1
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Giarmarco M, Seto J, Brock D, Brockerhoff S. Spatial detection of mitochondrial DNA and RNA in tissues. Front Cell Dev Biol 2024; 12:1346778. [PMID: 38808224 PMCID: PMC11130414 DOI: 10.3389/fcell.2024.1346778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/12/2024] [Indexed: 05/30/2024] Open
Abstract
Background Mitochondrial health has gained attention in a number of diseases, both as an indicator of disease state and as a potential therapeutic target. The quality and amount of mitochondrial DNA (mtDNA) and RNA (mtRNA) can be important indicators of mitochondrial and cell health, but are difficult to measure in complex tissues. Methods mtDNA and mtRNA in zebrafish retina samples were fluorescently labeled using RNAscope™ in situ hybridization, then mitochondria were stained using immunohistochemistry. Pretreatment with RNase was used for validation. Confocal images were collected and analyzed, and relative amounts of mtDNA and mtRNA were reported. Findings regarding mtDNA were confirmed using qPCR. Results Signals from probes detecting mtDNA and mtRNA were localized to mitochondria, and were differentially sensitive to RNase. This labeling strategy allows for quantification of relative mtDNA and mtRNA levels in individual cells. As a demonstration of the method in a complex tissue, single photoreceptors in zebrafish retina were analyzed for mtDNA and mtRNA content. An increase in mtRNA but not mtDNA coincides with proliferation of mitochondria at night in cones. A similar trend was measured in rods. Discussion Mitochondrial gene expression is an important component of cell adaptations to disease, stress, or aging. This method enables the study of mtDNA and mtRNA in single cells of an intact, complex tissue. The protocol presented here uses commercially-available tools, and is adaptable to a range of species and tissue types.
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Affiliation(s)
- Michelle Giarmarco
- Department of Ophthalmology, University of Washington, Seattle, WA, United States
| | - Jordan Seto
- Department of Ophthalmology, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Daniel Brock
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Susan Brockerhoff
- Department of Ophthalmology, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
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2
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Bulduk BK, Tortajada J, Valiente-Pallejà A, Callado LF, Torrell H, Vilella E, Meana JJ, Muntané G, Martorell L. High number of mitochondrial DNA alterations in postmortem brain tissue of patients with schizophrenia compared to healthy controls. Psychiatry Res 2024; 337:115928. [PMID: 38759415 DOI: 10.1016/j.psychres.2024.115928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Previous studies have shown mitochondrial dysfunction in schizophrenia (SZ) patients, which may be caused by mitochondrial DNA (mtDNA) alterations. However, there are few studies in SZ that have analyzed mtDNA in brain samples by next-generation sequencing (NGS). To address this gap, we used mtDNA-targeted NGS and qPCR to characterize mtDNA alterations in brain samples from patients with SZ (n = 40) and healthy controls (HC) (n = 40). 35 % of SZ patients showed mtDNA alterations, a significantly higher prevalence compared to 10 % of HC. Specifically, SZ patients had a significantly higher frequency of deletions (35 vs. 5 in HC), with a mean number of deletions of 3.8 in SZ vs. 1.0 in HC. Likely pathogenic missense variants were also significantly more frequent in patients with SZ than in HC (10 vs. three HC), encompassing 14 variants in patients and three in HC. The pathogenic tRNA variant m.3243A>G was identified in one SZ patient with a high heteroplasmy level of 32.2 %. While no significant differences in mtDNA copy number (mtDNA-CN) were observed between SZ and HC, antipsychotic users had significantly higher mtDNA-CN than non-users. These findings suggest a potential role for mtDNA alterations in the pathophysiology of SZ that require further validation and functional studies.
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Affiliation(s)
- Bengisu K Bulduk
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain
| | - Juan Tortajada
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain
| | - Alba Valiente-Pallejà
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Luís F Callado
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Department of Pharmacology, University of the Basque Country, UPV/EHU, Leioa, and BioBizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit URV-EURECAT Technology Centre of Catalonia, Unique Scientific and Technical Infrastructures, Reus, Catalonia, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - J Javier Meana
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Department of Pharmacology, University of the Basque Country, UPV/EHU, Leioa, and BioBizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Gerard Muntané
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Institut de Biologia Evolutiva (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain.
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.
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3
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Serrano IM, Hirose M, Valentine CC, Roesner S, Schmidt E, Pratt G, Williams L, Salk J, Ibrahim S, Sudmant PH. Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout ageing. Nat Ecol Evol 2024; 8:1021-1034. [PMID: 38361161 PMCID: PMC11090800 DOI: 10.1038/s41559-024-02338-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/22/2024] [Indexed: 02/17/2024]
Abstract
Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mitochondrial genome in different tissues throughout ageing. We used ultrasensitive duplex sequencing to profile ~2.5 million mitochondrial genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloguing ~1.2 million mitochondrial somatic and ultralow-frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the light strand origin of replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared with primates with a surfeit of reactive oxygen species-associated G > T/C > A mutations, and that somatic mutations in protein-coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that 're-align' mito-nuclear ancestry within an organism's lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.
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Affiliation(s)
- Isabel M Serrano
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | | | | | | | | | - Jesse Salk
- TwinStrand Biosciences, Seattle, WA, USA
| | - Saleh Ibrahim
- College of Medicine, Khalifa University, Abu Dhabi, UAE
| | - Peter H Sudmant
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
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4
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Bondy SC. Mitochondrial Dysfunction as the Major Basis of Brain Aging. Biomolecules 2024; 14:402. [PMID: 38672420 PMCID: PMC11048299 DOI: 10.3390/biom14040402] [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: 02/19/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
The changes in the properties of three biological events that occur with cerebral aging are discussed. These adverse changes already begin to develop early in mid-life and gradually become more pronounced with senescence. Essentially, they are reflections of the progressive decline in effectiveness of key processes, resulting in the deviation of essential biochemical trajectories to ineffective and ultimately harmful variants of these programs. The emphasis of this review is the major role played by the mitochondria in the transition of these three important processes toward more deleterious variants as brain aging proceeds. The immune system: the shift away from an efficient immune response to a more unfocused, continuing inflammatory condition. Such a state is both ineffective and harmful. Reactive oxygen species are important intracellular signaling systems. Additionally, microglial phagocytic activity utilizing short lived reactive oxygen species contribute to the removal of aberrant or dead cells and bacteria. These processes are transformed into an excessive, untargeted, and persistent generation of pro-oxidant free radicals (oxidative stress). The normal efficient neural transmission is modified to a state of undirected, chronic low-level excitatory activity. Each of these changes is characterized by the occurrence of continuous activity that is inefficient and diffused. The signal/noise ratio of several critical biological events is thus reduced as beneficial responses are gradually replaced by their impaired and deleterious variants.
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Affiliation(s)
- Stephen C. Bondy
- Department of Environmental & Occupational Health, University of California, Irvine, CA 92697, USA;
- Department of Medicine, University of California, Irvine, CA 92697, USA
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5
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Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nat Struct Mol Biol 2024; 31:568-577. [PMID: 38347148 DOI: 10.1038/s41594-024-01225-6] [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: 10/14/2022] [Accepted: 01/09/2024] [Indexed: 03/03/2024]
Abstract
Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.
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Affiliation(s)
- R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Thomas W Tullius
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Katja G Hansen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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6
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Sprason C, Tucker T, Clancy D. MtDNA deletions and aging. FRONTIERS IN AGING 2024; 5:1359638. [PMID: 38425363 PMCID: PMC10902006 DOI: 10.3389/fragi.2024.1359638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
Aging is the major risk factor in most of the leading causes of mortality worldwide, yet its fundamental causes mostly remain unclear. One of the clear hallmarks of aging is mitochondrial dysfunction. Mitochondria are best known for their roles in cellular energy generation, but they are also critical biosynthetic and signaling organelles. They also undergo multiple changes with organismal age, including increased genetic errors in their independent, circular genome. A key group of studies looking at mice with increased mtDNA mutations showed that premature aging phenotypes correlated with increased deletions but not point mutations. This generated an interest in mitochondrial deletions as a potential fundamental cause of aging. However, subsequent studies in different models have yielded diverse results. This review summarizes the research on mitochondrial deletions in various organisms to understand their possible roles in causing aging while identifying the key complications in quantifying deletions across all models.
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Affiliation(s)
| | | | - David Clancy
- Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
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7
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Shabalina IG, Edgar D, Gibanova N, Kalinovich AV, Petrovic N, Vyssokikh MY, Cannon B, Nedergaard J. Enhanced ROS Production in Mitochondria from Prematurely Aging mtDNA Mutator Mice. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:279-298. [PMID: 38622096 DOI: 10.1134/s0006297924020081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/20/2024] [Accepted: 01/21/2024] [Indexed: 04/17/2024]
Abstract
An increase in mitochondrial DNA (mtDNA) mutations and an ensuing increase in mitochondrial reactive oxygen species (ROS) production have been suggested to be a cause of the aging process ("the mitochondrial hypothesis of aging"). In agreement with this, mtDNA-mutator mice accumulate a large amount of mtDNA mutations, giving rise to defective mitochondria and an accelerated aging phenotype. However, incongruously, the rates of ROS production in mtDNA mutator mitochondria have generally earlier been reported to be lower - not higher - than in wildtype, thus apparently invalidating the "mitochondrial hypothesis of aging". We have here re-examined ROS production rates in mtDNA-mutator mice mitochondria. Using traditional conditions for measuring ROS (succinate in the absence of rotenone), we indeed found lower ROS in the mtDNA-mutator mitochondria compared to wildtype. This ROS mainly results from reverse electron flow driven by the membrane potential, but the membrane potential reached in the isolated mtDNA-mutator mitochondria was 33 mV lower than that in wildtype mitochondria, due to the feedback inhibition of succinate oxidation by oxaloacetate, and to a lower oxidative capacity in the mtDNA-mutator mice, explaining the lower ROS production. In contrast, in normal forward electron flow systems (pyruvate (or glutamate) + malate or palmitoyl-CoA + carnitine), mitochondrial ROS production was higher in the mtDNA-mutator mitochondria. Particularly, even during active oxidative phosphorylation (as would be ongoing physiologically), higher ROS rates were seen in the mtDNA-mutator mitochondria than in wildtype. Thus, when examined under physiological conditions, mitochondrial ROS production rates are indeed increased in mtDNA-mutator mitochondria. While this does not prove the validity of the mitochondrial hypothesis of aging, it may no longer be said to be negated in this respect. This paper is dedicated to the memory of Professor Vladimir P. Skulachev.
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Affiliation(s)
- Irina G Shabalina
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
| | - Daniel Edgar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
| | - Natalia Gibanova
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
| | - Anastasia V Kalinovich
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
| | - Natasa Petrovic
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
| | - Mikhail Yu Vyssokikh
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
| | - Barbara Cannon
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
| | - Jan Nedergaard
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden.
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8
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Serrano IM, Hirose M, Valentine CC, Roesner S, Schmidt E, Pratt G, Williams L, Salk J, Ibrahim S, Sudmant PH. Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531392. [PMID: 36945529 PMCID: PMC10028854 DOI: 10.1101/2023.03.06.531392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here, we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mt-genome in different tissues throughout aging. We used ultra-sensitive Duplex Sequencing to profile ~2.5 million mt-genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloging ~1.2 million mitochondrial somatic and ultra low frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the Light Strand Origin of Replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared to primates with a surfeit of reactive oxygen species-associated G>T/C>A mutations, and that somatic mutations in protein coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that "re-align" mito-nuclear ancestry within an organism's lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.
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Affiliation(s)
- Isabel M Serrano
- Center for Computational Biology, University of California, Berkeley
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck
| | | | | | | | | | | | | | - Saleh Ibrahim
- Department of Integrative Biology, University of California, Berkeley
| | - Peter H Sudmant
- Center for Computational Biology, University of California, Berkeley
- Department of Integrative Biology, University of California, Berkeley
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9
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Vandiver AR, Hoang AN, Herbst A, Lee CC, Aiken JM, McKenzie D, Teitell MA, Timp W, Wanagat J. Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging. Aging Cell 2023; 22:e13842. [PMID: 37132288 PMCID: PMC10265159 DOI: 10.1111/acel.13842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 05/04/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletion mutations cause many human diseases and are linked to age-induced mitochondrial dysfunction. Mapping the mutation spectrum and quantifying mtDNA deletion mutation frequency is challenging with next-generation sequencing methods. We hypothesized that long-read sequencing of human mtDNA across the lifespan would detect a broader spectrum of mtDNA rearrangements and provide a more accurate measurement of their frequency. We employed nanopore Cas9-targeted sequencing (nCATS) to map and quantitate mtDNA deletion mutations and develop analyses that are fit-for-purpose. We analyzed total DNA from vastus lateralis muscle in 15 males ranging from 20 to 81 years of age and substantia nigra from three 20-year-old and three 79-year-old men. We found that mtDNA deletion mutations detected by nCATS increased exponentially with age and mapped to a wider region of the mitochondrial genome than previously reported. Using simulated data, we observed that large deletions are often reported as chimeric alignments. To address this, we developed two algorithms for deletion identification which yield consistent deletion mapping and identify both previously reported and novel mtDNA deletion breakpoints. The identified mtDNA deletion frequency measured by nCATS correlates strongly with chronological age and predicts the deletion frequency as measured by digital PCR approaches. In substantia nigra, we observed a similar frequency of age-related mtDNA deletions to those observed in muscle samples, but noted a distinct spectrum of deletion breakpoints. NCATS-mtDNA sequencing allows the identification of mtDNA deletions on a single-molecule level, characterizing the strong relationship between mtDNA deletion frequency and chronological aging.
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Affiliation(s)
- Amy R. Vandiver
- Division of Dermatology, Department of MedicineUCLALos AngelesCaliforniaUSA
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
| | - Austin N. Hoang
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| | - Allen Herbst
- US Geological Survey National Wildlife Health CenterMadisonWisconsinUSA
| | - Cathy C. Lee
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| | - Judd M. Aiken
- Department of Agricultural, Food and Nutritional SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Debbie McKenzie
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Michael A. Teitell
- Molecular Biology InstituteUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Pathology and Laboratory Medicine, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Bioengineering, California NanoSystems Institute, Broad Center for Regenerative Medicine and Stem Cell ResearchUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Pediatrics, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Jonsson Comprehensive Cancer Center, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
| | - Winston Timp
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jonathan Wanagat
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
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10
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Jett S, Boneu C, Zarate C, Carlton C, Kodancha V, Nerattini M, Battista M, Pahlajani S, Williams S, Dyke JP, Mosconi L. Systematic review of 31P-magnetic resonance spectroscopy studies of brain high energy phosphates and membrane phospholipids in aging and Alzheimer's disease. Front Aging Neurosci 2023; 15:1183228. [PMID: 37273652 PMCID: PMC10232902 DOI: 10.3389/fnagi.2023.1183228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023] Open
Abstract
Many lines of evidence suggest that mitochondria have a central role in aging-related neurodegenerative diseases, such as Alzheimer's disease (AD). Mitochondrial dysfunction, cerebral energy dysmetabolism and oxidative damage increase with age, and are early event in AD pathophysiology and may precede amyloid beta (Aβ) plaques. In vivo probes of mitochondrial function and energy metabolism are therefore crucial to characterize the bioenergetic abnormalities underlying AD risk, and their relationship to pathophysiology and cognition. A majority of the research conducted in humans have used 18F-fluoro-deoxygluose (FDG) PET to image cerebral glucose metabolism (CMRglc), but key information regarding oxidative phosphorylation (OXPHOS), the process which generates 90% of the energy for the brain, cannot be assessed with this method. Thus, there is a crucial need for imaging tools to measure mitochondrial processes and OXPHOS in vivo in the human brain. 31Phosphorus-magnetic resonance spectroscopy (31P-MRS) is a non-invasive method which allows for the measurement of OXPHOS-related high-energy phosphates (HEP), including phosphocreatine (PCr), adenosine triphosphate (ATP), and inorganic phosphate (Pi), in addition to potential of hydrogen (pH), as well as components of phospholipid metabolism, such as phosphomonoesters (PMEs) and phosphodiesters (PDEs). Herein, we provide a systematic review of the existing literature utilizing the 31P-MRS methodology during the normal aging process and in patients with mild cognitive impairment (MCI) and AD, with an additional focus on individuals at risk for AD. We discuss the strengths and limitations of the technique, in addition to considering future directions toward validating the use of 31P-MRS measures as biomarkers for the early detection of AD.
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Affiliation(s)
- Steven Jett
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
| | - Camila Boneu
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
| | - Camila Zarate
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
| | - Caroline Carlton
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
| | - Vibha Kodancha
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
| | - Matilde Nerattini
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
- Nuclear Medicine Unit, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Michael Battista
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
| | - Silky Pahlajani
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
- Department of Radiology, Weill Cornell Medical College, New York, NY, United States
| | - Schantel Williams
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
| | - Jonathan P. Dyke
- Department of Radiology, Weill Cornell Medical College, New York, NY, United States
| | - Lisa Mosconi
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
- Department of Radiology, Weill Cornell Medical College, New York, NY, United States
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11
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Liu MH, Costa B, Choi U, Bandler RC, Lassen E, Grońska-Pęski M, Schwing A, Murphy ZR, Rosenkjær D, Picciotto S, Bianchi V, Stengs L, Edwards M, Loh CA, Truong TK, Brand RE, Pastinen T, Wagner JR, Skytte AB, Tabori U, Shoag JE, Evrony GD. Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.526140. [PMID: 36824744 PMCID: PMC9949150 DOI: 10.1101/2023.02.19.526140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other genetic diseases1-4. Almost all of these mosaic mutations begin as nucleotide mismatches or damage in only one of the two strands of the DNA prior to becoming double-strand mutations if unrepaired or misrepaired5. However, current DNA sequencing technologies cannot resolve these initial single-strand events. Here, we developed a single-molecule, long-read sequencing method that achieves single-molecule fidelity for single-base substitutions when present in either one or both strands of the DNA. It also detects single-strand cytosine deamination events, a common type of DNA damage. We profiled 110 samples from diverse tissues, including from individuals with cancer-predisposition syndromes, and define the first single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumors deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples deficient in only polymerase proofreading. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. Since the double-strand DNA mutations interrogated by prior studies are only the endpoint of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable new studies of how mutations arise in a variety of contexts, especially in cancer and aging.
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Affiliation(s)
- Mei Hong Liu
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Benjamin Costa
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Una Choi
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Rachel C. Bandler
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
| | | | - Marta Grońska-Pęski
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Adam Schwing
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Zachary R. Murphy
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | | | - Shany Picciotto
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, USA
| | - Vanessa Bianchi
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Canada
| | - Lucie Stengs
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Canada
| | - Caitlin A. Loh
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Tina K. Truong
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Randall E. Brand
- Department of Medicine, University of Pittsburgh School of Medicine, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Kansas City, USA
| | - J. Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Université de Sherbrooke, Canada
| | | | - Uri Tabori
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Canada
- Division of Haematology/Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Canada
| | - Jonathan E. Shoag
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, USA
| | - Gilad D. Evrony
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, USA
- Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
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12
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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.
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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
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13
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Manna S, Mc Elwain CJ, Maher GM, Giralt Martín M, Musumeci A, McCarthy FP, McCarthy C. Heterogenous Differences in Cellular Senescent Phenotypes in Pre-Eclampsia and IUGR following Quantitative Assessment of Multiple Biomarkers of Senescence. Int J Mol Sci 2023; 24:ijms24043101. [PMID: 36834513 PMCID: PMC9963163 DOI: 10.3390/ijms24043101] [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: 11/15/2022] [Revised: 12/20/2022] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Premature ageing of the placenta in pregnancy outcomes is associated with the persistent presence of oxidative stress and placental insufficiency reducing its functional capacity. In this study, we investigated cellular senescence phenotypes of pre-eclampsia and IUGR pregnancies by simultaneously measuring several biomarkers of senescence. Maternal plasma and placental samples were collected at term gestation from nulliparous women undergoing pre-labour elective caesarean section with pre-eclampsia without intrauterine growth restriction (PE; n = 5), pre-eclampsia associated with intrauterine growth restriction (n = 8), intrauterine growth restriction (IUGR < 10th centile; n = 6), and age-matched controls (n = 20). Placental absolute telomere length and senescence gene analysis was performed by RTqPCR. The expression of cyclin-dependent kinase inhibitors (p21 and p16) was determined by Western blot. Senescence-associated secretory phenotypes (SASPs) were evaluated in maternal plasma by multiplex ELISA assay. Placental expression of senescence-associated genes showed significant increases in CHEK1, PCNA, PTEN, CDKN2A, and CCNB-1 (p < 0.05) in pre-eclampsia, while TBX-2, PCNA, ATM, and CCNB-1 expression were evident (p < 0.05) and were significantly decreased in IUGR compared with controls. Placental p16 protein expression was significantly decreased in pre-eclampsia only compared with controls (p = 0.028). IL-6 was significantly increased in pre-eclampsia (0.54 pg/mL ± 0.271 vs. 0.3 pg/mL ± 0.102; p = 0.017) while IFN-γ was significantly increased in IUGR (4.6 pg/mL ± 2.2 vs. 2.17 pg/mL ± 0.8; p = 0.002) compared with controls. These results provide evidence of premature senescence in IUGR pregnancies, and while cell cycle checkpoint regulators are activated in pre-eclampsia, the cellular phenotype is one of cell repair and subsequent proliferation rather than progression to senescence. The heterogeneity of these cellular phenotypes highlights the complexity of characterising cellular senescence and may equally be indicative of the differing pathophysiological insults unique to each obstetric complication.
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Affiliation(s)
- Samprikta Manna
- Department of Obstetrics and Gynaecology, Cork University Maternity Hospital, University College Cork, T12 YE02 Cork, Ireland
- INFANT Research Centre, University College Cork, T12 K8AF Cork, Ireland
| | - Colm J. Mc Elwain
- Department of Pharmacology and Therapeutics, Western Gateway Building, University College Cork, T12 XF62 Cork, Ireland
| | - Gillian M. Maher
- INFANT Research Centre, University College Cork, T12 K8AF Cork, Ireland
- School of Public Health, Western Gateway Building, University College Cork, T12 XF62 Cork, Ireland
| | - Marta Giralt Martín
- Department of Pharmacology and Therapeutics, Western Gateway Building, University College Cork, T12 XF62 Cork, Ireland
| | - Andrea Musumeci
- Department of Pharmacology and Therapeutics, Western Gateway Building, University College Cork, T12 XF62 Cork, Ireland
| | - Fergus P. McCarthy
- Department of Obstetrics and Gynaecology, Cork University Maternity Hospital, University College Cork, T12 YE02 Cork, Ireland
- INFANT Research Centre, University College Cork, T12 K8AF Cork, Ireland
- Correspondence:
| | - Cathal McCarthy
- Department of Pharmacology and Therapeutics, Western Gateway Building, University College Cork, T12 XF62 Cork, Ireland
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14
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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: 997] [Impact Index Per Article: 997.0] [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.
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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.
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15
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López-Otín C, Pietrocola F, Roiz-Valle D, Galluzzi L, Kroemer G. Meta-hallmarks of aging and cancer. Cell Metab 2023; 35:12-35. [PMID: 36599298 DOI: 10.1016/j.cmet.2022.11.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
Abstract
Both aging and cancer are characterized by a series of partially overlapping "hallmarks" that we subject here to a meta-analysis. Several hallmarks of aging (i.e., genomic instability, epigenetic alterations, chronic inflammation, and dysbiosis) are very similar to specific cancer hallmarks and hence constitute common "meta-hallmarks," while other features of aging (i.e., telomere attrition and stem cell exhaustion) act likely to suppress oncogenesis and hence can be viewed as preponderantly "antagonistic hallmarks." Disabled macroautophagy and cellular senescence are two hallmarks of aging that exert context-dependent oncosuppressive and pro-tumorigenic effects. Similarly, the equivalence or antagonism between aging-associated deregulated nutrient-sensing and cancer-relevant alterations of cellular metabolism is complex. The agonistic and antagonistic relationship between the processes that drive aging and cancer has bearings for the age-related increase and oldest age-related decrease of cancer morbidity and mortality, as well as for the therapeutic management of malignant disease in the elderly.
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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.
| | - Federico Pietrocola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - David Roiz-Valle
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris Cité, 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.
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16
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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
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17
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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.
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18
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Desquiret-Dumas V, D’Ottavi M, Monnin A, Goudenège D, Méda N, Vizeneux A, Kankasa C, Tylleskar T, Bris C, Procaccio V, Nagot N, Van de Perre P, Reynier P, Molès JP. Long-Term Persistence of Mitochondrial DNA Instability in HIV-Exposed Uninfected Children during and after Exposure to Antiretroviral Drugs and HIV. Biomedicines 2022; 10:biomedicines10081786. [PMID: 35892686 PMCID: PMC9331317 DOI: 10.3390/biomedicines10081786] [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: 06/08/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-exposed uninfected (HEU) children show impaired health outcomes during childhood. A high rate of mitochondrial DNA (mtDNA) instability was reported in the blood of HEU at birth. We aimed to explore the relationship between these health outcomes and mtDNA deletions over time in a case series of 24 HEU children. MtDNA instability was assessed by deep sequencing and analyzed by eKLIPse-v2 algorithm at three time points, namely birth, 1 year, and 6 years of age. Association between mtDNA deletion and health outcomes, including growth, clinical, and neurodevelopmental parameters, were explored using univariate statistical analyses and after stratification with relevant variables. HEU children were selected with an equal male:female ratio. An elevated number of mtDNA deletions and duplications events was observed at 7 days’ post-partum. Median heteroplasmy increased at one year of life and then returned to baseline by six years of age. The mtDNA instability was acquired and was not transmitted by the mother. No risk factors were significantly associated with mtDNA instability. In this small case series, we did not detect any association between any health outcome at 6 years and mtDNA instability measures. A significant effect modification of the association between the duration of maternal prophylaxis and child growth was observed after stratification with heteroplasmy rate. Genomic instability persists over time among HEU children but, despite its extension, stays subclinical at six years.
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Affiliation(s)
- Valérie Desquiret-Dumas
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Morgana D’Ottavi
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - Audrey Monnin
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - David Goudenège
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Nicolas Méda
- Centre MURAZ, Bobo-Dioulasso 01 B.P. 390, Burkina Faso;
| | - Amélie Vizeneux
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - Chipepo Kankasa
- Department of Paediatrics and Child Health, University Teaching Hospital, Lusaka P.O. Box 50001, Zambia;
| | - Thorkild Tylleskar
- Centre for International Health, University of Bergen, N-5020 Bergen, Norway;
| | - Céline Bris
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Nicolas Nagot
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - Pascal Reynier
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
- Correspondence: ; Tel.: +33-434-35-91-07
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