1
|
Árnadóttir ER, Moore KHS, Guðmundsdóttir VB, Ebenesersdóttir SS, Guity K, Jónsson H, Stefánsson K, Helgason A. The rate and nature of mitochondrial DNA mutations in human pedigrees. Cell 2024; 187:3904-3918.e8. [PMID: 38851187 DOI: 10.1016/j.cell.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/06/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024]
Abstract
We examined the rate and nature of mitochondrial DNA (mtDNA) mutations in humans using sequence data from 64,806 contemporary Icelanders from 2,548 matrilines. Based on 116,663 mother-child transmissions, 8,199 mutations were detected, providing robust rate estimates by nucleotide type, functional impact, position, and different alleles at the same position. We thoroughly document the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants. The results reveal the impact of negative selection on viable deleterious mutations, including rapidly mutating disease-associated 3243A>G and 1555A>G and pre-natal selection that most likely occurs during the development of oocytes. Finally, we show that the fate of new mutations is determined by a drastic germline bottleneck, amounting to an average of 3 mtDNA units effectively transmitted from mother to child.
Collapse
Affiliation(s)
| | | | - Valdís B Guðmundsdóttir
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | - Kamran Guity
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kári Stefánsson
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland.
| |
Collapse
|
2
|
Somasundaram I, Jain SM, Blot-Chabaud M, Pathak S, Banerjee A, Rawat S, Sharma NR, Duttaroy AK. Mitochondrial dysfunction and its association with age-related disorders. Front Physiol 2024; 15:1384966. [PMID: 39015222 PMCID: PMC11250148 DOI: 10.3389/fphys.2024.1384966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
Aging is a complex process that features a functional decline in many organelles. Various factors influence the aging process, such as chromosomal abnormalities, epigenetic changes, telomere shortening, oxidative stress, and mitochondrial dysfunction. Mitochondrial dysfunction significantly impacts aging because mitochondria regulate cellular energy, oxidative balance, and calcium levels. Mitochondrial integrity is maintained by mitophagy, which helps maintain cellular homeostasis, prevents ROS production, and protects against mtDNA damage. However, increased calcium uptake and oxidative stress can disrupt mitochondrial membrane potential and permeability, leading to the apoptotic cascade. This disruption causes increased production of free radicals, leading to oxidative modification and accumulation of mitochondrial DNA mutations, which contribute to cellular dysfunction and aging. Mitochondrial dysfunction, resulting from structural and functional changes, is linked to age-related degenerative diseases. This review focuses on mitochondrial dysfunction, its implications in aging and age-related disorders, and potential anti-aging strategies through targeting mitochondrial dysfunction.
Collapse
Affiliation(s)
- Indumathi Somasundaram
- Biotechnology Engineering, Kolhapur Institute of Technology’s College of Engineering, Kolhapur, India
| | - Samatha M. Jain
- Department of Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Chennai, India
| | | | - Surajit Pathak
- Department of Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Chennai, India
| | - Antara Banerjee
- Department of Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Chennai, India
| | - Sonali Rawat
- Stem Cell Facility, DBT-Centre of Excellence for Stem Cell Research, All India Institute of Medical Sciences, New Delhi, India
| | - Neeta Raj Sharma
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Asim K. Duttaroy
- Department of Nutrition, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| |
Collapse
|
3
|
Bury A, Pyle A, Vincent AE, Actis P, Hudson G. Nanobiopsy investigation of the subcellular mtDNA heteroplasmy in human tissues. Sci Rep 2024; 14:13789. [PMID: 38877095 PMCID: PMC11178779 DOI: 10.1038/s41598-024-64455-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Mitochondrial function is critical to continued cellular vitality and is an important contributor to a growing number of human diseases. Mitochondrial dysfunction is typically heterogeneous, mediated through the clonal expansion of mitochondrial DNA (mtDNA) variants in a subset of cells in a given tissue. To date, our understanding of the dynamics of clonal expansion of mtDNA variants has been technically limited to the single cell-level. Here, we report the use of nanobiopsy for subcellular sampling from human tissues, combined with next-generation sequencing to assess subcellular mtDNA mutation load in human tissue from mitochondrial disease patients. The ability to map mitochondrial mutation loads within individual cells of diseased tissue samples will further our understanding of mitochondrial genetic diseases.
Collapse
Affiliation(s)
- Alexander Bury
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK
- Bragg Centre for Materials Research, Leeds, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK.
- Bragg Centre for Materials Research, Leeds, UK.
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
| |
Collapse
|
4
|
Bernardino Gomes TM, Vincent AE, Menger KE, Stewart JB, Nicholls TJ. Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation. Biochem J 2024; 481:683-715. [PMID: 38804971 DOI: 10.1042/bcj20230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.
Collapse
Affiliation(s)
- Tiago M Bernardino Gomes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- NHS England Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, U.K
| | - Amy E Vincent
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - James B Stewart
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| |
Collapse
|
5
|
Neueder A, Kojer K, Gu Z, Wang Y, Hering T, Tabrizi S, Taanman JW, Orth M. Huntington's disease affects mitochondrial network dynamics predisposing to pathogenic mitochondrial DNA mutations. Brain 2024; 147:2009-2022. [PMID: 38195181 DOI: 10.1093/brain/awae007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/27/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
Huntington's disease (HD) predominantly affects the brain, causing a mixed movement disorder, cognitive decline and behavioural abnormalities. It also causes a peripheral phenotype involving skeletal muscle. Mitochondrial dysfunction has been reported in tissues of HD models, including skeletal muscle, and lymphoblast and fibroblast cultures from patients with HD. Mutant huntingtin protein (mutHTT) expression can impair mitochondrial quality control and accelerate mitochondrial ageing. Here, we obtained fresh human skeletal muscle, a post-mitotic tissue expressing the mutated HTT allele at physiological levels since birth, and primary cell lines from HTT CAG repeat expansion mutation carriers and matched healthy volunteers to examine whether such a mitochondrial phenotype exists in human HD. Using ultra-deep mitochondrial DNA (mtDNA) sequencing, we showed an accumulation of mtDNA mutations affecting oxidative phosphorylation. Tissue proteomics indicated impairments in mtDNA maintenance with increased mitochondrial biogenesis of less efficient oxidative phosphorylation (lower complex I and IV activity). In full-length mutHTT expressing primary human cell lines, fission-inducing mitochondrial stress resulted in normal mitophagy. In contrast, expression of high levels of N-terminal mutHTT fragments promoted mitochondrial fission and resulted in slower, less dynamic mitophagy. Expression of high levels of mutHTT fragments due to somatic nuclear HTT CAG instability can thus affect mitochondrial network dynamics and mitophagy, leading to pathogenic mtDNA mutations. We show that life-long expression of mutant HTT causes a mitochondrial phenotype indicative of mtDNA instability in fresh post-mitotic human skeletal muscle. Thus, genomic instability may not be limited to nuclear DNA, where it results in somatic expansion of the HTT CAG repeat length in particularly vulnerable cells such as striatal neurons. In addition to efforts targeting the causative mutation, promoting mitochondrial health may be a complementary strategy in treating diseases with DNA instability such as HD.
Collapse
Affiliation(s)
| | - Kerstin Kojer
- Department of Neurology, Ulm University, 89081 Ulm, Germany
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Yiqin Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Tanja Hering
- Department of Neurology, Ulm University, 89081 Ulm, Germany
| | - Sarah Tabrizi
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
- Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Jan-Willem Taanman
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London NW3 2PF, UK
| | - Michael Orth
- Department of Neurology, Ulm University, 89081 Ulm, Germany
- Swiss Huntington Centre, Siloah AG, 3073 Gümligen, Switzerland
- University Hospital of Old Age Psychiatry and Psychotherapy, Bern University, CH-3000 Bern 60, Switzerland
| |
Collapse
|
6
|
Cai Y, Han Z, Cheng H, Li H, Wang K, Chen J, Liu ZX, Xie Y, Lin Y, Zhou S, Wang S, Zhou X, Jin S. The impact of ageing mechanisms on musculoskeletal system diseases in the elderly. Front Immunol 2024; 15:1405621. [PMID: 38774874 PMCID: PMC11106385 DOI: 10.3389/fimmu.2024.1405621] [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: 03/23/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Ageing is an inevitable process that affects various tissues and organs of the human body, leading to a series of physiological and pathological changes. Mechanisms such as telomere depletion, stem cell depletion, macrophage dysfunction, and cellular senescence gradually manifest in the body, significantly increasing the incidence of diseases in elderly individuals. These mechanisms interact with each other, profoundly impacting the quality of life of older adults. As the ageing population continues to grow, the burden on the public health system is expected to intensify. Globally, the prevalence of musculoskeletal system diseases in elderly individuals is increasing, resulting in reduced limb mobility and prolonged suffering. This review aims to elucidate the mechanisms of ageing and their interplay while exploring their impact on diseases such as osteoarthritis, osteoporosis, and sarcopenia. By delving into the mechanisms of ageing, further research can be conducted to prevent and mitigate its effects, with the ultimate goal of alleviating the suffering of elderly patients in the future.
Collapse
Affiliation(s)
- Yijin Cai
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhongyu Han
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hong Cheng
- School of Automation Engineering, University of Electronic Science and Technology, Chengdu, China
| | - Hongpeng Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ke Wang
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jia Chen
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhi-Xiang Liu
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yulong Xie
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yumeng Lin
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuwei Zhou
- Jiangsu Key Laboratory of Molecular and Functional Imaging, Department of Radiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Siyu Wang
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Xiao Zhou
- Second Clinical Medical College, Heilongjiang University of Chinese Medicine, Heilongjiang, China
| | - Song Jin
- Department of Rehabilitation, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| |
Collapse
|
7
|
Kotrys AV, Durham TJ, Guo XA, Vantaku VR, Parangi S, Mootha VK. Single-cell analysis reveals context-dependent, cell-level selection of mtDNA. Nature 2024; 629:458-466. [PMID: 38658765 PMCID: PMC11078733 DOI: 10.1038/s41586-024-07332-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024]
Abstract
Heteroplasmy occurs when wild-type and mutant mitochondrial DNA (mtDNA) molecules co-exist in single cells1. Heteroplasmy levels change dynamically in development, disease and ageing2,3, but it is unclear whether these shifts are caused by selection or drift, and whether they occur at the level of cells or intracellularly. Here we investigate heteroplasmy dynamics in dividing cells by combining precise mtDNA base editing (DdCBE)4 with a new method, SCI-LITE (single-cell combinatorial indexing leveraged to interrogate targeted expression), which tracks single-cell heteroplasmy with ultra-high throughput. We engineered cells to have synonymous or nonsynonymous complex I mtDNA mutations and found that cell populations in standard culture conditions purge nonsynonymous mtDNA variants, whereas synonymous variants are maintained. This suggests that selection dominates over simple drift in shaping population heteroplasmy. We simultaneously tracked single-cell mtDNA heteroplasmy and ancestry, and found that, although the population heteroplasmy shifts, the heteroplasmy of individual cell lineages remains stable, arguing that selection acts at the level of cell fitness in dividing cells. Using these insights, we show that we can force cells to accumulate high levels of truncating complex I mtDNA heteroplasmy by placing them in environments where loss of biochemical complex I activity has been reported to benefit cell fitness. We conclude that in dividing cells, a given nonsynonymous mtDNA heteroplasmy can be harmful, neutral or even beneficial to cell fitness, but that the 'sign' of the effect is wholly dependent on the environment.
Collapse
Affiliation(s)
- Anna V Kotrys
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoyan A Guo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Venkata R Vantaku
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sareh Parangi
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
8
|
Sequeira AN, O’Keefe IP, Katju V, Bergthorsson U. Friend turned foe: selfish behavior of a spontaneously arising mitochondrial deletion in an experimentally evolved Caenorhabditis elegans population. G3 (BETHESDA, MD.) 2024; 14:jkae018. [PMID: 38261394 PMCID: PMC11090458 DOI: 10.1093/g3journal/jkae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
Selfish mitochondrial DNA (mtDNA) mutations are variants that can proliferate within cells and enjoy a replication or transmission bias without fitness benefits for the host. mtDNA deletions in Caenorhabditis elegans can reach high heteroplasmic frequencies despite significantly reducing fitness, illustrating how new mtDNA variants can give rise to genetic conflict between different levels of selection and between the nuclear and mitochondrial genomes. During a mutation accumulation experiment in C. elegans, a 1,034-bp deletion originated spontaneously and reached an 81.7% frequency within an experimental evolution line. This heteroplasmic mtDNA deletion, designated as meuDf1, eliminated portions of 2 protein-coding genes (coxIII and nd4) and tRNA-thr in entirety. mtDNA copy number in meuDf1 heteroplasmic individuals was 35% higher than in individuals with wild-type mitochondria. After backcrossing into a common genetic background, the meuDf1 mitotype was associated with reduction in several fitness traits and independent competition experiments found a 40% reduction in composite fitness. Experiments that relaxed individual selection by single individual bottlenecks demonstrated that the deletion-bearing mtDNA possessed a strong transmission bias, thereby qualifying it as a novel selfish mitotype.
Collapse
Affiliation(s)
- Abigail N Sequeira
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
- Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| | - Ian P O’Keefe
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
- Department of Biochemistry and Molecular Biology, University of Maryland, 655 W. Baltimore Street, Baltimore, MD 21201, USA
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
- Program in Evolutionary Biology, Department of Ecology and Genetics (IEG), Evolutionsbiologiskt centrum, Norbyvägen 18D, Uppsala University, 752 36 Uppsala, Sweden
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
- Program in Evolutionary Biology, Department of Ecology and Genetics (IEG), Evolutionsbiologiskt centrum, Norbyvägen 18D, Uppsala University, 752 36 Uppsala, Sweden
| |
Collapse
|
9
|
Sanchez-Contreras M, Sweetwyne MT, Tsantilas KA, Whitson JA, Campbell MD, Kohrn BF, Kim HJ, Hipp MJ, Fredrickson J, Nguyen MM, Hurley JB, Marcinek DJ, Rabinovitch PS, Kennedy SR. The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging. eLife 2023; 12:e83395. [PMID: 36799304 PMCID: PMC10072880 DOI: 10.7554/elife.83395] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Accumulation of somatic mutations in the mitochondrial genome (mtDNA) has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction that occurs during aging. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low-frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue- and mutation type-dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age suggests a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.
Collapse
Affiliation(s)
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | | | - Jeremy A Whitson
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | | | - Brenden F Kohrn
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Hyeon Jeong Kim
- Department of Biology, University of WashingtonSeattleUnited States
| | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Megan M Nguyen
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - James B Hurley
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - David J Marcinek
- Department of Radiology, University of WashingtonSeattleUnited States
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| |
Collapse
|
10
|
López-Otín C, Blasco MA, Partridge L, Serrano M, Kroemer G. Hallmarks of aging: An expanding universe. Cell 2023; 186:243-278. [PMID: 36599349 DOI: 10.1016/j.cell.2022.11.001] [Citation(s) in RCA: 1099] [Impact Index Per Article: 1099.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/19/2022] [Accepted: 11/01/2022] [Indexed: 01/05/2023]
Abstract
Aging is driven by hallmarks fulfilling the following three premises: (1) their age-associated manifestation, (2) the acceleration of aging by experimentally accentuating them, and (3) the opportunity to decelerate, stop, or reverse aging by therapeutic interventions on them. We propose the following twelve hallmarks of aging: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, disabled macroautophagy, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation, and dysbiosis. These hallmarks are interconnected among each other, as well as to the recently proposed hallmarks of health, which include organizational features of spatial compartmentalization, maintenance of homeostasis, and adequate responses to stress.
Collapse
Affiliation(s)
- Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Linda Partridge
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK; Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; Altos Labs, Cambridge, UK
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| |
Collapse
|
11
|
Li Y, Yang S, Jin X, Li D, Lu J, Wang X, Wu M. Mitochondria as novel mediators linking gut microbiota to atherosclerosis that is ameliorated by herbal medicine: A review. Front Pharmacol 2023; 14:1082817. [PMID: 36733506 PMCID: PMC9886688 DOI: 10.3389/fphar.2023.1082817] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Atherosclerosis (AS) is the main cause of cardiovascular disease (CVD) and is characterized by endothelial damage, lipid deposition, and chronic inflammation. Gut microbiota plays an important role in the occurrence and development of AS by regulating host metabolism and immunity. As human mitochondria evolved from primordial bacteria have homologous characteristics, they are attacked by microbial pathogens as target organelles, thus contributing to energy metabolism disorders, oxidative stress, and apoptosis. Therefore, mitochondria may be a key mediator of intestinal microbiota disorders and AS aggravation. Microbial metabolites, such as short-chain fatty acids, trimethylamine, hydrogen sulfide, and bile acids, also affect mitochondrial function, including mtDNA mutation, oxidative stress, and mitophagy, promoting low-grade inflammation. This further damages cellular homeostasis and the balance of innate immunity, aggravating AS. Herbal medicines and their monomers can effectively ameliorate the intestinal flora and their metabolites, improve mitochondrial function, and inhibit atherosclerotic plaques. This review focuses on the interaction between gut microbiota and mitochondria in AS and explores a therapeutic strategy for restoring mitochondrial function and intestinal microbiota disorders using herbal medicines, aiming to provide new insights for the prevention and treatment of AS.
Collapse
Affiliation(s)
- Yujuan Li
- Guang’an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shengjie Yang
- Guang’an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiao Jin
- Guang’an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dan Li
- Guang’an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jing Lu
- Guang’an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China,Beijing University of Chinese Medicine, Beijing, China
| | - Xinyue Wang
- Guang’an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Min Wu
- Guang’an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China,*Correspondence: Min Wu,
| |
Collapse
|
12
|
High-frequency and functional mitochondrial DNA mutations at the single-cell level. Proc Natl Acad Sci U S A 2023; 120:e2201518120. [PMID: 36577067 PMCID: PMC9910596 DOI: 10.1073/pnas.2201518120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Decline in mitochondrial function underlies aging and age-related diseases, but the role of mitochondrial DNA (mtDNA) mutations in these processes remains elusive. To investigate patterns of mtDNA mutations, it is particularly important to quantify mtDNA mutations and their associated pathogenic effects at the single-cell level. However, existing single-cell mtDNA sequencing approaches remain inefficient due to high cost and low mtDNA on-target rates. In this study, we developed a cost-effective mtDNA targeted-sequencing protocol called single-cell sequencing by targeted amplification of multiplex probes (scSTAMP) and experimentally validated its reliability. We then applied our method to assess single-cell mtDNA mutations in 768 B lymphocytes and 768 monocytes from a 76-y-old female. Across 632 B lymphocyte and 617 monocytes with medium mtDNA coverage over >100×, our results indicated that over 50% of cells carried at least one mtDNA mutation with variant allele frequencies (VAFs) over 20%, and that cells carried an average of 0.658 and 0.712 such mutation for B lymphocytes and monocytes, respectively. Surprisingly, more than 20% of the observed mutations had VAFs of over 90% in either cell population. In addition, over 60% of the mutations were in protein-coding genes, of which over 70% were nonsynonymous, and more than 50% of the nonsynonymous mutations were predicted to be highly pathogenic. Interestingly, about 80% of the observed mutations were singletons in the respective cell populations. Our results revealed mtDNA mutations with functional significance might be prevalent at advanced age, calling further investigation on age-related mtDNA mutation dynamics at the single-cell level.
Collapse
|
13
|
Madan E, Palma AM, Vudatha V, Trevino JG, Natarajan KN, Winn RA, Won KJ, Graham TA, Drapkin R, McDonald SAC, Fisher PB, Gogna R. Cell Competition in Carcinogenesis. Cancer Res 2022; 82:4487-4496. [PMID: 36214625 PMCID: PMC9976200 DOI: 10.1158/0008-5472.can-22-2217] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/04/2022] [Accepted: 09/29/2022] [Indexed: 01/30/2023]
Abstract
The majority of human cancers evolve over time through the stepwise accumulation of somatic mutations followed by clonal selection akin to Darwinian evolution. However, the in-depth mechanisms that govern clonal dynamics and selection remain elusive, particularly during the earliest stages of tissue transformation. Cell competition (CC), often referred to as 'survival of the fittest' at the cellular level, results in the elimination of less fit cells by their more fit neighbors supporting optimal organism health and function. Alternatively, CC may allow an uncontrolled expansion of super-fit cancer cells to outcompete their less fit neighbors thereby fueling tumorigenesis. Recent research discussed herein highlights the various non-cell-autonomous principles, including interclonal competition and cancer microenvironment competition supporting the ability of a tumor to progress from the initial stages to tissue colonization. In addition, we extend current insights from CC-mediated clonal interactions and selection in normal tissues to better comprehend those factors that contribute to cancer development.
Collapse
Affiliation(s)
- Esha Madan
- Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
| | | | - Vignesh Vudatha
- Department of Surgery, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Jose G. Trevino
- Department of Surgery, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | | | - Robert A. Winn
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Kyoung Jae Won
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Trevor A. Graham
- Evolution and Cancer Laboratory, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, U.K
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stuart AC. McDonald
- Clonal Dynamics in Epithelia Laboratory, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square. London, EC1M 6BQ UK
| | - Paul B. Fisher
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Rajan Gogna
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| |
Collapse
|
14
|
Li YJ, Jin X, Li D, Lu J, Zhang XN, Yang SJ, Zhao YX, Wu M. New insights into vascular aging: Emerging role of mitochondria function. Biomed Pharmacother 2022; 156:113954. [DOI: 10.1016/j.biopha.2022.113954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
|
15
|
Chiaratti MR, Chinnery PF. Modulating mitochondrial DNA mutations: factors shaping heteroplasmy in the germ line and somatic cells. Pharmacol Res 2022; 185:106466. [PMID: 36174964 DOI: 10.1016/j.phrs.2022.106466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Until recently it was thought that most humans only harbor one type of mitochondrial DNA (mtDNA), however, deep sequencing and single-cell analysis has shown the converse - that mixed populations of mtDNA (heteroplasmy) are the norm. This is important because heteroplasmy levels can change dramatically during transmission in the female germ line, leading to high levels causing severe mitochondrial diseases. There is also emerging evidence that low level mtDNA mutations contribute to common late onset diseases such as neurodegenerative disorders and cardiometabolic diseases because the inherited mutation levels can change within developing organs and non-dividing cells over time. Initial predictions suggested that the segregation of mtDNA heteroplasmy was largely stochastic, with an equal tendency for levels to increase or decrease. However, transgenic animal work and single-cell analysis have shown this not to be the case during germ-line transmission and in somatic tissues during life. Mutation levels in specific mtDNA regions can increase or decrease in different contexts and the underlying molecular mechanisms are starting to be unraveled. In this review we provide a synthesis of recent literature on the mechanisms of selection for and against mtDNA variants. We identify the most pertinent gaps in our understanding and suggest ways these could be addressed using state of the art techniques.
Collapse
Affiliation(s)
- Marcos R Chiaratti
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
| |
Collapse
|
16
|
Zhang X, Englund DA, Aversa Z, Jachim SK, White TA, LeBrasseur NK. Exercise Counters the Age-Related Accumulation of Senescent Cells. Exerc Sport Sci Rev 2022; 50:213-221. [PMID: 35776782 PMCID: PMC9680689 DOI: 10.1249/jes.0000000000000302] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We propose the beneficial effects of exercise are in part mediated through the prevention and elimination of senescent cells. Exercise counters multiple forms of age-related molecular damage that initiate the senescence program and activates immune cells responsible for senescent cell clearance. Preclinical and clinical evidence for exercise as a senescence-targeting therapy and areas needing further investigation are discussed.
Collapse
Affiliation(s)
- Xu Zhang
- Robert and Arlene Kogod Center on Aging, Rochester, MN
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN
| | - Davis A. Englund
- Robert and Arlene Kogod Center on Aging, Rochester, MN
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN
| | - Zaira Aversa
- Robert and Arlene Kogod Center on Aging, Rochester, MN
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN
| | - Sarah K. Jachim
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN
| | | | - Nathan K. LeBrasseur
- Robert and Arlene Kogod Center on Aging, Rochester, MN
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN
| |
Collapse
|
17
|
Mitochondrial DNA Repair in Neurodegenerative Diseases and Ageing. Int J Mol Sci 2022; 23:ijms231911391. [PMID: 36232693 PMCID: PMC9569545 DOI: 10.3390/ijms231911391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the only organelles, along with the nucleus, that have their own DNA. Mitochondrial DNA (mtDNA) is a double-stranded circular molecule of ~16.5 kbp that can exist in multiple copies within the organelle. Both strands are translated and encode for 22 tRNAs, 2 rRNAs, and 13 proteins. mtDNA molecules are anchored to the inner mitochondrial membrane and, in association with proteins, form a structure called nucleoid, which exerts a structural and protective function. Indeed, mitochondria have evolved mechanisms necessary to protect their DNA from chemical and physical lesions such as DNA repair pathways similar to those present in the nucleus. However, there are mitochondria-specific mechanisms such as rapid mtDNA turnover, fission, fusion, and mitophagy. Nevertheless, mtDNA mutations may be abundant in somatic tissue due mainly to the proximity of the mtDNA to the oxidative phosphorylation (OXPHOS) system and, consequently, to the reactive oxygen species (ROS) formed during ATP production. In this review, we summarise the most common types of mtDNA lesions and mitochondria repair mechanisms. The second part of the review focuses on the physiological role of mtDNA damage in ageing and the effect of mtDNA mutations in neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. Considering the central role of mitochondria in maintaining cellular homeostasis, the analysis of mitochondrial function is a central point for developing personalised medicine.
Collapse
|
18
|
Miwa S, Kashyap S, Chini E, von Zglinicki T. Mitochondrial dysfunction in cell senescence and aging. J Clin Invest 2022; 132:158447. [PMID: 35775483 PMCID: PMC9246372 DOI: 10.1172/jci158447] [Citation(s) in RCA: 248] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial dysfunction and cell senescence are hallmarks of aging and are closely interconnected. Mitochondrial dysfunction, operationally defined as a decreased respiratory capacity per mitochondrion together with a decreased mitochondrial membrane potential, typically accompanied by increased production of oxygen free radicals, is a cause and a consequence of cellular senescence and figures prominently in multiple feedback loops that induce and maintain the senescent phenotype. Here, we summarize pathways that cause mitochondrial dysfunction in senescence and aging and discuss the major consequences of mitochondrial dysfunction and how these consequences contribute to senescence and aging. We also highlight the potential of senescence-associated mitochondrial dysfunction as an antiaging and antisenescence intervention target, proposing the combination of multiple interventions converging onto mitochondrial dysfunction as novel, potent senolytics.
Collapse
Affiliation(s)
- Satomi Miwa
- Newcastle University Biosciences Institute, Ageing Biology Laboratories, Newcastle upon Tyne, United Kingdom
| | - Sonu Kashyap
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Jacksonville, Florida, USA.,Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Eduardo Chini
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Jacksonville, Florida, USA.,Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Thomas von Zglinicki
- Newcastle University Biosciences Institute, Ageing Biology Laboratories, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
19
|
Abstract
Mitochondria are the main source of energy used to maintain cellular homeostasis. This aspect of mitochondrial biology underlies their putative role in age-associated tissue dysfunction. Proper functioning of the electron transport chain (ETC), which is partially encoded by the extra-nuclear mitochondrial genome (mtDNA), is key to maintaining this energy production. The acquisition of de novo somatic mutations that interrupt the function of the ETC have long been associated with aging and common diseases of the elderly. Yet, despite over 30 years of study, the exact role(s) mtDNA mutations play in driving aging and its associated pathologies remains under considerable debate. Furthermore, even fundamental aspects of age-related mtDNA mutagenesis, such as when mutations arise during aging, where and how often they occur across tissues, and the specific mechanisms that give rise to them, remain poorly understood. In this review, we address the current understanding of the somatic mtDNA mutations, with an emphasis of when, where, and how these mutations arise during aging. Additionally, we highlight current limitations in our knowledge and critically evaluate the controversies stemming from these limitations. Lastly, we highlight new and emerging technologies that offer potential ways forward in increasing our understanding of somatic mtDNA mutagenesis in the aging process.
Collapse
Affiliation(s)
- Monica Sanchez-Contreras
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| |
Collapse
|
20
|
Lima T, Li TY, Mottis A, Auwerx J. Pleiotropic effects of mitochondria in aging. NATURE AGING 2022; 2:199-213. [PMID: 37118378 DOI: 10.1038/s43587-022-00191-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/07/2022] [Indexed: 04/30/2023]
Abstract
Aging is typified by a progressive decline in mitochondrial activity and stress resilience. Here, we review how mitochondrial stress pathways have pleiotropic effects on cellular and systemic homeostasis, which can comprise protective or detrimental responses during aging. We describe recent evidence arguing that defects in these conserved adaptive pathways contribute to aging and age-related diseases. Signaling pathways regulating the mitochondrial unfolded protein response, mitochondrial membrane dynamics, and mitophagy are discussed, emphasizing how their failure contributes to heteroplasmy and de-regulation of key metabolites. Our current understanding of how these processes are controlled and interconnected explains how mitochondria can widely impact fundamental aspects of aging.
Collapse
Affiliation(s)
- Tanes Lima
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Terytty Yang Li
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Adrienne Mottis
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
21
|
Yang Q, Liu P, Anderson NS, Shpilka T, Du Y, Naresh NU, Li R, Zhu LJ, Luk K, Lavelle J, Zeinert RD, Chien P, Wolfe SA, Haynes CM. LONP-1 and ATFS-1 sustain deleterious heteroplasmy by promoting mtDNA replication in dysfunctional mitochondria. Nat Cell Biol 2022; 24:181-193. [PMID: 35165413 PMCID: PMC8868506 DOI: 10.1038/s41556-021-00840-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/29/2021] [Indexed: 12/13/2022]
Abstract
The accumulation of deleterious mitochondrial DNA (∆mtDNA) causes inherited mitochondrial diseases and ageing-associated decline in mitochondrial functions such as oxidative phosphorylation. Following mitochondrial perturbations, the bZIP protein ATFS-1 induces a transcriptional programme to restore mitochondrial function. Paradoxically, ATFS-1 is also required to maintain ∆mtDNAs in heteroplasmic worms. The mechanism by which ATFS-1 promotes ∆mtDNA accumulation relative to wild-type mtDNAs is unclear. Here we show that ATFS-1 accumulates in dysfunctional mitochondria. ATFS-1 is absent in healthy mitochondria owing to degradation by the mtDNA-bound protease LONP-1, which results in the nearly exclusive association between ATFS-1 and ∆mtDNAs in heteroplasmic worms. Moreover, we demonstrate that mitochondrial ATFS-1 promotes the binding of the mtDNA replicative polymerase (POLG) to ∆mtDNAs. Interestingly, inhibition of the mtDNA-bound protease LONP-1 increased ATFS-1 and POLG binding to wild-type mtDNAs. LONP-1 inhibition in Caenorhabditis elegans and human cybrid cells improved the heteroplasmy ratio and restored oxidative phosphorylation. Our findings suggest that ATFS-1 promotes mtDNA replication in dysfunctional mitochondria by promoting POLG-mtDNA binding, which is antagonized by LONP-1.
Collapse
Affiliation(s)
- Qiyuan Yang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nadine S Anderson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tomer Shpilka
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - YunGuang Du
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nandhitha Uma Naresh
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Josh Lavelle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rilee D Zeinert
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cole M Haynes
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| |
Collapse
|
22
|
Brunst KJ, Hsu HHL, Zhang L, Zhang X, Carroll KN, Just A, Coull BA, Kloog I, Wright RO, Baccarelli AA, Wright RJ. Prenatal particulate matter exposure and mitochondrial mutational load at the maternal-fetal interface: Effect modification by genetic ancestry. Mitochondrion 2022; 62:102-110. [PMID: 34785263 PMCID: PMC9175302 DOI: 10.1016/j.mito.2021.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/26/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022]
Abstract
Prenatal ambient particulate matter (PM2.5) exposure impacts infant development and alters placental mitochondrial DNA abundance. We investigated whether the timing of PM2.5 exposure predicts placental mitochondrial mutational load using NextGen sequencing in 283 multi-ethnic mother-infant dyads. We observed increased PM2.5exposure, particularly during mid- to late-pregnancy and among genes coding for NADH dehydrogenase and subunits of ATP synthase, was associated with a greater amount of nonsynonymous mutations. The strongest associations were observed for participants of African ancestry. Further work is needed to tease out the role of mitochondrial genetics and its impact on offspring development and emerging disease disparities.
Collapse
Affiliation(s)
- Kelly J Brunst
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267, USA.
| | - Hsiao-Hsien Leon Hsu
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St. New York, NY 10029, USA.
| | - Li Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267, USA.
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267, USA.
| | - Kecia N Carroll
- Kravis Children's Hospital, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St. New York, NY 10029, USA; Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St., New York, NY 10029, USA.
| | - Allan Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St. New York, NY 10029, USA
| | - Brent A Coull
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Ave., Boston, MA 02115, USA.
| | - Itai Kloog
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St. New York, NY 10029, USA; Department of Geography and Environmental Development, Ben-Gurion University of the Negev, P.O.B 653, Beer Sheva, Israel.
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St. New York, NY 10029, USA; Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St., New York, NY 10029, USA.
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, 722 W 168(th) St. New York, NY 10032, USA.
| | - Rosalind J Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St. New York, NY 10029, USA; Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 East 102(nd) St., New York, NY 10029, USA.
| |
Collapse
|
23
|
Wang Y, Zhao G, Fang Z, Pan H, Zhao Y, Wang Y, Zhou X, Wang X, Luo T, Zhang Y, Wang Z, Chen Q, Dong L, Huang Y, Zhou Q, Xia L, Li B, Guo J, Xia K, Tang B, Li J. Genetic landscape of human mitochondrial genome using whole genome sequencing. Hum Mol Genet 2021; 31:1747-1761. [PMID: 34897451 DOI: 10.1093/hmg/ddab358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/26/2021] [Accepted: 12/07/2021] [Indexed: 11/12/2022] Open
Abstract
Increasing evidences suggest that mitochondrial dysfunction is implicated in diseases and aging, and whole-genome sequencing (WGS) is the most unbiased method in analyzing the mitochondrial genome (mtDNA). However, the genetic landscape of mtDNA in the Chinese population has not been fully examined. Here, we described the genetic landscape of mtDNA using WGS data from Chinese individuals (n = 3241). We identified 3892 mtDNA variants, of which 3349 (86%) were rare variants. Interestingly, we observed a trend toward extreme heterogeneity of mtDNA variants. Our study observed a distinct purifying selection on mtDNA, which inhibits the accumulation of harmful heteroplasmies at the individual level: (1) mitochondrial dN/dS ratios were much less than 1; (2) the dN/dS ratio of heteroplasmies was higher than homoplasmies; (3) heteroplasmies had more indels and predicted deleterious variants than homoplasmies. Furthermore, we found that haplogroup M (20.27%) and D (20.15%) had the highest frequencies in the Chinese population, followed by B (18.51%) and F (16.45%). The number of variants per individual differed across haplogroup groups, with a higher number of homoplasmies for the M lineage. Meanwhile, mtDNA copy number was negatively correlated with age but positively correlated with the female sex. Finally, we developed an mtDNA variation database of Chinese populations called MTCards (http://genemed.tech/mtcards/) to facilitate the query of mtDNA variants in this study. In summary, these findings contribute to different aspects of understanding mtDNA, providing a better understanding of the genetic basis of mitochondrial-related diseases.
Collapse
Affiliation(s)
- Yijing Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhenghuan Fang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Hongxu Pan
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yuwen Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yige Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xun Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaomeng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Tengfei Luo
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lijie Dong
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Yuanfeng Huang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jifeng Guo
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| |
Collapse
|
24
|
McCastlain K, Howell CR, Welsh CE, Wang Z, Wilson CL, Mulder HL, Easton J, Mertens AC, Zhang J, Yasui Y, Hudson MM, Robison LL, Kundu M, Ness KK. The Association of Mitochondrial Copy Number With Sarcopenia in Adult Survivors of Childhood Cancer. J Natl Cancer Inst 2021; 113:1570-1580. [PMID: 33871611 PMCID: PMC8562958 DOI: 10.1093/jnci/djab084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Adult childhood cancer survivors are at risk for frailty, including low muscle mass and weakness (sarcopenia). Using peripheral blood mitochondrial DNA copy number (mtDNAcn) as a proxy for functional mitochondria, this study describes cross-sectional associations between mtDNAcn and sarcopenia among survivors. METHODS Among 1762 adult childhood cancer survivors (51.6% male; median age = 29.4 years, interquartile range [IQR] = 23.3-36.8), with a median of 20.6 years from diagnosis (IQR = 15.2-28.2), mtDNAcn estimates were derived from whole-genome sequencing. A subset was validated by quantitative polymerase chain reaction and evaluated cross-sectionally using multivariable logistic regression for their association with sarcopenia, defined by race-, age-, and sex-specific low lean muscle mass or weak grip strength. All statistical tests were 2-sided. RESULTS The prevalence of sarcopenia was 27.0%, higher among female than male survivors (31.5% vs 22.9%; P < .001) and associated with age at diagnosis; 51.7% of survivors with sarcopenia were diagnosed ages 4-13 years (P = .01). Sarcopenia was most prevalent (39.0%) among central nervous system tumor survivors. Cranial radiation (odds ratio [OR] = 1.84, 95% confidence interval [CI] = 1.32 to 2.59) and alkylating agents (OR = 1.34, 95% CI = 1.04 to 1.72) increased, whereas glucocorticoids decreased odds (OR = 0.72, 95% CI = 0.56 to 0.93) of sarcopenia. mtDNAcn decreased with age (β = -0.81, P = .002) and was higher among female survivors (β = 9.23, P = .01) and among survivors with a C allele at mt.204 (β = -17.9, P = .02). In adjusted models, every standard deviation decrease in mtDNAcn increased the odds of sarcopenia 20% (OR = 1.20, 95% CI = 1.07 to 1.34). CONCLUSIONS A growing body of evidence supports peripheral blood mtDNAcn as a biomarker for adverse health outcomes; however, this study is the first to report an association between mtDNAcn and sarcopenia among childhood cancer survivors.
Collapse
Affiliation(s)
- Kelly McCastlain
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Carrie R Howell
- Department of Preventive Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Catherine E Welsh
- Department of Mathematics & Computer Science, Rhodes College, Memphis, TN, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ann C Mertens
- Aflac Cancer & Blood Disorders Center at Children’s Healthcare of Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mondira Kundu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN, USA
| |
Collapse
|
25
|
Mitochondrial DNA in innate immune responses against infectious diseases. Biochem Soc Trans 2021; 48:2823-2838. [PMID: 33155647 DOI: 10.1042/bst20200687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/18/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022]
Abstract
Mitochondrial DNA (mtDNA) can initiate an innate immune response when mislocalized in a compartment other than the mitochondrial matrix. mtDNA plays significant roles in regulating mitochondrial dynamics as well as mitochondrial unfolded protein response (UPR). The mislocalized extra-mtDNA can elicit innate immune response via cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) pathway, inducing the expression of the interferon-stimulated genes (ISGs). Also, cytosolic damaged mtDNA is cleared up by various pathways which are responsible for participating in the activation of inflammatory responses. Four pathways of extra-mitochondrial mtDNA clearance are highlighted in this review - the inflammasome activation mechanism, neutrophil extracellular traps formation, recognition by Toll-like receptor 9 and transfer of mtDNA between cells packaged into extracellular vesicles. Anomalies in these pathways are associated with various diseases. We posit our review in the present pandemic situation and discuss how mtDNA elicits innate immune responses against different viruses and bacteria. This review gives a comprehensive picture of the role of extra-mitochondrial mtDNA in infectious diseases and speculates that research towards its understanding would help establish its therapeutic potential.
Collapse
|
26
|
Accelerated expansion of pathogenic mitochondrial DNA heteroplasmies in Huntington's disease. Proc Natl Acad Sci U S A 2021; 118:2014610118. [PMID: 34301881 PMCID: PMC8325154 DOI: 10.1073/pnas.2014610118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Decline of mitochondrial function may underlie the pathogenesis of many age-related diseases, such as Huntington’s disease (HD). Mitochondrial oxidative phosphorylation (OXPHOS) system is encoded partially by the mitochondrial genome (mtDNA). By investigating mtDNA in lymphoblast and blood samples of HD patients, we found that the expansion of OXPHOS-impairing mtDNA heteroplasmies (coexistence of mutated and wild-type mtDNA) is a molecular feature associated with the functional, motor, and cognitive aspects of HD progression, suggesting that improving mtDNA quality or restoring mitochondrial function could be a potential target for HD treatments. Mitochondrial dysfunction is found in the brain and peripheral tissues of patients diagnosed with Huntington’s disease (HD), an irreversible neurodegenerative disease of which aging is a major risk factor. Mitochondrial function is encoded by not only nuclear DNA but also DNA within mitochondria (mtDNA). Expansion of mtDNA heteroplasmies (coexistence of mutated and wild-type mtDNA) can contribute to age-related decline of mitochondrial function but has not been systematically investigated in HD. Here, by using a sensitive mtDNA-targeted sequencing method, we studied mtDNA heteroplasmies in lymphoblasts and longitudinal blood samples of HD patients. We found a significant increase in the fraction of mtDNA heteroplasmies with predicted pathogenicity in lymphoblasts from 1,549 HD patients relative to lymphoblasts from 182 healthy individuals. The increased fraction of pathogenic mtDNA heteroplasmies in HD lymphoblasts also correlated with advancing HD stages and worsened disease severity measured by HD motor function, cognitive function, and functional capacity. Of note, elongated CAG repeats in HTT promoted age-dependent expansion of pathogenic mtDNA heteroplasmies in HD lymphoblasts. We then confirmed in longitudinal blood samples of 169 HD patients that expansion of pathogenic mtDNA heteroplasmies was correlated with decline in functional capacity and exacerbation of HD motor and cognitive functions during a median follow-up of 6 y. The results of our study indicate accelerated decline of mtDNA quality in HD, and highlight monitoring mtDNA heteroplasmies longitudinally as a way to investigate the progressive decline of mitochondrial function in aging and age-related diseases.
Collapse
|
27
|
Fu L, Luo YX, Liu Y, Liu H, Li HZ, Yu Y. Potential of Mitochondrial Genome Editing for Human Fertility Health. Front Genet 2021; 12:673951. [PMID: 34354734 PMCID: PMC8329452 DOI: 10.3389/fgene.2021.673951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes vital proteins and RNAs for the normal functioning of the mitochondria. Mutations in mtDNA leading to mitochondrial dysfunction are relevant to a large spectrum of diseases, including fertility disorders. Since mtDNA undergoes rather complex processes during gametogenesis and fertilization, clarification of the changes and functions of mtDNA and its essential impact on gamete quality and fertility during this process is of great significance. Thanks to the emergence and rapid development of gene editing technology, breakthroughs have been made in mitochondrial genome editing (MGE), offering great potential for the treatment of mtDNA-related diseases. In this review, we summarize the features of mitochondria and their unique genome, emphasizing their inheritance patterns; illustrate the role of mtDNA in gametogenesis and fertilization; and discuss potential therapies based on MGE as well as the outlook in this field.
Collapse
Affiliation(s)
- Lin Fu
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu-Xin Luo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Ying Liu
- Food Inspection and Quarantine Technology Center of Shenzhen Customs District, FICS, Shenzhen, China
| | - Hui Liu
- Stem Cell Research Center, Peking University Third Hospital, Beijing, China
| | - Hong-Zhen Li
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yang Yu
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Stem Cell Research Center, Peking University Third Hospital, Beijing, China
| |
Collapse
|
28
|
The Isolation and Deep Sequencing of Mitochondrial DNA. Methods Mol Biol 2021. [PMID: 34080167 DOI: 10.1007/978-1-0716-1270-5_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In recent years, next-generation sequencing (NGS) has become a powerful tool for studying both inherited and somatic heteroplasmic mitochondrial DNA (mtDNA) variation. NGS has proved particularly powerful when combined with single-cell isolation techniques, allowing the investigation of low-level heteroplasmic variants both between cells and within tissues. Nevertheless, there remain significant challenges, especially around the selective enrichment of mtDNA from total cellular DNA and the avoidance of nuclear pseudogenes. This chapter summarizes the techniques needed to enrich, amplify, sequence, and analyse mtDNA using NGS .
Collapse
|
29
|
Pereira CV, Gitschlag BL, Patel MR. Cellular mechanisms of mtDNA heteroplasmy dynamics. Crit Rev Biochem Mol Biol 2021; 56:510-525. [PMID: 34120542 DOI: 10.1080/10409238.2021.1934812] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heteroplasmy refers to the coexistence of more than one variant of the mitochondrial genome (mtDNA). Mutated or partially deleted mtDNAs can induce chronic metabolic impairment and cause mitochondrial diseases when their heteroplasmy levels exceed a critical threshold. These mutant mtDNAs can be maternally inherited or can arise de novo. Compelling evidence has emerged showing that mutant mtDNA levels can vary and change in a nonrandom fashion across generations and amongst tissues of an individual. However, our lack of understanding of the basic cellular and molecular mechanisms of mtDNA heteroplasmy dynamics has made it difficult to predict who will inherit or develop mtDNA-associated diseases. More recently, with the advances in technology and the establishment of tractable model systems, insights into the mechanisms underlying the selection forces that modulate heteroplasmy dynamics are beginning to emerge. In this review, we summarize evidence from different organisms, showing that mutant mtDNA can experience both positive and negative selection. We also review the recently identified mechanisms that modulate heteroplasmy dynamics. Taken together, this is an opportune time to survey the literature and to identify key cellular pathways that can be targeted to develop therapies for diseases caused by heteroplasmic mtDNA mutations.
Collapse
Affiliation(s)
- Claudia V Pereira
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| |
Collapse
|
30
|
Sercel AJ, Carlson NM, Patananan AN, Teitell MA. Mitochondrial DNA Dynamics in Reprogramming to Pluripotency. Trends Cell Biol 2021; 31:311-323. [PMID: 33422359 PMCID: PMC7954944 DOI: 10.1016/j.tcb.2020.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/20/2022]
Abstract
Mammalian cells, with the exception of erythrocytes, harbor mitochondria, which are organelles that provide energy, intermediate metabolites, and additional activities to sustain cell viability, replication, and function. Mitochondria contain multiple copies of a circular genome called mitochondrial DNA (mtDNA), whose individual sequences are rarely identical (homoplasmy) because of inherited or sporadic mutations that result in multiple mtDNA genotypes (heteroplasmy). Here, we examine potential mechanisms for maintenance or shifts in heteroplasmy that occur in induced pluripotent stem cells (iPSCs) generated by cellular reprogramming, and further discuss manipulations that can alter heteroplasmy to impact stem and differentiated cell performance. This additional insight will assist in developing more robust iPSC-based models of disease and differentiated cell therapies.
Collapse
Affiliation(s)
- Alexander J Sercel
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Natasha M Carlson
- Department of Biology, California State University Northridge, CA, USA 91330; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Alexander N Patananan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Michael A Teitell
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA 90095; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research University of California, Los Angeles, Los Angeles, CA, USA 90095; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095.
| |
Collapse
|
31
|
Bury AG, Vincent AE, Turnbull DM, Actis P, Hudson G. Mitochondrial isolation: when size matters. Wellcome Open Res 2021; 5:226. [PMID: 33718619 PMCID: PMC7931255 DOI: 10.12688/wellcomeopenres.16300.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial vitality is critical to cellular function, with mitochondrial dysfunction linked to a growing number of human diseases. Tissue and cellular heterogeneity, in terms of genetics, dynamics and function means that increasingly mitochondrial research is conducted at the single cell level. Whilst there are several technologies that are currently available for single-cell analysis, each with their advantages, they cannot be easily adapted to study mitochondria with subcellular resolution. Here we review the current techniques and strategies for mitochondrial isolation, critically discussing each technology's limitations for future mitochondrial research. Finally, we highlight and discuss the recent breakthroughs in sub-cellular isolation techniques, with a particular focus on nanotechnologies that enable the isolation of mitochondria from subcellular compartments. This allows isolation of mitochondria with unprecedented spatial precision with minimal disruption to mitochondria and their immediate cellular environment.
Collapse
Affiliation(s)
- Alexander G Bury
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Amy E Vincent
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Paolo Actis
- Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Gavin Hudson
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| |
Collapse
|
32
|
Ishikawa K, Nakada K. Attempts to understand the mechanisms of mitochondrial diseases: The reverse genetics of mouse models for mitochondrial disease. Biochim Biophys Acta Gen Subj 2020; 1865:129835. [PMID: 33358867 DOI: 10.1016/j.bbagen.2020.129835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/25/2020] [Accepted: 12/18/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mitochondrial disease is a general term for a disease caused by a decline in mitochondrial function. The pathology of this disease is extremely diverse and complex, and the mechanism of its pathogenesis is still unknown. Using mouse models that develop the disease via the same processes as in humans is the easiest path to understanding the underlying mechanism. However, creating a mouse model is extremely difficult due to the lack of technologies that enable editing of mitochondrial DNA (mtDNA). SCOPE OF REVIEW This paper outlines the complex pathogenesis of mitochondrial disease, and the difficulties in producing relevant mouse models. Then, the paper provides a detailed discussion on several mice created with mutations in mtDNA. The paper also introduces the pathology of mouse models with mutations including knockouts of nuclear genes that directly affect mitochondrial function. MAJOR CONCLUSIONS Several mice with mtDNA mutations and those with nuclear DNA mutations have been established. Although these models help elucidate the pathological mechanism of mitochondrial disease, they lack sufficient diversity to enable a complete understanding. Considering the variety of factors that affect the cause and mechanism of mitochondrial disease, it is necessary to account for this background diversity in mouse models as well. GENERAL SIGNIFICANCE Mouse models are indispensable for understanding the pathological mechanism of mitochondrial disease, as well as for searching new treatments. There is a need for the creation and examination of mouse models with more diverse mutations and altered nuclear backgrounds and breeding environments.
Collapse
Affiliation(s)
- Kaori Ishikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
| |
Collapse
|
33
|
Bury AG, Vincent AE, Turnbull DM, Actis P, Hudson G. Mitochondrial isolation: when size matters. Wellcome Open Res 2020; 5:226. [PMID: 33718619 PMCID: PMC7931255 DOI: 10.12688/wellcomeopenres.16300.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 01/31/2024] Open
Abstract
Mitochondrial vitality is critical to cellular function, with mitochondrial dysfunction linked to a growing number of human diseases. Tissue and cellular heterogeneity, in terms of genetics, dynamics and function means that increasingly mitochondrial research is conducted at the single cell level. Whilst there are several technologies that are currently available for single-cell analysis, each with their advantages, they cannot be easily adapted to study mitochondria with subcellular resolution. Here we review the current techniques and strategies for mitochondrial isolation, critically discussing each technology's limitations for future mitochondrial research. Finally, we highlight and discuss the recent breakthroughs in sub-cellular isolation techniques, with a particular focus on nanotechnologies that enable the isolation of mitochondria from subcellular compartments. This allows isolation of mitochondria with unprecedented spatial precision with minimal disruption to mitochondria and their immediate cellular environment.
Collapse
Affiliation(s)
- Alexander G. Bury
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Amy E. Vincent
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Doug M. Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Paolo Actis
- Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Gavin Hudson
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| |
Collapse
|
34
|
Guo X, Wang Y, Zhang R, Gu Z. STAMP: a multiplex sequencing method for simultaneous evaluation of mitochondrial DNA heteroplasmies and content. NAR Genom Bioinform 2020; 2:lqaa065. [PMID: 33134911 DOI: 10.1093/nargab/lqaa065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/04/2020] [Accepted: 10/09/2020] [Indexed: 01/25/2023] Open
Abstract
Human mitochondrial genome (mtDNA) variations, such as mtDNA heteroplasmies (the co-existence of mutated and wild-type mtDNA), have received increasing attention in recent years for their clinical relevance to numerous diseases. But large-scale population studies of mtDNA heteroplasmies have been lagging due to the lack of a labor- and cost-effective method. Here, we present a novel human mtDNA sequencing method called STAMP (sequencing by targeted amplification of multiplex probes) for measuring mtDNA heteroplasmies and content in a streamlined workflow. We show that STAMP has high-mapping rates to mtDNA, deep coverage of unique reads and high tolerance to sequencing and polymerase chain reaction errors when applied to human samples. STAMP also has high sensitivity and low false positive rates in identifying artificial mtDNA variants at fractions as low as 0.5% in genomic DNA samples. We further extend STAMP, by including nuclear DNA-targeting probes, to enable assessment of relative mtDNA content in the same assay. The high cost-effectiveness of STAMP, along with the flexibility of using it for measuring various aspects of mtDNA variations, will accelerate the research of mtDNA heteroplasmies and content in large population cohorts, and in the context of human diseases and aging.
Collapse
Affiliation(s)
- Xiaoxian Guo
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Yiqin Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ruoyu Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
35
|
Wan Y, Finkel T. The mitochondria regulation of stem cell aging. Mech Ageing Dev 2020; 191:111334. [PMID: 32818514 PMCID: PMC7541753 DOI: 10.1016/j.mad.2020.111334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 01/07/2023]
Abstract
Mitochondrial dysfunction and stem cell exhaustion are among the nine separate hallmarks of aging. Emerging evidence however suggests that mitochondrial activity can have a profound influence on the self-renewal and function of stem cells, thus mechanistically linking mitochondrial function and stem cell decline. In this review, we discuss how accumulation of mtDNA mutations or alterations in mitochondrial dynamics, turnover, and signaling can modulate age-dependent stem cell function. Finally, we also describe how mitochondrial substrate utilization influences stem and progenitor activity. Together, this growing body of evidence suggests that modulation of mitochondrial activity might provide a strategy to slow or reverse age-dependent stem cell decline, and potentially, slow or reverse human aging.
Collapse
Affiliation(s)
- Yong Wan
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh/UPMC, USA; Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA 15219, USA
| | - Toren Finkel
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA 15219, USA; Division of Cardiology, Department of Medicine, University of Pittsburgh/UPMC, USA.
| |
Collapse
|
36
|
Smith AL, Whitehall JC, Bradshaw C, Gay D, Robertson F, Blain AP, Hudson G, Pyle A, Houghton D, Hunt M, Sampson JN, Stamp C, Mallett G, Amarnath S, Leslie J, Oakley F, Wilson L, Baker A, Russell OM, Johnson R, Richardson CA, Gupta B, McCallum I, McDonald SA, Kelly S, Mathers JC, Heer R, Taylor RW, Perkins ND, Turnbull DM, Sansom OJ, Greaves LC. Age-associated mitochondrial DNA mutations cause metabolic remodelling that contributes to accelerated intestinal tumorigenesis. NATURE CANCER 2020; 1:976-989. [PMID: 33073241 PMCID: PMC7116185 DOI: 10.1038/s43018-020-00112-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/05/2020] [Indexed: 01/15/2023]
Abstract
Oxidative phosphorylation (OXPHOS) defects caused by somatic mitochondrial DNA (mtDNA) mutations increase with age in human colorectal epithelium and are prevalent in colorectal tumours, but whether they actively contribute to tumorigenesis remains unknown. Here we demonstrate that mtDNA mutations causing OXPHOS defects are enriched during the human adenoma/carcinoma sequence, suggesting they may confer a metabolic advantage. To test this we deleted the tumour suppressor Apc in OXPHOS deficient intestinal stem cells in mice. The resulting tumours were larger than in control mice due to accelerated cell proliferation and reduced apoptosis. We show that both normal crypts and tumours undergo metabolic remodelling in response to OXPHOS deficiency by upregulating the de novo serine synthesis pathway (SSP). Moreover, normal human colonic crypts upregulate the SSP in response to OXPHOS deficiency prior to tumorigenesis. Our data show that age-associated OXPHOS deficiency causes metabolic remodelling that can functionally contribute to accelerated intestinal cancer development.
Collapse
Affiliation(s)
- Anna Lm Smith
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Julia C Whitehall
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Carla Bradshaw
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David Gay
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow. G61 1QH, UK
| | - Fiona Robertson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alasdair P Blain
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David Houghton
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthew Hunt
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - James N Sampson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Craig Stamp
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Grace Mallett
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Shoba Amarnath
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jack Leslie
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle upon Tyne, NE2 4HH, UK
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle upon Tyne, NE2 4HH, UK
| | - Laura Wilson
- Newcastle Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
| | - Angela Baker
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Oliver M Russell
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Riem Johnson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Claire A Richardson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Bhavana Gupta
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Iain McCallum
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Stuart Ac McDonald
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Seamus Kelly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - John C Mathers
- Human Nutrition Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH
| | - Rakesh Heer
- Newcastle Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Neil D Perkins
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow. G61 1QH, UK
| | - Laura C Greaves
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| |
Collapse
|
37
|
Nguyen H, LaFramboise T. Complexities and pitfalls in analyzing and interpreting mitochondrial DNA content in human cancer. J Genet Genomics 2020; 47:349-359. [PMID: 33004308 DOI: 10.1016/j.jgg.2020.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/01/2020] [Accepted: 04/20/2020] [Indexed: 11/29/2022]
Abstract
Mutations in the human mitochondrial genome have been observed in all types of human cancer, indicating that mutations might contribute to tumorigenesis, metastasis, recurrence, or drug response. This possibility is appealing because of the known shift from oxidative metabolism to glycolysis, known as the Warburg effect, that occurs in malignancy. Mitochondrial DNA (mtDNA) mutations could either be maternally inherited and predispose to cancer (germ line mutations) or occur sporadically in the mtDNA of specific tissues (tissue- or tumor-specific somatic mutations) and contribute to the tumor initiation and progression process. High-throughput sequencing technologies now enable comprehensive detection of mtDNA variation in tissues and bodily fluids, with the potential to be used as an early detection tool that may impact the treatment of cancer. Here, we discuss insights into the roles of mtDNA mutations in carcinogenesis, highlighting the complexities involved in the analysis and interpretation of mitochondrial genomic content, technical challenges in studying their contribution to pathogenesis, and the value of mtDNA mutations in developing early detection, diagnosis, prognosis, and therapeutic strategies for cancer.
Collapse
Affiliation(s)
- Hieu Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology (VRSIG), 458 Minh Khai, Vinh Tuy, Hai Ba Trung, Hanoi, Viet Nam; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
| |
Collapse
|
38
|
Arbeithuber B, Hester J, Cremona MA, Stoler N, Zaidi A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues. PLoS Biol 2020; 18:e3000745. [PMID: 32667908 PMCID: PMC7363077 DOI: 10.1371/journal.pbio.3000745] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
Mutations create genetic variation for other evolutionary forces to operate on and cause numerous genetic diseases. Nevertheless, how de novo mutations arise remains poorly understood. Progress in the area is hindered by the fact that error rates of conventional sequencing technologies (1 in 100 or 1,000 base pairs) are several orders of magnitude higher than de novo mutation rates (1 in 10,000,000 or 100,000,000 base pairs per generation). Moreover, previous analyses of germline de novo mutations examined pedigrees (and not germ cells) and thus were likely affected by selection. Here, we applied highly accurate duplex sequencing to detect low-frequency, de novo mutations in mitochondrial DNA (mtDNA) directly from oocytes and from somatic tissues (brain and muscle) of 36 mice from two independent pedigrees. We found mtDNA mutation frequencies 2- to 3-fold higher in 10-month-old than in 1-month-old mice, demonstrating mutation accumulation during the period of only 9 mo. Mutation frequencies and patterns differed between germline and somatic tissues and among mtDNA regions, suggestive of distinct mutagenesis mechanisms. Additionally, we discovered a more pronounced genetic drift of mitochondrial genetic variants in the germline of older versus younger mice, arguing for mtDNA turnover during oocyte meiotic arrest. Our study deciphered for the first time the intricacies of germline de novo mutagenesis using duplex sequencing directly in oocytes, which provided unprecedented resolution and minimized selection effects present in pedigree studies. Moreover, our work provides important information about the origins and accumulation of mutations with aging/maturation and has implications for delayed reproduction in modern human societies. Furthermore, the duplex sequencing method we optimized for single cells opens avenues for investigating low-frequency mutations in other studies.
Collapse
Affiliation(s)
- Barbara Arbeithuber
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - James Hester
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Marzia A. Cremona
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Nicholas Stoler
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Arslan Zaidi
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Bonnie Higgins
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kate Anthony
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Francesca Chiaromonte
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America
- EMbeDS, Sant’Anna School of Advanced Studies, Pisa, Italy
| | - Francisco J. Diaz
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kateryna D. Makova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| |
Collapse
|
39
|
Yin Q, Xu N, Xu D, Dong M, Shi X, Wang Y, Hao Z, Zhu S, Zhao D, Jin H, Liu W. Comparison of senescence-related changes between three- and two-dimensional cultured adipose-derived mesenchymal stem cells. Stem Cell Res Ther 2020; 11:226. [PMID: 32517737 PMCID: PMC7285747 DOI: 10.1186/s13287-020-01744-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/18/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Adipose-derived mesenchymal stem cells (ADMSCs) have attracted widespread interest as cell-based tissue repair systems. To obtain adequate quantities of ADMSCs for therapeutic applications, extensive in vitro expansion is required. However, under current two-dimensional (2D) approaches, ADMSCs rapidly undergo replicative senescence, and cell growth is impeded and stem cell properties are eliminated by mechanisms that are poorly understood. These issues limit the extensive applications of ADMSCs. In this study, we investigated senescence-related changes in mesenchymal stem cells (MSCs) isolated from human adipose tissue in 2D and three-dimensional (3D) cultures. METHODS We studied cell growth over a given period (21 days) to determine if modes of culture were associated with ADMSC senescence. ADMSCs were isolated from healthy females by liposuction surgery and then were grown in 2D and 3D cultures. The cell morphology was observed during cell culture. Every other time of culture, senescence-associated β-galactosidase (SA-β-gal) expression, cell viability, proliferation, and differentiation potential of ADMSCs from 2D and 3D cultures were detected. Also, senescence- and stemness-related gene expression, telomere length, telomerase activity, and energy metabolism of ADMSCs for different culture times were evaluated. RESULTS With long-term propagation, we observed significant changes in cell morphology, proliferation, differentiation abilities, and energy metabolism, which were associated with increases in SA-β-gal activity and decreases in telomere length and telomerase activity. Notably, when cultured in 3D, these changes were improved. CONCLUSIONS Our results indicate that 3D culture is able to ameliorate senescence-related changes in ADMSCs.
Collapse
Affiliation(s)
- Qiliang Yin
- Cancer Center at the First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021, People's Republic of China
| | - Na Xu
- Jilin Medical University, Jilin, 132013, People's Republic of China
| | - Dongsheng Xu
- Cancer Center at the First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021, People's Republic of China
| | - Mingxin Dong
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Zoonosis Prevention and Control Key Laboratory, Changchun, 130122, People's Republic of China
| | - Xiumin Shi
- Cancer Center at the First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021, People's Republic of China
| | - Yan Wang
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Zoonosis Prevention and Control Key Laboratory, Changchun, 130122, People's Republic of China
| | - Zhuo Hao
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Zoonosis Prevention and Control Key Laboratory, Changchun, 130122, People's Republic of China
| | - Shuangshuang Zhu
- Cancer Center at the First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021, People's Republic of China
| | - Donghai Zhao
- Jilin Medical University, Jilin, 132013, People's Republic of China
| | - Haofan Jin
- Cancer Center at the First Hospital of Jilin University, 1 Xinmin Street, Changchun, 130021, People's Republic of China.
| | - Wensen Liu
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Zoonosis Prevention and Control Key Laboratory, Changchun, 130122, People's Republic of China.
| |
Collapse
|
40
|
Lawless C, Greaves L, Reeve AK, Turnbull DM, Vincent AE. The rise and rise of mitochondrial DNA mutations. Open Biol 2020; 10:200061. [PMID: 32428418 PMCID: PMC7276526 DOI: 10.1098/rsob.200061] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022] Open
Abstract
How mitochondrial DNA mutations clonally expand in an individual cell is a question that has perplexed mitochondrial biologists for decades. A growing body of literature indicates that mitochondrial DNA mutations play a major role in ageing, metabolic diseases, neurodegenerative diseases, neuromuscular disorders and cancers. Importantly, this process of clonal expansion occurs for both inherited and somatic mitochondrial DNA mutations. To complicate matters further there are fundamental differences between mitochondrial DNA point mutations and deletions, and between mitotic and post-mitotic cells, that impact this pathogenic process. These differences, along with the challenges of investigating a longitudinal process occurring over decades in humans, have so far hindered progress towards understanding clonal expansion. Here we summarize our current understanding of the clonal expansion of mitochondrial DNA mutations in different tissues and highlight key unanswered questions. We then discuss the various existing biological models, along with their advantages and disadvantages. Finally, we explore what has been achieved with mathematical modelling so far and suggest future work to advance this important area of research.
Collapse
Affiliation(s)
| | | | | | - Doug M. Turnbull
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, UK
| | - Amy E. Vincent
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, UK
| |
Collapse
|
41
|
Chen D, Zhao Q, Xiong J, Lou X, Han Q, Wei X, Xie J, Li X, Zhou H, Shen L, Yang Y, Fang H, Lyu J. Systematic analysis of a mitochondrial disease-causing ND6 mutation in mitochondrial deficiency. Mol Genet Genomic Med 2020; 8:e1199. [PMID: 32162843 PMCID: PMC7216815 DOI: 10.1002/mgg3.1199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 12/24/2022] Open
Abstract
Background The m.14487T>C mutation is recognized as a diagnostic mutation of mitochondrial disease during the past 16 years, emerging evidence suggests that mutant loads of m.14487T>C and disease phenotype are not closely correlated. Methods Immortalized lymphocytes were generated by coculturing the Epstein–Barr virus and lymphocytes from m.14487T>C carrier Chinese patient with Leigh syndrome. Fifteen cytoplasmic hybrid (cybrid) cell lines were generated by fusing mtDNA lacking 143B cells with platelets donated by patients. Mitochondrial function was systematically analyzed at transcriptomic, metabolomic, and biochemical levels. Results Unlike previous reports, we found that the assembly of mitochondrial respiratory chain complexes, mitochondrial respiration, and mitochondrial OXPHOS function was barely affected in cybrid cells carrying homoplastic m.14487T>C mutation. Mitochondrial dysfunction associated transcriptomic and metabolomic reprogramming were not detected in cybrid carrying homoplastic m.14487T>C. However, we found that mitochondrial function was impaired in patient‐derived immortalized lymphocytes. Conclusion Our data revealed that m.14487T>C mutation is insufficient to cause mitochondrial deficiency; additional modifier genes may be involved in m.14487T>C‐associated mitochondrial disease. Our results further demonstrated that a caution should be taken by solely use of m.14487T>C mutation for molecular diagnosis of mitochondrial disease.
Collapse
Affiliation(s)
- Deyu Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiongya Zhao
- Zhejiang Provincial People's Hospital, Affiliated People's Hospital of Hangzhou Medical College, College of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Jingting Xiong
- Department of Laboratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoting Lou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Qinxia Han
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiujuan Wei
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Jie Xie
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueyun Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Huaibin Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Lijun Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China.,Zhejiang Provincial People's Hospital, Affiliated People's Hospital of Hangzhou Medical College, College of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| |
Collapse
|
42
|
Abstract
The past two centuries have witnessed an unprecedented rise in human life expectancy. Sustaining longer lives with reduced periods of disability will require an understanding of the underlying mechanisms of ageing, and genetics is a powerful tool for identifying these mechanisms. Large-scale genome-wide association studies have recently identified many loci that influence key human ageing traits, including lifespan. Multi-trait loci have been linked with several age-related diseases, suggesting shared ageing influences. Mutations that drive accelerated ageing in prototypical progeria syndromes in humans point to an important role for genome maintenance and stability. Together, these different strands of genetic research are highlighting pathways for the discovery of anti-ageing interventions that may be applicable in humans.
Collapse
|
43
|
Matkarimov BT, Saparbaev MK. DNA Repair and Mutagenesis in Vertebrate Mitochondria: Evidence for Asymmetric DNA Strand Inheritance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:77-100. [DOI: 10.1007/978-3-030-41283-8_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
44
|
Whitehall JC, Greaves LC. Aberrant mitochondrial function in ageing and cancer. Biogerontology 2019; 21:445-459. [PMID: 31802313 PMCID: PMC7347693 DOI: 10.1007/s10522-019-09853-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/23/2019] [Indexed: 12/12/2022]
Abstract
Alterations in mitochondrial metabolism have been described as one of the major hallmarks of both ageing cells and cancer. Age is the biggest risk factor for the development of a significant number of cancer types and this therefore raises the question of whether there is a link between age-related mitochondrial dysfunction and the advantageous changes in mitochondrial metabolism prevalent in cancer cells. A common underlying feature of both ageing and cancer cells is the presence of somatic mutations of the mitochondrial genome (mtDNA) which we postulate may drive compensatory alterations in mitochondrial metabolism that are advantageous for tumour growth. In this review, we discuss basic mitochondrial functions, mechanisms of mtDNA mutagenesis and their metabolic consequences, and review the evidence for and against a role for mtDNA mutations in cancer development.
Collapse
Affiliation(s)
- Julia C Whitehall
- The Medical School, Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Laura C Greaves
- The Medical School, Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| |
Collapse
|
45
|
Dubie JJ, Caraway AR, Stout MM, Katju V, Bergthorsson U. The conflict within: origin, proliferation and persistence of a spontaneously arising selfish mitochondrial genome. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190174. [PMID: 31787044 DOI: 10.1098/rstb.2019.0174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial genomes can sustain mutations that are simultaneously detrimental to individual fitness and yet, can proliferate within individuals owing to a replicative advantage. We analysed the fitness effects and population dynamics of a mitochondrial genome containing a novel 499 bp deletion in the cytochrome b(1) (ctb-1) gene (Δctb-1) encoding the cytochrome b of complex III in Caenorhabditis elegans. Δctb-1 reached a high heteroplasmic frequency of 96% in one experimental line during a mutation accumulation experiment and was linked to additional spontaneous mutations in nd5 and tRNA-Asn. The Δctb-1 mutant mitotype imposed a significant fitness cost including a 65% and 52% reduction in productivity and competitive fitness, respectively, relative to individuals bearing wild-type (WT) mitochondria. Deletion-bearing worms were rapidly purged within a few generations when competed against WT mitochondrial DNA (mtDNA) bearing worms in experimental populations. By contrast, the Δctb-1 mitotype was able to persist in large populations comprising heteroplasmic individuals only, although the average intracellular frequency of Δctb-1 exhibited a slow decline owing to competition among individuals bearing different frequencies of the heteroplasmy. Within experimental lines subjected to severe population bottlenecks (n = 1), the relative intracellular frequency of Δctb-1 increased, which is a hallmark of selfish drive. A positive correlation between Δctb-1 and WT mtDNA copy-number suggests a mechanism that increases total mtDNA per se, and does not discern the Δctb-1 mitotype from the WT mtDNA. This study demonstrates the selfish nature of the Δctb-1 mitotype, given its transmission advantage and substantial fitness load for the host, and highlights the importance of population size for the population dynamics of selfish mtDNA. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
Collapse
Affiliation(s)
- Joseph James Dubie
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| | - Avery Robert Caraway
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| | - McKenna Margaret Stout
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| |
Collapse
|
46
|
Koolkarnkhai P, Intakham C, Sangthong P, Surat W, Wonnapinij P. Portunus pelagicus mtDNA heteroplasmy inheritance and its effect on the use of mtCR and mtCOI sequence data. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:848-860. [PMID: 31766903 DOI: 10.1080/24701394.2019.1693549] [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: 10/25/2022]
Abstract
Mitochondrial DNA (mtDNA) sequences, especially mitochondrial control region (mtCR) and mitochondrial cytochrome c oxidase subunit I (mtCOI), have been widely used in population and evolutionary genetic analyses of metazoan. The presence of mtDNA heteroplasmy - a mixture of mtDNA haplotypes - possibly affects these analyses. This study aimed to reveal mtDNA heteroplasmy in mtCR, mtCOI, and mtND2 (mitochondrial NADH dehydrogenase subunit 2) of Portunus pelagicus, and examine its effect on the use of mtCR and mtCOI sequences. The screening result showed that the probability of observing mtDNA heteroplasmy was approximately 8%. Across the three targeted regions, 92 heteroplasmic variants were observed from seven samples comprising three mothers and four offspring. Most inherited heteroplasmy presented transition and silence mutation. By comparing the proportion of shared variants among maternal relatives to that among non-relatives, the result suggested that most heteroplasmic variants observed in an individual are inherited. Statistical analyses carried out on the inter-generational differences suggested that random drift and purifying selection play roles in determining the offspring's heteroplasmy level. The size of the random shift varies according to the location of variants and the mothers. The phylogenetic analysis showed that the presence of mtDNA heteroplasmy in mtCR and mtCOI does not affect familial and species identification, respectively. This study firstly reported the mtDNA heteroplasmy in P. pelagicus, its inheritance pattern, and its effect on the use of mtDNA sequence data. This basic knowledge would be useful for the study based on mtDNA sequence data, especially in other invertebrates.
Collapse
Affiliation(s)
| | - Chidchanok Intakham
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pradit Sangthong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
| | - Wunrada Surat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| |
Collapse
|
47
|
Sundermann EE, Erlandson KM, Pope CN, Rubtsova A, Montoya J, Moore AA, Marzolini C, O'Brien KK, Pahwa S, Payne BA, Rubin LH, Walmsley S, Haughey NJ, Montano M, Karris MY, Margolick JB, Moore DJ. Current Challenges and Solutions in Research and Clinical Care of Older Persons Living with HIV: Findings Presented at the 9th International Workshop on HIV and Aging. AIDS Res Hum Retroviruses 2019; 35:985-998. [PMID: 31373216 PMCID: PMC6862962 DOI: 10.1089/aid.2019.0100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In the era of effective antiretroviral therapy, the number of older people with HIV (PWH) is increasing, and those aging with HIV are experiencing an increasing burden of age-associated comorbidities. Life expectancy among older PWH is approaching that of demographically comparable HIV-uninfected (HIV-) adults. With this changing demographic of PWH come new challenges for researchers and clinicians in how to identify, address, and manage the complex interplay of treated HIV infection and aging-associated factors. In response to these challenges, the annual International Workshop on HIV and Aging was initiated in 2009 as a multidisciplinary platform for scientific discourse on the research and clinical complications arising from the aging population of PWH. The multidisciplinary nature of the workshop has resulted in a wide range of topics addressed over the past 9 years, from basic mechanisms in aging and HIV pathogenesis, to epidemiology of aging within large cohorts, interventions, and implementation of clinical programs. Herein, we summarize the key topics discussed at the 9th Annual International Workshop on HIV and Aging 2018, including "inflammaging," mitochondrial dysfunction, exercise interventions, HIV-associated neurocognitive impairment, metabolic dysfunction, menopause, and polypharmacy. In addition to recent developments in research and clinical care, we discuss open questions and future research directions required to better understand the interaction of HIV and aging.
Collapse
Affiliation(s)
- Erin E. Sundermann
- Department of Psychiatry, University of California, San Diego, La Jolla, California
| | - Kristine M. Erlandson
- Department of Medicine, University of Colorado-Anschutz Medical Center, Aurora, Colorado
- Department of Epidemiology, School of Public Health, University of Colorado-Anschutz Medical Center, Aurora, Colorado
| | - Caitlin N. Pope
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Anna Rubtsova
- Department of Behavioral Sciences and Health Education, Emory University Rollins School of Public Health, Atlanta, Georgia
| | - Jessica Montoya
- Department of Psychiatry, University of California, San Diego, La Jolla, California
| | - Alison A. Moore
- Division of Geriatrics and Gerontology, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Catia Marzolini
- Division of Infectious Diseases and Hospital Epidemiology, Departments of Medicine and Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
- The Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Kelly K. O'Brien
- Department of Physical Therapy, University of Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation (IHPME), University of Toronto, Toronto, Ontario, Canada
- The Rehabilitation Sciences Institute (RSI), University of Toronto, Toronto, Ontario, Canada
| | - Savita Pahwa
- Department of Microbiology and Immunology and the Miami CFAR, University of Miami Miller School of Medicine, Miami, Florida
| | - Brendan A.I. Payne
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Leah H. Rubin
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sharon Walmsley
- Toronto General Hospital, University Health Network, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Norman J. Haughey
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Monty Montano
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Maile Y. Karris
- Division of Infectious Diseases and Global Public Health, Department of Medicine, Unviersity of California San Diego, San Diego, California
| | - Joseph B. Margolick
- Department of Molecular Microbiology and Immunology, Environmental Health and Engineering, and Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David J. Moore
- Department of Psychiatry, University of California, San Diego, La Jolla, California
| |
Collapse
|
48
|
Malcomson FC, Breininger SP, ElGendy K, Joel A, Ranathunga R, Hill TR, Bradburn DM, Turnbull DM, Greaves LC, Mathers JC. Design and baseline characteristics of the Biomarkers Of Risk In Colorectal Cancer (BORICC) Follow-Up study: A 12+ years follow-up. Nutr Health 2019; 25:231-238. [PMID: 31370734 DOI: 10.1177/0260106019866963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most common cancer worldwide. Age is the strongest non-modifiable risk factor but it is estimated that over half of CRC cases are linked with lifestyle factors such as diet. The Biomarkers Of RIsk of Colorectal Cancer (BORICC) Study recruited 363 participants in 2005 to investigate the effects of lifestyle factors on biomarkers of CRC risk. AIM In the present BORICC Follow-Up (BFU) Study, we are using a longitudinal study design to investigate the effects of ageing (12+ years) and lifestyle factors on biomarkers of CRC risk and on healthy ageing. METHODS BFU Study participants attended a study visit at North Tyneside General Hospital (UK) for collection of biological samples, including blood and rectal biopsies, and information collected included anthropometric measurements, a Health & Medications Questionnaire, physical activity and sedentary behaviour, and habitual diet. Furthermore, musculoskeletal function was assessed by heel bone densitometry, timed up and go and hand grip strength as markers of healthy ageing. The BFU Study outcomes will be similar to those measured at baseline in the BORICC Study, such as DNA methylation and mitochondrial function, with additional measurements including the gut microbiome, faecal short-chain fatty acid concentrations and expression of genes associated with CRC. RESULTS Participants' recruitment to BFU Study and all sample and data collection have been completed. Forty-seven of the original BORICC participants were re-recruited to the BFU Study (mean age 67 years, 51% female). The recruits included 37 initially healthy participants and 10 participants who had adenomatous polyps at baseline. Approximately 70% of participants were over-weight or obese. CONCLUSION Ultimately, identifying lifestyle factors that can reduce CRC risk, and understanding the underlying mechanisms for the effects of lifestyle and ageing on CRC risk, could lead to early prevention strategies.
Collapse
Affiliation(s)
- F C Malcomson
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- LLHW Centre for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
| | - S P Breininger
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- LLHW Centre for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - K ElGendy
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- LLHW Centre for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
| | - A Joel
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- LLHW Centre for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
| | - Rmtk Ranathunga
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Department of Applied Nutrition, Wayamba University of Sri Lanka, Faculty of Livestock, Fisheries and Nutrition, Makandura, Gonawila, Sri Lanka
| | - T R Hill
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - D Michael Bradburn
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - D M Turnbull
- LLHW Centre for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - L C Greaves
- LLHW Centre for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - J C Mathers
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- LLHW Centre for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
| |
Collapse
|
49
|
Mitochondria in the signaling pathways that control longevity and health span. Ageing Res Rev 2019; 54:100940. [PMID: 31415807 PMCID: PMC7479635 DOI: 10.1016/j.arr.2019.100940] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022]
Abstract
Genetic and pharmacological intervention studies have identified evolutionarily conserved and functionally interconnected networks of cellular energy homeostasis, nutrient-sensing, and genome damage response signaling pathways, as prominent regulators of longevity and health span in various species. Mitochondria are the primary sites of ATP production and are key players in several other important cellular processes. Mitochondrial dysfunction diminishes tissue and organ functional performance and is a commonly considered feature of the aging process. Here we review the evidence that through reciprocal and multilevel functional interactions, mitochondria are implicated in the lifespan modulation function of these pathways, which altogether constitute a highly dynamic and complex system that controls the aging process. An important characteristic of these pathways is their extensive crosstalk and apparent malleability to modification by non-invasive pharmacological, dietary, and lifestyle interventions, with promising effects on lifespan and health span in animal models and potentially also in humans.
Collapse
|
50
|
Benayoun BA, Lee C. MOTS-c: A Mitochondrial-Encoded Regulator of the Nucleus. Bioessays 2019; 41:e1900046. [PMID: 31378979 PMCID: PMC8224472 DOI: 10.1002/bies.201900046] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/28/2019] [Indexed: 12/25/2022]
Abstract
Mitochondria are increasingly being recognized as information hubs that sense cellular changes and transmit messages to other cellular components, such as the nucleus, the endoplasmic reticulum (ER), the Golgi apparatus, and lysosomes. Nonetheless, the interaction between mitochondria and the nucleus is of special interest because they both host part of the cellular genome. Thus, the communication between genome-bearing organelles would likely include gene expression regulation. Multiple nuclear-encoded proteins have been known to regulate mitochondrial gene expression. On the contrary, no mitochondrial-encoded factors are known to actively regulate nuclear gene expression. MOTS-c (mitochondrial open reading frame of the 12S ribosomal RNA type-c) is a recently identified peptide encoded within the mitochondrial 12S ribosomal RNA gene that has metabolic functions. Notably, MOTS-c can translocate to the nucleus upon metabolic stress (e.g., glucose restriction and oxidative stress) and directly regulate adaptive nuclear gene expression to promote cellular homeostasis. It is hypothesized that cellular fitness requires the coevolved mitonuclear genomes to coordinate adaptive responses using gene-encoded factors that cross-regulate the opposite genome. This suggests that cellular gene expression requires the bipartite split genomes to operate as a unified system, rather than the nucleus being the sole master regulator.
Collapse
Affiliation(s)
- Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation Program, Los Angeles, CA, 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation Program, Los Angeles, CA, 90089, USA
- Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, Republic of Korea
| |
Collapse
|