1
|
Kayhan M, Vouillamoz J, Rodriguez DG, Bugarski M, Mitamura Y, Gschwend J, Schneider C, Hall A, Legouis D, Akdis CA, Peter L, Rehrauer H, Gewin L, Wenger RH, Khodo SN. Intrinsic TGF-β signaling attenuates proximal tubule mitochondrial injury and inflammation in chronic kidney disease. Nat Commun 2023; 14:3236. [PMID: 37270534 PMCID: PMC10239443 DOI: 10.1038/s41467-023-39050-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/26/2023] [Indexed: 06/05/2023] Open
Abstract
Excessive TGF-β signaling and mitochondrial dysfunction fuel chronic kidney disease (CKD) progression. However, inhibiting TGF-β failed to impede CKD in humans. The proximal tubule (PT), the most vulnerable renal segment, is packed with giant mitochondria and injured PT is pivotal in CKD progression. How TGF-β signaling affects PT mitochondria in CKD remained unknown. Here, we combine spatial transcriptomics and bulk RNAseq with biochemical analyses to depict the role of TGF-β signaling on PT mitochondrial homeostasis and tubulo-interstitial interactions in CKD. Male mice carrying specific deletion of Tgfbr2 in the PT have increased mitochondrial injury and exacerbated Th1 immune response in the aristolochic acid model of CKD, partly, through impaired complex I expression and mitochondrial quality control associated with a metabolic rewiring toward aerobic glycolysis in the PT cells. Injured S3T2 PT cells are identified as the main mediators of the maladaptive macrophage/dendritic cell activation in the absence of Tgfbr2. snRNAseq database analyses confirm decreased TGF-β receptors and a metabolic deregulation in the PT of CKD patients. This study describes the role of TGF-β signaling in PT mitochondrial homeostasis and inflammation in CKD, suggesting potential therapeutic targets that might be used to mitigate CKD progression.
Collapse
Affiliation(s)
- Merve Kayhan
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | | | - Milica Bugarski
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Yasutaka Mitamura
- Swiss Institute of Allergy and Asthma Research, University of Zurich, Zurich, Switzerland
| | - Julia Gschwend
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Andrew Hall
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - David Legouis
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, Hospital and University of Geneva, Geneva, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research, University of Zurich, Zurich, Switzerland
| | - Leary Peter
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Leslie Gewin
- Department of Internal Medicine, Division of Nephrology, Washington University, St. Louis, USA
- Department of Medicine, St. Louis Veterans Affairs, St. Louis, USA
| | - Roland H Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | |
Collapse
|
2
|
Tiberi J, Segatto M, Fiorenza MT, La Rosa P. Apparent Opportunities and Hidden Pitfalls: The Conflicting Results of Restoring NRF2-Regulated Redox Metabolism in Friedreich's Ataxia Pre-Clinical Models and Clinical Trials. Biomedicines 2023; 11:biomedicines11051293. [PMID: 37238963 DOI: 10.3390/biomedicines11051293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/18/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
Friedreich's ataxia (FRDA) is an autosomal, recessive, inherited neurodegenerative disease caused by the loss of activity of the mitochondrial protein frataxin (FXN), which primarily affects dorsal root ganglia, cerebellum, and spinal cord neurons. The genetic defect consists of the trinucleotide GAA expansion in the first intron of FXN gene, which impedes its transcription. The resulting FXN deficiency perturbs iron homeostasis and metabolism, determining mitochondrial dysfunctions and leading to reduced ATP production, increased reactive oxygen species (ROS) formation, and lipid peroxidation. These alterations are exacerbated by the defective functionality of the nuclear factor erythroid 2-related factor 2 (NRF2), a transcription factor acting as a key mediator of the cellular redox signalling and antioxidant response. Because oxidative stress represents a major pathophysiological contributor to FRDA onset and progression, a great effort has been dedicated to the attempt to restore the NRF2 signalling axis. Despite this, the beneficial effects of antioxidant therapies in clinical trials only partly reflect the promising results obtained in preclinical studies conducted in cell cultures and animal models. For these reasons, in this critical review, we overview the outcomes obtained with the administration of various antioxidant compounds and critically analyse the aspects that may have contributed to the conflicting results of preclinical and clinical studies.
Collapse
Affiliation(s)
- Jessica Tiberi
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Via dei Marsi 78, 00185 Rome, Italy
- PhD Program in Behavioral Neuroscience, Sapienza University of Rome, Via dei Marsi 78, 00185 Rome, Italy
| | - Marco Segatto
- Department of Bioscience and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Maria Teresa Fiorenza
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Via dei Marsi 78, 00185 Rome, Italy
- European Center for Brain Research, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00179 Rome, Italy
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Via dei Marsi 78, 00185 Rome, Italy
- European Center for Brain Research, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00179 Rome, Italy
| |
Collapse
|
3
|
Park J, Baruch-Torres N, Yin YW. Structural and Molecular Basis for Mitochondrial DNA Replication and Transcription in Health and Antiviral Drug Toxicity. Molecules 2023; 28:1796. [PMID: 36838782 PMCID: PMC9961925 DOI: 10.3390/molecules28041796] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Human mitochondrial DNA (mtDNA) is a 16.9 kbp double-stranded, circular DNA, encoding subunits of the oxidative phosphorylation electron transfer chain and essential RNAs for mitochondrial protein translation. The minimal human mtDNA replisome is composed of the DNA helicase Twinkle, DNA polymerase γ, and mitochondrial single-stranded DNA-binding protein. While the mitochondrial RNA transcription is carried out by mitochondrial RNA polymerase, mitochondrial transcription factors TFAM and TFB2M, and a transcription elongation factor, TEFM, both RNA transcriptions, and DNA replication machineries are intertwined and control mtDNA copy numbers, cellular energy supplies, and cellular metabolism. In this review, we discuss the mechanisms governing these main pathways and the mtDNA diseases that arise from mutations in transcription and replication machineries from a structural point of view. We also address the adverse effect of antiviral drugs mediated by mitochondrial DNA and RNA polymerases as well as possible structural approaches to develop nucleoside reverse transcriptase inhibitor and ribonucleosides analogs with reduced toxicity.
Collapse
Affiliation(s)
- Joon Park
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Noe Baruch-Torres
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| |
Collapse
|
4
|
Golubickaite I, Ugenskiene R, Bartnykaite A, Poskiene L, Vegiene A, Padervinskis E, Rudzianskas V, Juozaityte E. Mitochondria-Related TFAM and POLG Gene Variants and Associations with Tumor Characteristics and Patient Survival in Head and Neck Cancer. Genes (Basel) 2023; 14:434. [PMID: 36833361 PMCID: PMC9956916 DOI: 10.3390/genes14020434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
In 2020, 878,348 newly reported cases and 444,347 deaths related to head and neck cancer were reported. These numbers suggest that there is still a need for molecular biomarkers for the diagnosis and prognosis of the disease. In this study, we aimed to analyze mitochondria-related mitochondrial transcription factor A (TFAM) and DNA polymerase γ (POLG) single-nucleotide polymorphisms (SNPs) in the head and neck cancer patient group and evaluate associations between SNPs, disease characteristics, and patient outcomes. Genotyping was performed using TaqMan probes with Real-Time polymerase chain reaction. We found associations between TFAM gene SNPs rs11006129 and rs3900887 and patient survival status. We found that patients with the TFAM rs11006129 CC genotype and non-carriers of the T allele had longer survival times than those with the CT genotype or T-allele carriers. Additionally, patients with the TFAM rs3900887 A allele tended to have shorter survival times than non-carriers of the A allele. Our findings suggest that variants in the TFAM gene may play an important role in head and neck cancer patient survival and could be considered and further evaluated as prognostic biomarkers. However, due to the limited sample size (n = 115), further studies in larger and more diverse cohorts are needed to confirm these findings.
Collapse
Affiliation(s)
- Ieva Golubickaite
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Agne Bartnykaite
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathological Anatomy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Aurelija Vegiene
- Department of Otorhinolaryngology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Evaldas Padervinskis
- Department of Otorhinolaryngology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Viktoras Rudzianskas
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Elona Juozaityte
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| |
Collapse
|
5
|
Verma M, Francis L, Lizama BN, Callio J, Fricklas G, Wang KZQ, Kaufman BA, D'Aiuto L, Stolz DB, Watkins SC, Nimgaonkar VL, Soto-Gutierrez A, Goldstein A, Chu CT. iPSC-Derived Neurons from Patients with POLG Mutations Exhibit Decreased Mitochondrial Content and Dendrite Simplification. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:201-212. [PMID: 36414085 PMCID: PMC9976192 DOI: 10.1016/j.ajpath.2022.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
Abstract
Mutations in POLG, the gene encoding the catalytic subunit of DNA polymerase gamma, result in clinical syndromes characterized by mitochondrial DNA (mtDNA) depletion in affected tissues with variable organ involvement. The brain is one of the most affected organs, and symptoms include intractable seizures, developmental delay, dementia, and ataxia. Patient-derived induced pluripotent stem cells (iPSCs) provide opportunities to explore mechanisms in affected cell types and potential therapeutic strategies. Fibroblasts from two patients were reprogrammed to create new iPSC models of POLG-related mitochondrial diseases. Compared with iPSC-derived control neurons, mtDNA depletion was observed upon differentiation of the POLG-mutated lines to cortical neurons. POLG-mutated neurons exhibited neurite simplification with decreased mitochondrial content, abnormal mitochondrial structure and function, and increased cell death. Expression of the mitochondrial kinase PTEN-induced kinase 1 (PINK1) mRNA was decreased in patient neurons. Overexpression of PINK1 increased mitochondrial content and ATP:ADP ratios in neurites, decreasing cell death and rescuing neuritic complexity. These data indicate an intersection of polymerase gamma and PINK1 pathways that may offer a novel therapeutic option for patients affected by this spectrum of disorders.
Collapse
Affiliation(s)
- Manish Verma
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lily Francis
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Britney N Lizama
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jason Callio
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Gabriella Fricklas
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kent Z Q Wang
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Brett A Kaufman
- Department of Medicine, Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Leonardo D'Aiuto
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Donna B Stolz
- Center for Biologic Imaging (CBI), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Simon C Watkins
- Center for Biologic Imaging (CBI), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Vishwajit L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | | | - Amy Goldstein
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charleen T Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
| |
Collapse
|
6
|
Meyrick J, Stefanetti RJ, Errington L, McFarland R, Gorman GS, Lax NZ. Model systems informing mechanisms and drug discovery: a systematic review of POLG-related disease models. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18637.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Introduction Pathogenic variants in the gene encoding the catalytic subunit of DNA polymerase gamma (POLG), comprise an important single-gene cause of inherited mitochondrial disorders. Clinical manifestations are now recognised as an array of overlapping clinical features rather than discrete syndromes as originally conceptualised. Animal and cellular models have been used to address numerous scientific questions, from basic science to the development and assessment of novel therapies. Here, we sought to perform a systematic review of the existing models used in mitochondrial research and their effectiveness in recapitulating POLG-related disease. Methods Four databases were searched from inception to May 31, 2022: MEDLINE, Scopus, Web of Science, and Cochrane Review. Original articles available in English, reporting the use of a model system designed to recapitulate POLG-related disease, or related pathogenicity, were eligible for inclusion. Risk of bias and the methodological quality of articles were assessed by an adapted version of the Cochrane Risk of Bias Tool, with the quality of evidence synthesized across each model. Results A total of 55 articles, including seven model organisms (Human, yeast [Saccharomyces cerevisiae and Schizosaccharomyces pombe], Drosophila, Mouse, Nematoda, and Zebrafish) with 258 distinct variants were included. Of these, 66% (N=38) of articles recapitulated mitochondrial DNA (mtDNA) depletion and 42% (N=23) recapitulated POLG-related disease. Thirty-three percent of articles (N=18/55) utilised tissue-specific models of POLG-related dysfunction, while 13% (N=7) investigated the effect of potential therapeutics in POLG-related mitochondrial disorders. Discussion The available evidence supporting the ability of models for POLG-related disease to recapitulate molecular mechanisms and phenotype is limited, inconsistent and of poor methodologic quality. Further success in examining and translating novel therapies into effective treatments will be enhanced by the availability of more robust models that better recapitulate the entire spectrum of POLG-related disease. PROSPERO registration: CRD42021234883
Collapse
|
7
|
Targeting Mitochondria as a Therapeutic Approach for Parkinson's Disease. Cell Mol Neurobiol 2022; 43:1499-1518. [PMID: 35951210 DOI: 10.1007/s10571-022-01265-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/21/2022] [Indexed: 11/03/2022]
Abstract
Neurodegeneration is among the most critical challenges that involve modern societies and annually influences millions of patients worldwide. While the pathophysiology of Parkinson's disease (PD) is complicated, the role of mitochondrial is demonstrated. The in vitro and in vivo models and genome-wide association studies in human cases proved that specific genes, including PINK1, Parkin, DJ-1, SNCA, and LRRK2, linked mitochondrial dysfunction with PD. Also, mitochondrial DNA (mtDNA) plays an essential role in the pathophysiology of PD. Targeting mitochondria as a therapeutic approach to inhibit or slow down PD formation and progression seems to be an exciting issue. The current review summarized known mutations associated with both mitochondrial dysfunction and PD. The significance of mtDNA in Parkinson's disease pathogenesis and potential PD therapeutic approaches targeting mitochondrial dysfunction was then discussed.
Collapse
|
8
|
Carvalho G, Repolês BM, Mendes I, Wanrooij PH. Mitochondrial DNA Instability in Mammalian Cells. Antioxid Redox Signal 2022; 36:885-905. [PMID: 34015960 PMCID: PMC9127837 DOI: 10.1089/ars.2021.0091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023]
Abstract
Significance: The small, multicopy mitochondrial genome (mitochondrial DNA [mtDNA]) is essential for efficient energy production, as alterations in its coding information or a decrease in its copy number disrupt mitochondrial ATP synthesis. However, the mitochondrial replication machinery encounters numerous challenges that may limit its ability to duplicate this important genome and that jeopardize mtDNA stability, including various lesions in the DNA template, topological stress, and an insufficient nucleotide supply. Recent Advances: An ever-growing array of DNA repair or maintenance factors are being reported to localize to the mitochondria. We review current knowledge regarding the mitochondrial factors that may contribute to the tolerance or repair of various types of changes in the mitochondrial genome, such as base damage, incorporated ribonucleotides, and strand breaks. We also discuss the newly discovered link between mtDNA instability and activation of the innate immune response. Critical Issues: By which mechanisms do mitochondria respond to challenges that threaten mtDNA maintenance? What types of mtDNA damage are repaired, and when are the affected molecules degraded instead? And, finally, which forms of mtDNA instability trigger an immune response, and how? Future Directions: Further work is required to understand the contribution of the DNA repair and damage-tolerance factors present in the mitochondrial compartment, as well as the balance between mtDNA repair and degradation. Finally, efforts to understand the events underlying mtDNA release into the cytosol are warranted. Pursuing these and many related avenues can improve our understanding of what goes wrong in mitochondrial disease. Antioxid. Redox Signal. 36, 885-905.
Collapse
Affiliation(s)
- Gustavo Carvalho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Bruno Marçal Repolês
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela Mendes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Paulina H. Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| |
Collapse
|
9
|
Chemotherapy Resistance: Role of Mitochondrial and Autophagic Components. Cancers (Basel) 2022; 14:cancers14061462. [PMID: 35326612 PMCID: PMC8945922 DOI: 10.3390/cancers14061462] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Chemotherapy resistance is a common occurrence during cancer treatment that cancer researchers are attempting to understand and overcome. Mitochondria are a crucial intracellular signaling core that are becoming important determinants of numerous aspects of cancer genesis and progression, such as metabolic reprogramming, metastatic capability, and chemotherapeutic resistance. Mitophagy, or selective autophagy of mitochondria, can influence both the efficacy of tumor chemotherapy and the degree of drug resistance. Regardless of the fact that mitochondria are well-known for coordinating ATP synthesis from cellular respiration in cellular bioenergetics, little is known its mitophagy regulation in chemoresistance. Recent advancements in mitochondrial research, mitophagy regulatory mechanisms, and their implications for our understanding of chemotherapy resistance are discussed in this review. Abstract Cancer chemotherapy resistance is one of the most critical obstacles in cancer therapy. One of the well-known mechanisms of chemotherapy resistance is the change in the mitochondrial death pathways which occur when cells are under stressful situations, such as chemotherapy. Mitophagy, or mitochondrial selective autophagy, is critical for cell quality control because it can efficiently break down, remove, and recycle defective or damaged mitochondria. As cancer cells use mitophagy to rapidly sweep away damaged mitochondria in order to mediate their own drug resistance, it influences the efficacy of tumor chemotherapy as well as the degree of drug resistance. Yet despite the importance of mitochondria and mitophagy in chemotherapy resistance, little is known about the precise mechanisms involved. As a consequence, identifying potential therapeutic targets by analyzing the signal pathways that govern mitophagy has become a vital research goal. In this paper, we review recent advances in mitochondrial research, mitophagy control mechanisms, and their implications for our understanding of chemotherapy resistance.
Collapse
|
10
|
Dohrn MF, Heller C, Zengeler D, Obermaier CD, Biskup S, Weis J, Nikolin S, Claeys KG, Schöne U, Beijer D, Winter N, Achenbach P, Gess B, Schulz JB, Mulahasanovic L. Heterozygous POLG variant Ser1181Asn co-segregating in a family with autosomal dominant axonal neuropathy, proximal muscle fatigability, ptosis, and ragged red fibers. Neurol Res Pract 2022; 4:5. [PMID: 35101151 PMCID: PMC8805222 DOI: 10.1186/s42466-022-00169-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022] Open
Abstract
By whole-exome sequencing, we found the heterozygous POLG variant c.3542G>A; p.Ser1181Asn in a family of four affected individuals, presenting with a mixed neuro-myopathic phenotype. The variant is located within the active site of polymerase gamma, in a cluster region associated with an autosomal dominant inheritance. In adolescence, the index developed distal atrophies and weakness, sensory loss, afferent ataxia, double vision, and bilateral ptosis. One older sister presented with Charcot-Marie-Tooth-like symptoms, while the youngest sister and father reported exercise-induced muscle pain and proximal weakness. In none of the individuals, we observed any involvement of the central nervous system. Muscle biopsies obtained from the father and the older sister showed ragged-red fibers, and electron microscopy confirmed mitochondrial damage. We conclude that this novel POLG variant explains this family’s phenotype.
Collapse
|
11
|
Singh A, Patel SS. Quantitative methods to study helicase, DNA polymerase, and exonuclease coupling during DNA replication. Methods Enzymol 2022; 672:75-102. [PMID: 35934486 PMCID: PMC9933136 DOI: 10.1016/bs.mie.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genome replication is accomplished by highly regulated activities of enzymes in a multi-protein complex called the replisome. Two major enzymes, DNA polymerase and helicase, catalyze continuous DNA synthesis on the leading strand of the parental DNA duplex while the lagging strand is synthesized discontinuously. The helicase and DNA polymerase on their own are catalytically inefficient and weak motors for unwinding/replicating double-stranded DNA. However, when a helicase and DNA polymerase are functionally and physically coupled, they catalyze fast and highly processive leading strand DNA synthesis. DNA polymerase has a 3'-5' exonuclease activity, which removes nucleotides misincorporated in the nascent DNA. DNA synthesis kinetics, processivity, and accuracy are governed by the interplay of the helicase, DNA polymerase, and exonuclease activities within the replisome. This chapter describes quantitative biochemical and biophysical methods to study the coupling of these three critical activities during DNA replication. The methods include real-time quantitation of kinetics of DNA unwinding-synthesis by a coupled helicase-DNA polymerase complex, a 2-aminopurine fluorescence-based assay to map the precise positions of helicase and DNA polymerase with respect to the replication fork junction, and a radiometric assay to study the coupling of DNA polymerase, exonuclease, and helicase activities during processive leading strand DNA synthesis. These methods are presented here with bacteriophage T7 replication proteins as an example but can be applied to other systems with appropriate modifications.
Collapse
|
12
|
DNA Damage Response Genes in Osteosarcoma. JOURNAL OF ONCOLOGY 2021; 2021:9365953. [PMID: 35251167 PMCID: PMC8894034 DOI: 10.1155/2021/9365953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Improving the osteosarcoma (OS) patients' survival has long been a challenge, even though the disease's treatment is on the verge of progress. DNA damage response (DDR) has traditionally been associated with carcinogenesis, tumor growth, and genomic instability. No study has used DDR genes as a signature to identify the prognosis of OS. The goal of this work was to find an effective possible DDR gene biomarker for predicting OS prognosis, which may be useful in clinical diagnosis and therapy. METHODS To assess gene methylation, univariate and multivariate cox regression analyses were performed on data from OS patients. The data were retrieved from public databases, including the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and the Gene Expression Omnibus (GEO). RESULTS The DDR gene signature was chosen, which included seven genes (NHEJ1, RMI2, SWI5, ERCC2, CLK2, POLG, and MLH1). In the TARGET dataset, patients were categorized into two groups: high-risk and low-risk. Patients with a high-risk score revealed a shorter OS rate (hazard ratio (HR): 3.15, 95% confidence interval (CI): 1.38-4.34, P < 0.001) in comparison with the patients with a low-risk score in the TARGET as a training group. The validation of the prognostic signature accuracy was carried out in relapse and validation cohorts (TARGET, n = 75; GSE21257, n = 53). The signature was found to be an independent predictive factor for OS in multivariate cox regression analysis, and a nomogram model was developed to predict an individual's risk of OS. DDR gene signature involved in Fanconi anemia pathway, nonhomologous end-joining pathway, mismatch repair, and nucleotide excision repair pathway. CONCLUSIONS Our study suggests that the identified novel DDR genes could be a powerful prognostic tool for prognosis evaluation and a valuable tool in predicting the risk factors in OS patients.
Collapse
|
13
|
Allkanjari K, Baldock RA. Beyond base excision repair: an evolving picture of mitochondrial DNA repair. Biosci Rep 2021; 41:BSR20211320. [PMID: 34608928 PMCID: PMC8527207 DOI: 10.1042/bsr20211320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are highly specialised organelles required for key cellular processes including ATP production through cellular respiration and controlling cell death via apoptosis. Unlike other organelles, mitochondria contain their own DNA genome which encodes both protein and RNA required for cellular respiration. Each cell may contain hundreds to thousands of copies of the mitochondrial genome, which is essential for normal cellular function - deviation of mitochondrial DNA (mtDNA) copy number is associated with cellular ageing and disease. Furthermore, mtDNA lesions can arise from both endogenous or exogenous sources and must either be tolerated or corrected to preserve mitochondrial function. Importantly, replication of damaged mtDNA can lead to stalling and introduction of mutations or genetic loss, mitochondria have adapted mechanisms to repair damaged DNA. These mechanisms rely on nuclear-encoded DNA repair proteins that are translocated into the mitochondria. Despite the presence of many known nuclear DNA repair proteins being found in the mitochondrial proteome, it remains to be established which DNA repair mechanisms are functional in mammalian mitochondria. Here, we summarise the existing and emerging research, alongside examining proteomic evidence, demonstrating that mtDNA damage can be repaired using Base Excision Repair (BER), Homologous Recombination (HR) and Microhomology-mediated End Joining (MMEJ). Critically, these repair mechanisms do not operate in isolation and evidence for interplay between pathways and repair associated with replication is discussed. Importantly, characterising non-canonical functions of key proteins and understanding the bespoke pathways used to tolerate, repair or bypass DNA damage will be fundamental in fully understanding the causes of mitochondrial genome mutations and mitochondrial dysfunction.
Collapse
Affiliation(s)
- Kathrin Allkanjari
- Formerly: Solent University Southampton, East Park Terrace, Southampton, SO14 0YN, UK
| | - Robert A. Baldock
- School of Natural and Social Sciences, University of Gloucestershire, Francis Close Hall, Swindon Road, Cheltenham GL50 4AZ, UK
| |
Collapse
|
14
|
Bris C, Goudenège D, Desquiret-Dumas V, Gueguen N, Bannwarth S, Gaignard P, Rucheton B, Trimouille A, Allouche S, Rouzier C, Saadi S, Jardel C, Slama A, Barth M, Verny C, Spinazzi M, Cassereau J, Colin E, Armelle M, Pereon Y, Martin-Negrier ML, Paquis-Flucklinger V, Letournel F, Lenaers G, Bonneau D, Reynier P, Amati-Bonneau P, Procaccio V. Improved detection of mitochondrial DNA instability in mitochondrial genome maintenance disorders. Genet Med 2021; 23:1769-1778. [PMID: 34040194 DOI: 10.1038/s41436-021-01206-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Diseases caused by defects in mitochondrial DNA (mtDNA) maintenance machinery, leading to mtDNA deletions, form a specific group of disorders. However, mtDNA deletions also appear during aging, interfering with those resulting from mitochondrial disorders. METHODS Here, using next-generation sequencing (NGS) data processed by eKLIPse and data mining, we established criteria distinguishing age-related mtDNA rearrangements from those due to mtDNA maintenance defects. MtDNA deletion profiles from muscle and urine patient samples carrying pathogenic variants in nuclear genes involved in mtDNA maintenance (n = 40) were compared with age-matched controls (n = 90). Seventeen additional patient samples were used to validate the data mining model. RESULTS Overall, deletion number, heteroplasmy level, deletion locations, and the presence of repeats at deletion breakpoints were significantly different between patients and controls, especially in muscle samples. The deletion number was significantly relevant in adults, while breakpoint repeat lengths surrounding deletions were discriminant in young subjects. CONCLUSION Altogether, eKLIPse analysis is a powerful tool for measuring the accumulation of mtDNA deletions between patients of different ages, as well as in prioritizing novel variants in genes involved in mtDNA stability.
Collapse
Affiliation(s)
- Celine Bris
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - David Goudenège
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Valerie Desquiret-Dumas
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Naig Gueguen
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Pauline Gaignard
- Service de Biochimie, CHU Bicêtre, APHP Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Benoit Rucheton
- Département de Biochimie et Génétique, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Aurelien Trimouille
- Service de Génétique médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Stephane Allouche
- Service de Biochimie, EA4650, Centre Hospitalier Universitaire, Caen, France
| | - Cecile Rouzier
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Samira Saadi
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Claude Jardel
- Département de Biochimie et Génétique, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Abdel Slama
- Service de Biochimie, CHU Bicêtre, APHP Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Magalie Barth
- Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Christophe Verny
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Marco Spinazzi
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Julien Cassereau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Estelle Colin
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Magot Armelle
- Centre de Référence Maladies Neuromusculaires, CHU Nantes, Nantes, France
| | - Yann Pereon
- Centre de Référence Maladies Neuromusculaires, CHU Nantes, Nantes, France
| | | | | | - Franck Letournel
- UF de Neurobiologie-Neuropathologie, UMR INSERM 1066 - CNRS 6021, MINT, Angers, France
| | - Guy Lenaers
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Dominique Bonneau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Pascal Reynier
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Patrizia Amati-Bonneau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France. .,Département de Biochimie et Génétique, CHU d'Angers, Angers, France.
| |
Collapse
|
15
|
Chen C, McDonald D, Blain A, Sachdeva A, Bone L, Smith ALM, Warren C, Pickett SJ, Hudson G, Filby A, Vincent AE, Turnbull DM, Reeve AK. Imaging mass cytometry reveals generalised deficiency in OXPHOS complexes in Parkinson's disease. NPJ Parkinsons Dis 2021; 7:39. [PMID: 33980828 PMCID: PMC8115071 DOI: 10.1038/s41531-021-00182-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Abstract
Here we report the application of a mass spectrometry-based technology, imaging mass cytometry, to perform in-depth proteomic profiling of mitochondrial complexes in single neurons, using metal-conjugated antibodies to label post-mortem human midbrain sections. Mitochondrial dysfunction, particularly deficiency in complex I has previously been associated with the degeneration of dopaminergic neurons in Parkinson's disease. To further our understanding of the nature of this dysfunction, and to identify Parkinson's disease specific changes, we validated a panel of antibodies targeting subunits of all five mitochondrial oxidative phosphorylation complexes in dopaminergic neurons from Parkinson's disease, mitochondrial disease, and control cases. Detailed analysis of the expression profile of these proteins, highlighted heterogeneity between individuals. There is a widespread decrease in expression of all complexes in Parkinson's neurons, although more severe in mitochondrial disease neurons, however, the combination of affected complexes varies between the two groups. We also provide evidence of a potential neuronal response to mitochondrial dysfunction through a compensatory increase in mitochondrial mass. This study highlights the use of imaging mass cytometry in the assessment and analysis of expression of oxidative phosphorylation proteins, revealing the complexity of deficiencies of these proteins within individual neurons which may contribute to and drive neurodegeneration in Parkinson's disease.
Collapse
Affiliation(s)
- Chun Chen
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - David McDonald
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Flow Cytometry Core Facility, Newcastle University, Newcastle upon Tyne, UK
| | - Alasdair Blain
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ashwin Sachdeva
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Bone
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Anna L M Smith
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Charlotte Warren
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Filby
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Flow Cytometry Core Facility, Newcastle University, Newcastle upon Tyne, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amy K Reeve
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
| |
Collapse
|
16
|
Golubickaite I, Ugenskiene R, Ziliene E, Beniusyte J, Inciura A, Poskiene L, Juozaityte E. POLG Gene Variants in Cervical Cancer Patients and Their Associations with Clinical and Pathomorphological Tumor Characteristics. J Clin Med 2021; 10:1838. [PMID: 33922707 PMCID: PMC8123044 DOI: 10.3390/jcm10091838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/09/2022] Open
Abstract
Cervical cancer is one of the most common cancers in women worldwide. Human papillomaviruses are known to be the main, but not the only risk factor, of this cancer type. Despite all the knowledge on this cancer type, it is still a challenge to predict the course of the disease, and therefore, minimally invasive biomarkers are needed. This study aimed to analyze single-nucleotide variants in the POLG gene and assess the associations with tumor phenotype and patient outcome. A total of 172 cervical cancer patients were included in this study. Clinical and tumor data were gathered from medical records retrospectively. Single nucleotide variations were determined using TaqMan probes with Real-Time PCR. Significant associations between POLG rs3087374 and cervical cancer patients' tumor histological type, stage, and tumor size were determined. The CA genotype and A allele of rs3087374 increased the probability of adenocarcinoma histological tumor type, IIIA stage, and T3 tumor size compared to CC genotype and C allele, respectively. Furthermore, patients with AA genotype in rs2072267 had longer metastasis-free survival than those with the GG genotype. Our data suggest that mitochondrial polymerase gamma encoded by nuclear POLG gene is important for specific tumor phenotype formation and patient outcome in cervical cancer.
Collapse
Affiliation(s)
- Ieva Golubickaite
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania;
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania;
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (E.Z.); (J.B.); (A.I.); (E.J.)
| | - Egle Ziliene
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (E.Z.); (J.B.); (A.I.); (E.J.)
| | - Jurgita Beniusyte
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (E.Z.); (J.B.); (A.I.); (E.J.)
| | - Arturas Inciura
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (E.Z.); (J.B.); (A.I.); (E.J.)
| | - Lina Poskiene
- Department of Pathological Anatomy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania;
| | - Elona Juozaityte
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (E.Z.); (J.B.); (A.I.); (E.J.)
| |
Collapse
|
17
|
Role of Oxidative DNA Damage and Repair in Atrial Fibrillation and Ischemic Heart Disease. Int J Mol Sci 2021; 22:ijms22083838. [PMID: 33917194 PMCID: PMC8068079 DOI: 10.3390/ijms22083838] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
Atrial fibrillation (AF) and ischemic heart disease (IHD) represent the two most common clinical cardiac diseases, characterized by angina, arrhythmia, myocardial damage, and cardiac dysfunction, significantly contributing to cardiovascular morbidity and mortality and posing a heavy socio-economic burden on society worldwide. Current treatments of these two diseases are mainly symptomatic and lack efficacy. There is thus an urgent need to develop novel therapies based on the underlying pathophysiological mechanisms. Emerging evidence indicates that oxidative DNA damage might be a major underlying mechanism that promotes a variety of cardiac diseases, including AF and IHD. Antioxidants, nicotinamide adenine dinucleotide (NAD+) boosters, and enzymes involved in oxidative DNA repair processes have been shown to attenuate oxidative damage to DNA, making them potential therapeutic targets for AF and IHD. In this review, we first summarize the main molecular mechanisms responsible for oxidative DNA damage and repair both in nuclei and mitochondria, then describe the effects of oxidative DNA damage on the development of AF and IHD, and finally discuss potential targets for oxidative DNA repair-based therapeutic approaches for these two cardiac diseases.
Collapse
|
18
|
MITOL-dependent ubiquitylation negatively regulates the entry of PolγA into mitochondria. PLoS Biol 2021; 19:e3001139. [PMID: 33657094 PMCID: PMC7959396 DOI: 10.1371/journal.pbio.3001139] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 03/15/2021] [Accepted: 02/04/2021] [Indexed: 02/01/2023] Open
Abstract
Mutations in mitochondrial replicative polymerase PolγA lead to progressive external ophthalmoplegia (PEO). While PolγA is the known central player in mitochondrial DNA (mtDNA) replication, it is unknown whether a regulatory process exists on the mitochondrial outer membrane which controlled its entry into the mitochondria. We now demonstrate that PolγA is ubiquitylated by mitochondrial E3 ligase, MITOL (or MARCH5, RNF153). Ubiquitylation in wild-type (WT) PolγA occurs at Lysine 1060 residue via K6 linkage. Ubiquitylation of PolγA negatively regulates its binding to Tom20 and thereby its mitochondrial entry. While screening different PEO patients for mitochondrial entry, we found that a subset of the PolγA mutants is hyperubiquitylated by MITOL and interact less with Tom20. These PolγA variants cannot enter into mitochondria, instead becomes enriched in the insoluble fraction and undergo enhanced degradation. Hence, mtDNA replication, as observed via BrdU incorporation into the mtDNA, was compromised in these PEO mutants. However, by manipulating their ubiquitylation status by 2 independent techniques, these PEO mutants were reactivated, which allowed the incorporation of BrdU into mtDNA. Thus, regulated entry of non-ubiquitylated PolγA may have beneficial consequences for certain PEO patients. This study shows that mitochondrial entry of the replicative polymerase PolgA is regulated by ubiquitylation by the E3 ligase MITOL; however, by manipulating their ubiquitylation status, some progressive external ophthalmoplegia mutants whose PolgA is polyubiquitylated and cannot enter the mitochondrion can be reactivated and hence become functionally active.
Collapse
|
19
|
Feric M, Demarest TG, Tian J, Croteau DL, Bohr VA, Misteli T. Self-assembly of multi-component mitochondrial nucleoids via phase separation. EMBO J 2021; 40:e107165. [PMID: 33619770 DOI: 10.15252/embj.2020107165] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/08/2021] [Accepted: 01/19/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondria contain an autonomous and spatially segregated genome. The organizational unit of their genome is the nucleoid, which consists of mitochondrial DNA (mtDNA) and associated architectural proteins. Here, we show that phase separation is the primary physical mechanism for assembly and size control of the mitochondrial nucleoid (mt-nucleoid). The major mtDNA-binding protein TFAM spontaneously phase separates in vitro via weak, multivalent interactions into droplets with slow internal dynamics. TFAM and mtDNA form heterogenous, viscoelastic structures in vitro, which recapitulate the dynamics and behavior of mt-nucleoids in vivo. Mt-nucleoids coalesce into larger droplets in response to various forms of cellular stress, as evidenced by the enlarged and transcriptionally active nucleoids in mitochondria from patients with the premature aging disorder Hutchinson-Gilford Progeria Syndrome (HGPS). Our results point to phase separation as an evolutionarily conserved mechanism of genome organization.
Collapse
Affiliation(s)
- Marina Feric
- National Cancer Institute, NIH, Bethesda, MD, USA.,National Institute of General Medical Sciences, NIH, Bethesda, MD, USA
| | | | - Jane Tian
- National Institute on Aging, NIH, Baltimore, MD, USA
| | | | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
| |
Collapse
|
20
|
Borsche M, Pereira SL, Klein C, Grünewald A. Mitochondria and Parkinson's Disease: Clinical, Molecular, and Translational Aspects. JOURNAL OF PARKINSONS DISEASE 2021; 11:45-60. [PMID: 33074190 PMCID: PMC7990451 DOI: 10.3233/jpd-201981] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial dysfunction represents a well-established player in the pathogenesis of both monogenic and idiopathic Parkinson’s disease (PD). Initially originating from the observation that mitochondrial toxins cause PD, findings from genetic PD supported a contribution of mitochondrial dysfunction to the disease. Here, proteins encoded by the autosomal recessively inherited PD genes Parkin, PTEN-induced kinase 1 (PINK1), and DJ-1 are involved in mitochondrial pathways. Additional evidence for mitochondrial dysfunction stems from models of autosomal-dominant PD due to mutations in alpha-synuclein (SNCA) and leucine-rich repeat kinase 2 (LRRK2). Moreover, patients harboring alterations in mitochondrial polymerase gamma (POLG) often exhibit signs of parkinsonism. While some molecular studies suggest that mitochondrial dysfunction is a primary event in PD, others speculate that it is the result of impaired mitochondrial clearance. Most recent research even implicated damage-associated molecular patterns released from non-degraded mitochondria in neuroinflammatory processes in PD. Here, we summarize the manifold literature dealing with mitochondria in the context of PD. Moreover, in light of recent advances in the field of personalized medicine, patient stratification according to the degree of mitochondrial impairment followed by mitochondrial enhancement therapy may hold potential for at least a subset of genetic and idiopathic PD cases. Thus, in the second part of this review, we discuss therapeutic approaches targeting mitochondrial dysfunction with the aim to prevent or delay neurodegeneration in PD.
Collapse
Affiliation(s)
- Max Borsche
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Sandro L Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| |
Collapse
|
21
|
Kierdaszuk B, Kaliszewska M, Rusecka J, Kosińska J, Bartnik E, Tońska K, Kamińska AM, Kostera-Pruszczyk A. Progressive External Ophthalmoplegia in Polish Patients-From Clinical Evaluation to Genetic Confirmation. Genes (Basel) 2020; 12:genes12010054. [PMID: 33396418 PMCID: PMC7824435 DOI: 10.3390/genes12010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial encephalomyopathies comprise a group of heterogeneous disorders resulting from impaired oxidative phosphorylation (OxPhos). Among a variety of symptoms progressive external ophthalmoplegia (PEO) seems to be the most common. The aim of this study is to present clinical and genetic characteristics of Polish patients with PEO. Clinical, electrophysiological, neuroradiological, and morphological data of 84 patients were analyzed. Genetic studies of mitochondrial DNA (mtDNA) were performed in all patients. Among nuclear DNA (nDNA) genes POLG was sequenced in 41 patients, TWNK (C10orf2) in 13 patients, and RNASEH1 in 2 patients. Total of 27 patients were included in the chronic progressive external ophthalmoplegia (CPEO) group, 24 in the CPEO+ group. Twenty-six patients had mitochondrial encephalomyopathy (ME), six patients Kearns-Sayre syndrome (KSS), and one patient sensory ataxic neuropathy, dysarthria, ophthalmoparesis (SANDO) syndrome. Genetic analysis of nDNA genes revealed the presence of pathogenic or possibly pathogenic variants in the POLG gene in nine patients, the TWNK gene in five patients and the RNASEH1 gene in two patients. Detailed patients' history and careful assessment of family history are essential in the diagnostic work-up. Genetic studies of both mtDNA and nDNA are necessary for the final diagnosis of progressive external ophthalmoplegia and for genetic counseling.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Cerebellum/diagnostic imaging
- Cerebellum/metabolism
- Cerebellum/pathology
- Cerebrum/diagnostic imaging
- Cerebrum/metabolism
- Cerebrum/pathology
- Child
- DNA Helicases/genetics
- DNA Helicases/metabolism
- DNA Polymerase gamma/genetics
- DNA Polymerase gamma/metabolism
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- Diagnosis, Differential
- Female
- Gene Expression
- Humans
- Kearns-Sayre Syndrome/diagnostic imaging
- Kearns-Sayre Syndrome/genetics
- Kearns-Sayre Syndrome/metabolism
- Kearns-Sayre Syndrome/pathology
- Male
- Middle Aged
- Mitochondria/metabolism
- Mitochondria/pathology
- Mitochondrial Diseases/diagnostic imaging
- Mitochondrial Diseases/genetics
- Mitochondrial Diseases/metabolism
- Mitochondrial Diseases/pathology
- Mitochondrial Encephalomyopathies/diagnostic imaging
- Mitochondrial Encephalomyopathies/genetics
- Mitochondrial Encephalomyopathies/metabolism
- Mitochondrial Encephalomyopathies/pathology
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Ophthalmoplegia, Chronic Progressive External/diagnostic imaging
- Ophthalmoplegia, Chronic Progressive External/genetics
- Ophthalmoplegia, Chronic Progressive External/metabolism
- Ophthalmoplegia, Chronic Progressive External/pathology
- Pedigree
- Poland
- Polymorphism, Genetic
- Ribonuclease H/genetics
- Ribonuclease H/metabolism
- Sequence Deletion
Collapse
Affiliation(s)
- Biruta Kierdaszuk
- Department of Neurology, Medical University of Warsaw, Banacha 1a, 02-097 Warsaw, Poland; (A.M.K.); (A.K.-P.)
- Correspondence: ; Tel.: +48-22-599-2858; Fax: +48-22-599-1857
| | - Magdalena Kaliszewska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.K.); (J.R.); (E.B.); (K.T.)
| | - Joanna Rusecka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.K.); (J.R.); (E.B.); (K.T.)
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Pawinskiego 3c, 02-106 Warsaw, Poland;
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.K.); (J.R.); (E.B.); (K.T.)
| | - Katarzyna Tońska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.K.); (J.R.); (E.B.); (K.T.)
| | - Anna M. Kamińska
- Department of Neurology, Medical University of Warsaw, Banacha 1a, 02-097 Warsaw, Poland; (A.M.K.); (A.K.-P.)
| | - Anna Kostera-Pruszczyk
- Department of Neurology, Medical University of Warsaw, Banacha 1a, 02-097 Warsaw, Poland; (A.M.K.); (A.K.-P.)
| |
Collapse
|
22
|
Zhao L, Sumberaz P. Mitochondrial DNA Damage: Prevalence, Biological Consequence, and Emerging Pathways. Chem Res Toxicol 2020; 33:2491-2502. [PMID: 32486637 DOI: 10.1021/acs.chemrestox.0c00083] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria have a plethora of functions within a eukaryotic cell, ranging from energy production, cell signaling, and protein cofactor synthesis to various aspects of metabolism. Mitochondrial dysfunction is known to cause over 200 named disorders and has been implicated in many human diseases and aging. Mitochondria have their own genetic material, mitochondrial DNA (mtDNA), which encodes 13 protein subunits in the oxidative phosphorylation system and a full set of transfer and rRNAs. Although more than 99% of the proteins in mitochondria are nuclear DNA (nDNA)-encoded, the integrity of mtDNA is critical for mitochondrial functions, as evidenced by mitochondrial diseases sourced from mtDNA mutations and depletions and the vital role of fragmented mtDNA molecules in cell signaling pathways. Previous research has shown that mtDNA is an important target of genotoxic assaults by a variety of chemical and physical factors. This Perspective discusses the prevalence of mtDNA damage by comparing the abundance of lesions in mDNA and nDNA and summarizes current knowledge on the biological pathways to cope with mtDNA damage, including mtDNA repair, mtDNA degradation, and mitochondrial fission and fusion. Also, emerging roles of mtDNA damage in mutagenesis and immune responses are reviewed.
Collapse
Affiliation(s)
- Linlin Zhao
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| | - Philip Sumberaz
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| |
Collapse
|
23
|
Brown SA, Ray JC, Herrmann J. Precision Cardio-Oncology: a Systems-Based Perspective on Cardiotoxicity of Tyrosine Kinase Inhibitors and Immune Checkpoint Inhibitors. J Cardiovasc Transl Res 2020; 13:402-416. [PMID: 32253744 PMCID: PMC8855704 DOI: 10.1007/s12265-020-09992-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023]
Abstract
Cancer therapies have been evolving from conventional chemotherapeutics to targeted agents. This has fulfilled the hope of greater efficacy but unfortunately not of greater safety. In fact, a broad spectrum of toxicities can be seen with targeted therapies, including cardiovascular toxicities. Among these, cardiomyopathy and heart failure have received greatest attention, given their profound implications for continuation of cancer therapies and cardiovascular morbidity and mortality. Prediction of risk has always posed a challenge and even more so with the newer targeted agents. The merits of accurate risk prediction, however, are very evident, e.g. facilitating treatment decisions even before the first dose is given. This is important for agents with a long half-life and high potential to induced life-threatening cardiac complications, such as myocarditis with immune checkpoint inhibitors. An opportunity to address these needs in the field of cardio-oncology is provided by the expanding repertoire of "-omics" and other tools in precision medicine and their integration in a systems biology approach. This may allow for new insights into patho-mechanisms and the creation of more precise and cost-effective risk prediction tools with the ultimate goals of improved therapy decisions and prevention of cardiovascular complications. Herein, we explore this topic as a future approach to translating the complexity of cardio-oncology to the reality of patient care.
Collapse
Affiliation(s)
- Sherry-Ann Brown
- Department of Cardiovascular Diseases, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Jordan C Ray
- Department of Cardiovascular Diseases, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Joerg Herrmann
- Department of Cardiovascular Diseases, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA.
| |
Collapse
|
24
|
Hoyos-Gonzalez N, Trasviña-Arenas CH, Degiorgi A, Castro-Lara AY, Peralta-Castro A, Jimenez-Sandoval P, Diaz-Quezada C, Lodi T, Baruffini E, Brieba LG. Modeling of pathogenic variants of mitochondrial DNA polymerase: insight into the replication defects and implication for human disease. Biochim Biophys Acta Gen Subj 2020; 1864:129608. [PMID: 32234506 DOI: 10.1016/j.bbagen.2020.129608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 03/07/2020] [Accepted: 03/25/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Mutations in human gene encoding the mitochondrial DNA polymerase γ (HsPolγ) are associated with a broad range of mitochondrial diseases. Here we studied the impact on DNA replication by disease variants clustered around residue HsPolγ-K1191, a residue that in several family-A DNA polymerases interacts with the 3' end of the primer. METHODS Specifically, we examined the effect of HsPolγ carrying pathogenic variants in residues D1184, I1185, C1188, K1191, D1196, and a stop codon at residue T1199, using as a model the yeast mitochondrial DNA polymerase protein, Mip1p. RESULTS The introduction of pathogenic variants C1188R (yV945R), and of a stop codon at residue T1199 (yT956X) abolished both polymerization and exonucleolysis in vitro. HsPolγ substitutions in residues D1184 (yD941), I1185 (yI942), K1191 (yK948) and D1196 (yD953) shifted the balance between polymerization and exonucleolysis in favor of exonucleolysis. HsPolγ pathogenic variants at residue K1191 (yK948) and D1184 (yD941) were capable of nucleotide incorporation albeit with reduced processivity. Structural analysis of mitochondrial DNAPs showed that residue HsPolγ-N864 is placed in an optimal distance to interact with the 3' end of the primer and the phosphate backbone previous to the 3' end. Amino acid changes in residue HsPolγ-N864 to Ala, Ser or Asp result in enzymes that did not decrease their polymerization activity on short templates but exhibited a substantial decrease for processive DNA synthesis. CONCLUSION Our data suggest that in mitochondrial DNA polymerases multiple amino acids are involved in the primer-stand stabilization.
Collapse
Affiliation(s)
- Nallely Hoyos-Gonzalez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Andrea Degiorgi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Atzimaba Y Castro-Lara
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Antolín Peralta-Castro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Pedro Jimenez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36821 Irapuato, Guanajuato, Mexico
| | - Tiziana Lodi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy.
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36821 Irapuato, Guanajuato, Mexico.
| |
Collapse
|
25
|
Oliveira MT, Pontes CDB, Ciesielski GL. Roles of the mitochondrial replisome in mitochondrial DNA deletion formation. Genet Mol Biol 2020; 43:e20190069. [PMID: 32141473 PMCID: PMC7197994 DOI: 10.1590/1678-4685-gmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/12/2019] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletions are a common cause of human mitochondrial
diseases. Mutations in the genes encoding components of the mitochondrial
replisome, such as DNA polymerase gamma (Pol γ) and the mtDNA helicase Twinkle,
have been associated with the accumulation of such deletions and the development
of pathological conditions in humans. Recently, we demonstrated that changes in
the level of wild-type Twinkle promote mtDNA deletions, which implies that not
only mutations in, but also dysregulation of the stoichiometry between the
replisome components is potentially pathogenic. The mechanism(s) by which
alterations to the replisome function generate mtDNA deletions is(are) currently
under debate. It is commonly accepted that stalling of the replication fork at
sites likely to form secondary structures precedes the deletion formation. The
secondary structural elements can be bypassed by the replication-slippage
mechanism. Otherwise, stalling of the replication fork can generate single- and
double-strand breaks, which can be repaired through recombination leading to the
elimination of segments between the recombination sites. Here, we discuss
aberrances of the replisome in the context of the two debated outcomes, and
suggest new mechanistic explanations based on replication restart and template
switching that could account for all the deletion types reported for
patients.
Collapse
Affiliation(s)
- Marcos T Oliveira
- Universidade Estadual Paulista Júlio de Mesquita Filho, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | | | | |
Collapse
|
26
|
A Genome-wide Screen Reveals that Reducing Mitochondrial DNA Polymerase Can Promote Elimination of Deleterious Mitochondrial Mutations. Curr Biol 2019; 29:4330-4336.e3. [PMID: 31786061 PMCID: PMC6926476 DOI: 10.1016/j.cub.2019.10.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 10/09/2019] [Accepted: 10/29/2019] [Indexed: 02/05/2023]
Abstract
A mutant mitochondrial genome arising amid the pool of mitochondrial genomes within a cell must compete with existing genomes to survive to the next generation. Even weak selective forces can bias transmission of one genome over another to affect the inheritance of mitochondrial diseases and guide the evolution of mitochondrial DNA (mtDNA). Studies in several systems suggested that purifying selection in the female germline reduces transmission of detrimental mitochondrial mutations [1, 2, 3, 4, 5, 6, 7]. In contrast, some selfish genomes can take over despite a cost to host fitness [8, 9, 10, 11, 12, 13]. Within individuals, the outcome of competition is therefore influenced by multiple selective forces. The nuclear genome, which encodes most proteins within mitochondria, and all external regulators of mitochondrial biogenesis and dynamics can influence the competition between mitochondrial genomes [14, 15, 16, 17, 18], yet little is known about how this works. Previously, we established a Drosophila line transmitting two mitochondrial genomes in a stable ratio enforced by purifying selection benefiting one genome and a selfish advantage favoring the other [8]. Here, to find nuclear genes that impact mtDNA competition, we screened heterozygous deletions tiling ∼70% of the euchromatic regions and examined their influence on this ratio. This genome-wide screen detected many nuclear modifiers of this ratio and identified one as the catalytic subunit of mtDNA polymerase gene (POLG), tam. A reduced dose of tam drove elimination of defective mitochondrial genomes. This study suggests that our approach will uncover targets for interventions that would block propagation of pathogenic mitochondrial mutations. Multiple nuclear factors affect selective transmission of mitochondrial genomes Reducing mtDNA polymerase restricts the transmission of detrimental mtDNA mutants
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Homozygous R627W mutations in POLG cause mitochondrial DNA depletion leading to encephalopathy, seizures and stroke-like episodes. Mitochondrion 2019; 48:78-83. [DOI: 10.1016/j.mito.2019.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/05/2019] [Accepted: 08/14/2019] [Indexed: 01/21/2023]
|
29
|
Amino and carboxy-terminal extensions of yeast mitochondrial DNA polymerase assemble both the polymerization and exonuclease active sites. Mitochondrion 2019; 49:166-177. [PMID: 31445096 DOI: 10.1016/j.mito.2019.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/11/2019] [Accepted: 08/19/2019] [Indexed: 11/24/2022]
Abstract
Human and yeast mitochondrial DNA polymerases (DNAPs), POLG and Mip1, are related by evolution to bacteriophage DNAPs. However, mitochondrial DNAPs contain unique amino and carboxyl-terminal extensions that physically interact. Here we describe that N-terminal deletions in Mip1 polymerases abolish polymerization and decrease exonucleolytic degradation, whereas moderate C-terminal deletions reduce polymerization. Similarly, to the N-terminal deletions, an extended C-terminal deletion of 298 amino acids is deficient in nucleotide addition and exonucleolytic degradation of double and single-stranded DNA. The latter observation suggests that the physical interaction between the amino and carboxyl-terminal regions of Mip1 may be related to the spread of pathogenic POLG mutant along its primary sequence.
Collapse
|
30
|
Sowers ML, Anderson APP, Wrabl JO, Yin YW. Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase. J Am Chem Soc 2019; 141:10821-10829. [PMID: 31251605 PMCID: PMC7119269 DOI: 10.1021/jacs.9b04655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High fidelity human mitochondrial DNA polymerase (Pol γ) contains two active sites, a DNA polymerization site (pol) and a 3'-5' exonuclease site (exo) for proofreading. Although separated by 35 Å, coordination between the pol and exo sites is crucial to high fidelity replication. The biophysical mechanisms for this coordination are not completely understood. To understand the communication between the two active sites, we used a statistical-mechanical model of the protein ensemble to calculate the energetic landscape and local stability. We compared a series of structures of Pol γ, complexed with primer/template DNA, and either a nucleotide substrate or a series of nucleotide analogues, which are differentially incorporated and excised by pol and exo activity. Despite the nucleotide or its analogues being bound in the pol, Pol γ residue stability varied across the protein, particularly in the exo domain. This suggests that substrate presence in the pol can be "sensed" in the exo domain. Consistent with this hypothesis, in silico mutations made in one active site mutually perturbed the energetics of the other. To identify specific regions of the polymerase that contributed to this communication, we constructed an allosteric network connectivity map that further demonstrates specific pol-exo cooperativity. Thus, a cooperative network underlies energetic connectivity. We propose that Pol γ and other dual-function polymerases exploit an energetic coupling network that facilitates domain-domain communication to enhance discrimination between correct and incorrect nucleotides.
Collapse
Affiliation(s)
- Mark L. Sowers
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Andrew P. P. Anderson
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 71115, United States
| | - James O. Wrabl
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Y. Whitney Yin
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 71115, United States
| |
Collapse
|
31
|
Hsieh PC, Wang CC, Tsai CL, Yeh YM, Lee YS, Wu YR. POLG R964C and GBA L444P mutations in familial Parkinson's disease: Case report and literature review. Brain Behav 2019; 9:e01281. [PMID: 30941926 PMCID: PMC6520296 DOI: 10.1002/brb3.1281] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/08/2019] [Accepted: 03/15/2019] [Indexed: 02/06/2023] Open
Abstract
Polymerase gamma (POLG) is an enzyme responsible for the replication and repair of mitochondrial DNA. Mutations in POLG may cause variable clinical manifestations, including parkinsonism, epilepsy, cerebellar ataxia, neuropathy, and progressive external ophthalmoplegia. However, mutations of this gene are rare in patients with typical Parkinson's disease (PD). We report a man (current age: 59 years) without any underlying disease presenting with right-hand tremor at the age of 39 years, followed by slow movement, rigidity, and postural instability. He developed motor fluctuation and levodopa-induced dyskinesia 8 years later. At the age of 58 years, cognitive decline and visual hallucination ensued; he was institutionalized thereafter. We used multiplex ligation-dependent probe amplification, which demonstrated no large deletions or duplications of relevant PD genes. Next, targeted sequencing panel covering 51 genes causative for PD was applied for the proband; it revealed a heterozygous missense substitution R964C in POLG and a heterozygous missense substitution L444P in GBA. The patient's father, who had been diagnosed as having PD and type 2 diabetes mellitus at the age of 70 years, demonstrated identical mutations. This is the first report of familial PD combined with POLG R964C and GBA L444P mutations. Two pathogenic gene mutations potentially cause double hit in pathological neurodegeneration. This finding extends our understanding of the PD genotype-phenotype correlation.
Collapse
Affiliation(s)
- Pei-Chen Hsieh
- Department of Neurology, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan
| | - Chun-Chieh Wang
- Department of Neurology, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yun Shien Lee
- Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan
| | - Yih-Ru Wu
- Department of Neurology, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan.,Department of Neurology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| |
Collapse
|
32
|
Yehudai D, Liyanage SU, Hurren R, Rizoska B, Albertella M, Gronda M, Jeyaraju DV, Wang X, Barghout SH, MacLean N, Siriwardena TP, Jitkova Y, Targett-Adams P, Schimmer AD. The thymidine dideoxynucleoside analog, alovudine, inhibits the mitochondrial DNA polymerase γ, impairs oxidative phosphorylation and promotes monocytic differentiation in acute myeloid leukemia. Haematologica 2018; 104:963-972. [PMID: 30573504 PMCID: PMC6518883 DOI: 10.3324/haematol.2018.195172] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/17/2018] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial DNA encodes 13 proteins that comprise components of the respiratory chain that maintain oxidative phosphorylation. The replication of mitochondrial DNA is performed by the sole mitochondrial DNA polymerase γ. As acute myeloid leukemia (AML) cells and stem cells have an increased reliance on oxidative phosphorylation, we sought to evaluate polymerase γ inhibitors in AML. The thymidine dideoxynucleoside analog, alovudine, is an inhibitor of polymerase γ. In AML cells, alovudine depleted mitochondrial DNA, reduced mitochondrial encoded proteins, decreased basal oxygen consumption, and decreased cell proliferation and viability. To evaluate the effects of polymerase γ inhibition with alovudine in vivo, mice were xenografted with OCI-AML2 cells and then treated with alovudine. Systemic administration of alovudine reduced leukemic growth without evidence of toxicity and decreased levels of mitochondrial DNA in the leukemic cells. We also showed that alovudine increased the monocytic differentiation of AML cells. Genetic knockdown and other chemical inhibitors of polymerase γ also promoted AML differentiation, but the effects on AML differentiation were independent of reductions in oxidative phosphorylation or respiratory chain proteins. Thus, we have identified a novel mechanism by which mitochondria regulate AML fate and differentiation independent of oxidative phosphorylation. Moreover, we highlight polymerase γ inhibitors, such as alovudine, as novel therapeutic agents for AML.
Collapse
Affiliation(s)
- Dana Yehudai
- Princess Margaret Cancer Centre, University Health Network, ON, Canada.,Medivir AB, Huddinge, Sweden
| | | | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | | | - Mark Albertella
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Danny V Jeyaraju
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Samir H Barghout
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | | | - Yulia Jitkova
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | | | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| |
Collapse
|
33
|
Hynynen J, Pokka T, Komulainen-Ebrahim J, Myllynen P, Kärppä M, Pylvänen L, Kälviäinen R, Sokka A, Jyrkilä A, Lähdetie J, Haataja L, Mäkitalo A, Ylikotila P, Eriksson K, Haapala P, Ansakorpi H, Hinttala R, Vieira P, Majamaa K, Rantala H, Uusimaa J. Variants p.Q1236H and p.E1143G in mitochondrial DNA polymerase gamma POLG1 are not associated with increased risk for valproate-induced hepatotoxicity or pancreatic toxicity: A retrospective cohort study of patients with epilepsy. Epilepsia 2018; 59:2125-2136. [PMID: 30255931 DOI: 10.1111/epi.14568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Previous studies have suggested that heterozygous variants p.Q1236H and p.E1143G in mitochondrial DNA polymerase gamma (POLG1) increase the risk for liver injury for patients on valproate (VPA) therapy. We assessed the prevalence of these common variants and seven other pathogenic mutations in POLG1 and determined the occurrence of VPA-induced hepatotoxicity (VHT) or pancreatic toxicity in a cohort of patients with epilepsy. METHODS Patients with epilepsy (N = 367) were retrospectively identified from medical record files and screened for mutations in POLG1. Patients who had received VPA monotherapy and carried either of the two variants, p.Q1236H or p.E1143G, without other pathogenic mutations in POLG1 (n = 33, variant group) and patients without these variants (n = 28, nonvariant group) were included in the study. Clinical data on epilepsy, characteristics of VPA treatment, risk factors for VHT, laboratory data on liver and pancreas functions, and adverse effects were collected. RESULTS A total of 122 patients had either the POLG1 p.Q1236H (n = 99) or p.E1143G (n = 24) variant in the heterozygous or homozygous state. Transient liver dysfunction was identified in three (n = 33, 9.1%) variant group patients and in one (n = 28, 3.6%) nonvariant group patient (P = 0.62). Mild to moderate elevations in liver enzymes were encountered in both groups. Furthermore, two patients on VPA polytherapy developed acute pancreatitis, and two pediatric patients with heterozygous p.Q1236H variants and mutations in IQSEC2 and GLDC, respectively, had elevated levels of VPA metabolites in urine, elevated plasma glycine, and/or increased acylglycine excretion. SIGNIFICANCE POLG1 p.Q1236H and p.E1143G variants could not be identified as statistically significant risk factors for VHT or pancreatic toxicity. We suggest that VPA treatment could be suitable for patients who harbor these common variants in the absence of other pathogenic mutations in POLG1.
Collapse
Affiliation(s)
- Johanna Hynynen
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Tytti Pokka
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Jonna Komulainen-Ebrahim
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | | | - Mikko Kärppä
- Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland
| | - Laura Pylvänen
- Department of Neurology, Oulu University Hospital, Oulu, Finland
| | - Reetta Kälviäinen
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Arja Sokka
- Institute of Clinical Medicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.,Department of Pediatric Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Aino Jyrkilä
- Institute of Clinical Medicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.,Department of Pediatric Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana Lähdetie
- Department of Child Neurology, University of Turku and Turku University Central Hospital, Turku, Finland
| | - Leena Haataja
- Department of Pediatric Neurology, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anna Mäkitalo
- Department of Child Neurology, University of Turku and Turku University Central Hospital, Turku, Finland.,Department of Geriatric Medicine, University of Turku, Turku, Finland
| | - Pauli Ylikotila
- Department of Neurology, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Division of Clinical Neurosciences, Turku University Hospital, Turku, Finland
| | - Kai Eriksson
- Tampere Center for Child Health Research and Pediatric Neurology, Tampere University Hospital, Tampere, Finland
| | - Piia Haapala
- Outpatient Intellectual Disabilities Clinic, Tampere University Hospital, Tampere, Finland
| | - Hanna Ansakorpi
- Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland
| | - Reetta Hinttala
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Päivi Vieira
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Kari Majamaa
- Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland
| | - Heikki Rantala
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Johanna Uusimaa
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| |
Collapse
|
34
|
Mitochondrial DNA replication: clinical syndromes. Essays Biochem 2018; 62:297-308. [PMID: 29950321 DOI: 10.1042/ebc20170101] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/17/2018] [Accepted: 05/23/2018] [Indexed: 02/08/2023]
Abstract
Each nucleated cell contains several hundreds of mitochondria, which are unique organelles in being under dual genome control. The mitochondria contain their own DNA, the mtDNA, but most of mitochondrial proteins are encoded by nuclear genes, including all the proteins required for replication, transcription, and repair of mtDNA. MtDNA replication is a continuous process that requires coordinated action of several enzymes that are part of the mtDNA replisome. It also requires constant supply of deoxyribonucleotide triphosphates(dNTPs) and interaction with other mitochondria for mixing and unifying the mitochondrial compartment. MtDNA maintenance defects are a growing list of disorders caused by defects in nuclear genes involved in different aspects of mtDNA replication. As a result of defects in these genes, mtDNA depletion and/or multiple mtDNA deletions develop in affected tissues resulting in variable manifestations that range from adult-onset mild disease to lethal presentation early in life.
Collapse
|
35
|
Hikmat O, Naess K, Engvall M, Klingenberg C, Rasmussen M, Tallaksen CME, Brodtkorb E, Fiskerstrand T, Isohanni P, Uusimaa J, Darin N, Rahman S, Bindoff LA. Elevated cerebrospinal fluid protein inPOLG-related epilepsy: Diagnostic and prognostic implications. Epilepsia 2018; 59:1595-1602. [DOI: 10.1111/epi.14459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Omar Hikmat
- Department of Pediatrics; Haukeland University Hospital; Bergen Norway
- Department of Clinical Medicine (K1); University of Bergen; Bergen Norway
| | - Karin Naess
- Center for Inherited Metabolic Diseases; Karolinska University Hospital; Stockholm Sweden
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; Stockholm Sweden
| | - Martin Engvall
- Center for Inherited Metabolic Diseases; Karolinska University Hospital; Stockholm Sweden
- Department of Molecular Medicine and Surgery; Karolinska Institute; Stockholm Sweden
| | - Claus Klingenberg
- Department of Pediatric and Adolescent Medicine; University Hospital of North Norway; Tromso Norway
- Pediatric Research Group; Department of Clinical Medicine; UiT-Arctic University of Norway; Tromso Norway
| | - Magnhild Rasmussen
- Women and Children's Division; Department of Clinical Neurosciences for Children; Oslo University Hospital; Oslo Norway
- Unit for Congenital and Hereditary Neuromuscular Disorders; Department of Neurology; Oslo University Hospital; Oslo Norway
| | - Chantal M. E. Tallaksen
- Department of Neurology; Oslo University Hospital; Oslo Norway
- Institute of Clinical Medicine; Faculty of Medicine; University of Oslo; Oslo Norway
| | - Eylert Brodtkorb
- Department of Neuroscience; Norwegian University of Science and Technology; Trondheim Norway
- Department of Neurology and Clinical Neurophysiology; St. Olav's University Hospital; Trondheim Norway
| | - Torunn Fiskerstrand
- Department of Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
- Department of Clinical Science (K2); University of Bergen; Bergen Norway
| | - Pirjo Isohanni
- Department of Pediatric Neurology; Children's Hospital; University of Helsinki and Helsinki University Hospital; Helsinki Finland
- Research Programs Unit; Molecular Neurology; Biomedicum Helsinki; University of Helsinki; Helsinki Finland
| | - Johanna Uusimaa
- PEDEGO Research Unit and Biocenter Oulu; University of Oulu; Oulu Finland
- Department of Children and Adolescents; Medical Research Center; Oulu University Hospital; Oulu Finland
| | - Niklas Darin
- Department of Pediatrics; Queen Silvia Children's Hospital; University of Gothenburg; Gothenburg Sweden
| | - Shamima Rahman
- Mitochondrial Research Group; University College London Great Ormond Street Institute of Child Health; London UK
- Metabolic Unit; Great Ormond Street Hospital for Children; National Health Service Foundation Trust; London UK
| | - Laurence A. Bindoff
- Department of Clinical Medicine (K1); University of Bergen; Bergen Norway
- Department of Neurology; Haukeland University Hospital; Bergen Norway
| |
Collapse
|
36
|
Prasad R, Çağlayan M, Dai DP, Nadalutti CA, Zhao ML, Gassman NR, Janoshazi AK, Stefanick DF, Horton JK, Krasich R, Longley MJ, Copeland WC, Griffith JD, Wilson SH. DNA polymerase β: A missing link of the base excision repair machinery in mammalian mitochondria. DNA Repair (Amst) 2017; 60:77-88. [PMID: 29100041 PMCID: PMC5919216 DOI: 10.1016/j.dnarep.2017.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mitochondrial genome integrity is fundamental to mammalian cell viability. Since mitochondrial DNA is constantly under attack from oxygen radicals released during ATP production, DNA repair is vital in removing oxidatively generated lesions in mitochondrial DNA, but the presence of a strong base excision repair system has not been demonstrated. Here, we addressed the presence of such a system in mammalian mitochondria involving the primary base lesion repair enzyme DNA polymerase (pol) β. Pol β was localized to mammalian mitochondria by electron microscopic-immunogold staining, immunofluorescence co-localization and biochemical experiments. Extracts from purified mitochondria exhibited base excision repair activity that was dependent on pol β. Mitochondria from pol β-deficient mouse fibroblasts had compromised DNA repair and showed elevated levels of superoxide radicals after hydrogen peroxide treatment. Mitochondria in pol β-deficient fibroblasts displayed altered morphology by electron microscopy. These results indicate that mammalian mitochondria contain an efficient base lesion repair system mediated in part by pol β and thus pol β plays a role in preserving mitochondrial genome stability.
Collapse
Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Melike Çağlayan
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Da-Peng Dai
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Cristina A Nadalutti
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ming-Lang Zhao
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Natalie R Gassman
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA; University of South Alabama Mitchell Cancer Institute, 1660 Springhill Ave, Mobile, AL 36604, USA
| | - Agnes K Janoshazi
- Signal Transduction Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Donna F Stefanick
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Rachel Krasich
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
37
|
Wang D, Li GD, Fan Y, Zhang DF, Bi R, Yu XF, Long H, Li YY, Yao YG. The mtDNA replication-related genes TFAM and POLG are associated with leprosy in Han Chinese from Southwest China. J Dermatol Sci 2017; 88:349-356. [PMID: 28958595 DOI: 10.1016/j.jdermsci.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND The pathogen Mycobacterium leprae of leprosy is heavily dependent on the host energy metabolites and nutritional products for survival. Previously we and others have identified associations of several mitochondrion-related genes and mitochondrial DNA (mtDNA) copy number alterations with leprosy and/or its subtype. We hypothesized that genetic variants of mtDNA replication-related genes would affect leprosy. OBJECTIVE We aimed to identify genetic associations between the mtDNA replication-related genes TFAM, POLG and leprosy. METHODS Genetic association study was performed in 2898 individuals from two independent sample sets in Yunnan Province, China. We first screened 7 tag SNPs of TFAM and POLG in 527 leprosy cases and 583 controls (Sample I). Expression quantitative trait loci (eQTL) analysis and differential mRNA expression were analyzed to discern potential effect of risk variants. The entire exon region of TFAM and POLG were further analyzed in 798 leprosy cases and 990 controls (Sample II; 4327 East Asians from the ExAC dataset was included as a reference control) by using targeted gene sequencing for fine mapping potentially causal variants. RESULTS Two tag SNPs of TFAM (rs1049432, P=0.007) and POLG (rs3176238, P=0.006) were associated with multibacillary leprosy (MB) in Sample I and the significance survived correction for multiple comparisons. SNPs rs1937 of TFAM (which was linked with rs1049432) and rs61756401 of POLG were associated with leprosy, whereas no potentially causative coding variants were identified in Sample II. The eQTL analysis showed that rs1049432 was a significant cis eQTL for TFAM in nerve tissue (P=1.20×10-12), and rs3176238 was a significant cis eQTL for POLG in nerve (P=3.90×10-13) and skin tissues (P=2.50×10-11). Consistently, mRNA level of POLG was differentially expressed in leprotic skin lesions. CONCLUSIONS Genetic variants of TFAM and POLG were associated with leprosy in Han Chinese, presumably by affecting gene expression.
Collapse
Affiliation(s)
- Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Guo-Dong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Xiu-Feng Yu
- Wenshan Institute of Dermatology, Wenshan, Yunnan, 663000, China
| | - Heng Long
- Wenshan Institute of Dermatology, Wenshan, Yunnan, 663000, China
| | - Yu-Ye Li
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| |
Collapse
|
38
|
Hikmat O, Eichele T, Tzoulis C, Bindoff LA. Understanding the Epilepsy in POLG Related Disease. Int J Mol Sci 2017; 18:ijms18091845. [PMID: 28837072 PMCID: PMC5618494 DOI: 10.3390/ijms18091845] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 12/31/2022] Open
Abstract
Epilepsy is common in polymerase gamma (POLG) related disease and is associated with high morbidity and mortality. Epileptiform discharges typically affect the occipital regions initially and focal seizures, commonly evolving to bilateral convulsive seizures which are the most common seizure types in both adults and children. Our work has shown that mtDNA depletion—i.e., the quantitative loss of mtDNA—in neurones is the earliest and most important factor of the subsequent development of cellular dysfunction. Loss of mtDNA leads to loss of mitochondrial respiratory chain (MRC) components that, in turn, progressively disables energy metabolism. This critically balanced neuronal energy metabolism leads to both a chronic and continuous attrition (i.e., neurodegeneration) and it leaves the neurone unable to cope with increased demand that can trigger a potentially catastrophic cycle that results in acute focal necrosis. We believe that it is the onset of epilepsy that triggers the cascade of damage. These events can be identified in the stepwise evolution that characterizes the clinical, Electroencephalography (EEG), neuro-imaging, and neuropathology findings. Early recognition with prompt and aggressive seizure management is vital and may play a role in modifying the epileptogenic process and improving survival.
Collapse
Affiliation(s)
- Omar Hikmat
- Department of Pediatrics, Haukeland University Hospital, 5021 Bergen, Norway.
- Department of Clinical Medicine (K1), University of Bergen, 5020 Bergen, Norway.
| | - Tom Eichele
- K.G. Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, 5009 Bergen, Norway.
- Department of Biological and Medical Psychology, University of Bergen, 5009 Bergen, Norway.
- Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway.
| | - Charalampos Tzoulis
- Department of Clinical Medicine (K1), University of Bergen, 5020 Bergen, Norway.
- Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway.
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, 5020 Bergen, Norway.
- Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway.
| |
Collapse
|
39
|
Chan SSL. Inherited mitochondrial genomic instability and chemical exposures. Toxicology 2017; 391:75-83. [PMID: 28756246 DOI: 10.1016/j.tox.2017.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/12/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022]
Abstract
There are approximately 1500 proteins that are needed for mitochondrial structure and function, most of which are encoded in the nuclear genome (Calvo et al., 2006). Each mitochondrion has its own genome (mtDNA), which in humans encodes 13 polypeptides, 22 tRNAs and 2 rRNAs required for oxidative phosphorylation. The mitochondrial genome of humans and most vertebrates is approximately 16.5kbp, double-stranded, circular, with few non-coding bases. Thus, maintaining mtDNA stability, that is, the ability of the cell to maintain adequate levels of mtDNA template for oxidative phosphorylation is essential and can be impacted by the level of mtDNA mutation currently within the cell or mitochondrion, but also from errors made during normal mtDNA replication, defects in mitochondrial quality control mechanisms, and exacerbated by exposures to exogenous and/or endogenous genotoxic agents. In this review, we expand on the origins and consequences of mtDNA instability, the current state of research regarding the mechanisms by which mtDNA instability can be overcome by cellular and chemical interventions, and the future of research and treatments for mtDNA instability.
Collapse
Affiliation(s)
- Sherine S L Chan
- Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, SC 29425, United States; Neuroene Therapeutics, Mt. Pleasant, SC 29464, United States.
| |
Collapse
|
40
|
Saki M, Prakash A. DNA damage related crosstalk between the nucleus and mitochondria. Free Radic Biol Med 2017; 107:216-227. [PMID: 27915046 PMCID: PMC5449269 DOI: 10.1016/j.freeradbiomed.2016.11.050] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/25/2016] [Accepted: 11/29/2016] [Indexed: 12/18/2022]
Abstract
The electron transport chain is the primary pathway by which a cell generates energy in the form of ATP. Byproducts of this process produce reactive oxygen species that can cause damage to mitochondrial DNA. If not properly repaired, the accumulation of DNA damage can lead to mitochondrial dysfunction linked to several human disorders including neurodegenerative diseases and cancer. Mitochondria are able to combat oxidative DNA damage via repair mechanisms that are analogous to those found in the nucleus. Of the repair pathways currently reported in the mitochondria, the base excision repair pathway is the most comprehensively described. Proteins that are involved with the maintenance of mtDNA are encoded by nuclear genes and translocate to the mitochondria making signaling between the nucleus and mitochondria imperative. In this review, we discuss the current understanding of mitochondrial DNA repair mechanisms and also highlight the sensors and signaling pathways that mediate crosstalk between the nucleus and mitochondria in the event of mitochondrial stress.
Collapse
Affiliation(s)
- Mohammad Saki
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604, United States
| | - Aishwarya Prakash
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604, United States.
| |
Collapse
|
41
|
DeBalsi KL, Longley MJ, Hoff KE, Copeland WC. Synergistic Effects of the in cis T251I and P587L Mitochondrial DNA Polymerase γ Disease Mutations. J Biol Chem 2017; 292:4198-4209. [PMID: 28154168 DOI: 10.1074/jbc.m116.773341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/26/2017] [Indexed: 01/28/2023] Open
Abstract
Human mitochondrial DNA (mtDNA) polymerase γ (Pol γ) is the only polymerase known to replicate the mitochondrial genome. The Pol γ holoenzyme consists of the p140 catalytic subunit (POLG) and the p55 homodimeric accessory subunit (POLG2), which enhances binding of Pol γ to DNA and promotes processivity of the holoenzyme. Mutations within POLG impede maintenance of mtDNA and cause mitochondrial diseases. Two common POLG mutations usually found in cis in patients primarily with progressive external ophthalmoplegia generate T251I and P587L amino acid substitutions. To determine whether T251I or P587L is the primary pathogenic allele or whether both substitutions are required to cause disease, we overproduced and purified WT, T251I, P587L, and T251I + P587L double variant forms of recombinant Pol γ. Biochemical characterization of these variants revealed impaired DNA binding affinity, reduced thermostability, diminished exonuclease activity, defective catalytic activity, and compromised DNA processivity, even in the presence of the p55 accessory subunit. However, physical association with p55 was unperturbed, suggesting intersubunit affinities similar to WT. Notably, although the single mutants were similarly impaired, a dramatic synergistic effect was found for the double mutant across all parameters. In conclusion, our analyses suggest that individually both T251I and P587L substitutions functionally impair Pol γ, with greater pathogenicity predicted for the single P587L variant. Combining T251I and P587L induces extreme thermal lability and leads to synergistic nucleotide and DNA binding defects, which severely impair catalytic activity and correlate with presentation of disease in patients.
Collapse
Affiliation(s)
- Karen L DeBalsi
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Matthew J Longley
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Kirsten E Hoff
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - William C Copeland
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| |
Collapse
|
42
|
Da Pozzo P, Cardaioli E, Rubegni A, Gallus GN, Malandrini A, Rufa A, Battisti C, Carluccio MA, Rocchi R, Giannini F, Bianchi A, Mancuso M, Siciliano G, Dotti MT, Federico A. Novel POLG mutations and variable clinical phenotypes in 13 Italian patients. Neurol Sci 2017; 38:563-570. [DOI: 10.1007/s10072-016-2734-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/07/2016] [Indexed: 11/29/2022]
|
43
|
Liyanage SU, Coyaud E, Laurent EMN, Hurren R, Maclean N, Wood SR, Kazak L, Shamas-Din A, Holt I, Raught B, Schimmer A. Characterizing the mitochondrial DNA polymerase gamma interactome by BioID identifies Ruvbl2 localizes to the mitochondria. Mitochondrion 2016; 32:31-35. [PMID: 27845271 DOI: 10.1016/j.mito.2016.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/13/2016] [Accepted: 11/02/2016] [Indexed: 10/20/2022]
Abstract
Human mitochondrial DNA (mtDNA) is replicated by the mitochondrial DNA polymerase gamma (POLG). Using proximity dependent biotin labelling (BioID), we characterized the POLG interactome and identified new interaction partners involved in mtDNA maintenance, transcription, translation and protein quality control. We also identified interaction with the nuclear AAA+ ATPase Ruvbl2, suggesting mitochondrial localization for this protein. Ruvbl2 was detected in mitochondria-enriched fractions in leukemic cells. Additionally, transgenic overexpression of Ruvbl2 from an alternative translation initiation site resulted in mitochondrial co-localization. Overall, POLG interactome mapping identifies novel proteins which support mitochondrial biogenesis and a potential novel mitochondrial isoform of Ruvbl2.
Collapse
Affiliation(s)
- Sanduni U Liyanage
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, ON, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Neil Maclean
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Stuart R Wood
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Lawrence Kazak
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Aisha Shamas-Din
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ian Holt
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aaron Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, ON, Canada.
| |
Collapse
|
44
|
Adjusting MtDNA Quantification in Whole Blood for Peripheral Blood Platelet and Leukocyte Counts. PLoS One 2016; 11:e0163770. [PMID: 27736919 PMCID: PMC5063275 DOI: 10.1371/journal.pone.0163770] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/14/2016] [Indexed: 12/28/2022] Open
Abstract
Alterations of mitochondrial DNA copy number (mtDNAcn) in the blood (mitochondrial to nuclear DNA ratio) appear associated with several systemic diseases, including primary mitochondrial disorders, carcinogenesis, and hematologic diseases. Measuring mtDNAcn in DNA extracted from whole blood (WB) instead of from peripheral blood mononuclear cells or buffy coat may yield different results due to mitochondrial DNA present in platelets. The aim of this work is to quantify the contribution of platelets to mtDNAcn in whole blood [mtDNAcn(WB)] and to propose a correction formula to estimate leukocytes' mtDNAcn [mtDNAcn(L)] from mtDNAcn(WB). Blood samples from 10 healthy adults were combined with platelet-enriched plasma and saline solution to produce artificial blood preparations. Aliquots of each sample were combined with five different platelet concentrations. In 46 of these blood preparations, mtDNAcn was measured by qPCR. MtDNAcn(WB) increased 1.07 (95%CI 0.86, 1.29; p<0.001) per 1000 platelets present in the preparation. We proved that leukocyte count should also be taken into account as mtDNAcn(WB) was inversely associated with leukocyte count; it increased 1.10 (95%CI 0.95, 1.25, p<0.001) per unit increase of the ratio between platelet and leukocyte counts. If hematological measurements are available, subtracting 1.10 the platelets/leukocyte ratio from mtDNAcn(WB) may serve as an estimation for mtDNAcn(L). Both platelet and leukocyte counts in the sample are important sources of variation if comparing mtDNAcn among groups of patients when mtDNAcn is measured in DNA extracted from whole blood. Not taking the platelet/leukocyte ratio into account in whole blood measurements, may lead to overestimation and misclassification if interpreted as leukocytes' mtDNAcn.
Collapse
|
45
|
Saneto RP. Alpers-Huttenlocher syndrome: the role of a multidisciplinary health care team. J Multidiscip Healthc 2016; 9:323-33. [PMID: 27555780 PMCID: PMC4968991 DOI: 10.2147/jmdh.s84900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Alpers–Huttenlocher syndrome (AHS) is a mitochondrial DNA-depletion syndrome. Age of onset is bimodal: early onset at 2–4 years and later adolescent onset at 17–24 years of age. Early development is usually normal, with epilepsy heralding the disorder in ~50% of patients. The onset of seizures is coupled with progressive cognitive decline. Hepatopathy is variable, and when present is a progressive dysfunction leading to liver failure in many cases. These features of seizures, cognitive degeneration, and hepatopathy represent the “classic triad” of AHS. However, most patients develop other system involvement. Therefore, although AHS is ultimately a lethal disorder, medical care is required for sustained quality of life. Frequently, additional organ systems – gastrointestinal, respiratory, nutritional, and psychiatric – abnormalities appear and need treatment. Rarely, cardiovascular dysfunction and even pregnancy complicate medical treatment. Optimal care requires a team of physicians and caretakers to make sure quality of life is optimized. The care team, together with the family and palliative care specialists, need to be in communication as the disease progresses and medical changes occur. Although the unpredictable losses of function challenge medical care, the team approach can foster the individual quality-of-life care needed for the patient and family.
Collapse
Affiliation(s)
- Russell P Saneto
- Department of Neurology, University of Washington; Division of Pediatric Neurology, Seattle Children's Hospital, Seattle, WA, USA
| |
Collapse
|
46
|
Chuquilin M, Govindarajan R, Peck D, Font-Montgomery E. Response to immunotherapy in a patient with adult onset Leigh syndrome and T9176C mtDNA mutation. Mol Genet Metab Rep 2016; 8:28-32. [PMID: 27408822 PMCID: PMC4932611 DOI: 10.1016/j.ymgmr.2016.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 01/06/2023] Open
Abstract
Leigh syndrome is a mitochondrial disease caused by mutations in different genes, including ATP6A for which no known therapy is available. We report a case of adult-onset Leigh syndrome with response to immunotherapy. A twenty year-old woman with baseline learning difficulties was admitted with progressive behavioral changes, diplopia, headaches, bladder incontinence, and incoordination. Brain MRI and PET scan showed T2 hyperintensity and increased uptake in bilateral basal ganglia, respectively. Autoimmune encephalitis was suspected and she received plasmapheresis with clinical improvement. She was readmitted 4 weeks later with dysphagia and aspiration pneumonia. Plasmapheresis was repeated with resolution of her symptoms. Given the multisystem involvement and suggestive MRI changes, genetic testing was done, revealing a homoplasmic T9176C ATPase 6 gene mtDNA mutation. Monthly IVIG provided clinical improvement with worsening when infusions were delayed. Leigh syndrome secondary to mtDNA T9176C mutations could have an autoimmune mechanism that responds to immunotherapy.
Collapse
Affiliation(s)
- Miguel Chuquilin
- Department of Neurology, University of Missouri in Columbia, Five Hospital Drive CE 537 DC 047.00, Columbia, MO 65212, USA
| | - Raghav Govindarajan
- Department of Neurology, University of Missouri in Columbia, Five Hospital Drive CE 537, Columbia, MO 65212, USA
| | - Dawn Peck
- Department of Genetics, University of Missouri in Columbia, 404 N Keene St, Suite 101, Columbia, MO 65201, USA
| | - Esperanza Font-Montgomery
- Department of Genetics, University of Missouri in Columbia, 404 N Keene St, Suite 101, Columbia, MO 65201, USA
| |
Collapse
|
47
|
Souren NYP, Gerdes LA, Kümpfel T, Lutsik P, Klopstock T, Hohlfeld R, Walter J. Mitochondrial DNA Variation and Heteroplasmy in Monozygotic Twins Clinically Discordant for Multiple Sclerosis. Hum Mutat 2016; 37:765-75. [PMID: 27119776 DOI: 10.1002/humu.23003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/10/2016] [Indexed: 12/22/2022]
Abstract
We examined the debated link between mitochondrial DNA (mtDNA) variation and multiple sclerosis (MS) using 49 monozygotic (MZ) twin pairs clinically discordant for MS, which enables to associate de novo mtDNA variants, skewed heteroplasmy, and mtDNA copy number with MS manifestation. Ultra-deep sequencing of blood-derived mtDNA revealed 25 heteroplasmic variants with potentially pathogenic features in 18 pairs. All variants were pair-specific and had low and/or similar heteroplasmy levels in both cotwins. In one pair, a confirmed pathogenic variant (m.11778G>A, heteroplasmy ∼50%) associated with Leber hereditary optic neuropathy was detected. Detailed diagnostic investigation revealed subclinical MS signs in the prior nondiseased cotwin. Moreover, neither mtDNA deletions nor copy-number variations were involved. Furthermore, the majority of heteroplasmic variants were shared among MZ twins and exhibited more similar heteroplasmy levels in the same tissue of MZ twins as compared with different tissues of the same individual. Heteroplasmy levels were also more similar within MZ twins compared with nonidentical siblings. Our analysis excludes mtDNA variation as a major driver of the discordant clinical manifestation of MS in MZ twins, and provides valuable insights into the occurrence and distribution of heteroplasmic variants within MZ twins and nonidentical siblings, and across different tissues.
Collapse
Affiliation(s)
- Nicole Y P Souren
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Lisa A Gerdes
- Institute of Clinical Neuroimmunology, Medical Campus Großhadern, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, Medical Campus Großhadern, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Pavlo Lutsik
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,DZNE - German Center for Neurodegenerative Diseases, Munich, Germany
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, Medical Campus Großhadern, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| |
Collapse
|
48
|
Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions. Sci Rep 2016; 6:25186. [PMID: 27122135 PMCID: PMC4848546 DOI: 10.1038/srep25186] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 04/12/2016] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are a common cause of primary mitochondrial disorders, and have also been implicated in a broad collection of conditions, including aging, neurodegeneration, and cancer. Prevalent among these pathogenic variants are mtDNA deletions, which show a strong bias for the loss of sequence in the major arc between, but not including, the heavy and light strand origins of replication. Because individual mtDNA deletions can accumulate focally, occur with multiple mixed breakpoints, and in the presence of normal mtDNA sequences, methods that detect broad-spectrum mutations with enhanced sensitivity and limited costs have both research and clinical applications. In this study, we evaluated semi-quantitative and digital PCR-based methods of mtDNA deletion detection using double-stranded reference templates or biological samples. Our aim was to describe key experimental assay parameters that will enable the analysis of low levels or small differences in mtDNA deletion load during disease progression, with limited false-positive detection. We determined that the digital PCR method significantly improved mtDNA deletion detection sensitivity through absolute quantitation, improved precision and reduced assay standard error.
Collapse
|
49
|
Young MJ, Copeland WC. Human mitochondrial DNA replication machinery and disease. Curr Opin Genet Dev 2016; 38:52-62. [PMID: 27065468 DOI: 10.1016/j.gde.2016.03.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/03/2016] [Accepted: 03/08/2016] [Indexed: 12/21/2022]
Abstract
The human mitochondrial genome is replicated by DNA polymerase γ in concert with key components of the mitochondrial DNA (mtDNA) replication machinery. Defects in mtDNA replication or nucleotide metabolism cause deletions, point mutations, or depletion of mtDNA. The resulting loss of cellular respiration ultimately induces mitochondrial genetic diseases, including mtDNA depletion syndromes (MDS) such as Alpers or early infantile hepatocerebral syndromes, and mtDNA deletion disorders such as progressive external ophthalmoplegia, ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy. Here we review the current literature regarding human mtDNA replication and heritable disorders caused by genetic changes of the POLG, POLG2, Twinkle, RNASEH1, DNA2, and MGME1 genes.
Collapse
Affiliation(s)
- Matthew J Young
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC 27709, United States
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC 27709, United States.
| |
Collapse
|
50
|
Singh B, Owens KM, Bajpai P, Desouki MM, Srinivasasainagendra V, Tiwari HK, Singh KK. Mitochondrial DNA Polymerase POLG1 Disease Mutations and Germline Variants Promote Tumorigenic Properties. PLoS One 2015; 10:e0139846. [PMID: 26468652 PMCID: PMC4607296 DOI: 10.1371/journal.pone.0139846] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/17/2015] [Indexed: 02/04/2023] Open
Abstract
Germline mutations in mitochondrial DNA polymerase gamma (POLG1) induce mitochondrial DNA (mtDNA) mutations, depletion, and decrease oxidative phosphorylation. Earlier, we identified somatic mutations in POLG1 and the contribution of these mutations in human cancer. However, a role for germline variations in POLG1 in human cancers is unknown. In this study, we examined a role for disease associated germline variants of POLG1, POLG1 gene expression, copy number variation and regulation in human cancers. We analyzed the mutations, expression and copy number variation in POLG1 in several cancer databases and validated the analyses in primary breast tumors and breast cancer cell lines. We discovered 5-aza-2'-deoxycytidine led epigenetic regulation of POLG1, mtDNA-encoded genes and increased mitochondrial respiration. We conducted comprehensive race based bioinformatics analyses of POLG1 gene in more than 33,000 European-Americans and 5,000 African-Americans. We identified a mitochondrial disease causing missense variation in polymerase domain of POLG1 protein at amino acid 1143 (E1143G) to be 25 times more prevalent in European-Americans (allele frequency 0.03777) when compared to African-American (allele frequency 0.00151) population. We identified T251I and P587L missense variations in exonuclease and linker region of POLG1 also to be more prevalent in European-Americans. Expression of these variants increased glucose consumption, decreased ATP production and increased matrigel invasion. Interestingly, conditional expression of these variants revealed that matrigel invasion properties conferred by these germline variants were reversible suggesting a role of epigenetic regulators. Indeed, we identified a set of miRNA whose expression was reversible after variant expression was turned off. Together, our studies demonstrate altered genetic and epigenetic regulation of POLG1 in human cancers and suggest a role for POLG1 germline variants in promoting tumorigenic properties.
Collapse
Affiliation(s)
- Bhupendra Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Kjerstin M. Owens
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, United States of America
| | - Prachi Bajpai
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Mohamed Mokhtar Desouki
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, United States of America
| | - Vinodh Srinivasasainagendra
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Hemant K. Tiwari
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Keshav K. Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Environmental Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Center for Aging, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Birmingham Veterans Affairs Medical Center, Birmingham, AL, 35294, United States of America
- * E-mail:
| |
Collapse
|