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Tapanainen R, Aasumets K, Fekete Z, Goffart S, Dufour E, L O Pohjoismäki J. Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution. Gene 2024; 926:148644. [PMID: 38851366 DOI: 10.1016/j.gene.2024.148644] [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: 03/09/2024] [Revised: 04/23/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
The non-coding regions of the mitochondrial DNAs (mtDNAs) of hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) and long (130-160 bp) tandem repeats, absent in related mammalian orders. In the presented study, we provide in-depth analysis for mountain hare (Lepus timidus) and brown hare (L. europaeus) mtDNA non-coding regions, together with a species- and population-level analysis of tandem repeat variation. Mountain hare short tandem repeats (SRs) as well as other analyzed hare species consist of two conserved 10 bp motifs, with only brown hares exhibiting a single, more variable motif. Long tandem repeats (LRs) also differ in sequence and copy number between species. Mountain hares have four to seven LRs, median value five, while brown hares exhibit five to nine LRs, median value six. Interestingly, introgressed mountain hare mtDNA in brown hares obtained an intermediate LR length distribution, with median copy number being the same as with conspecific brown hare mtDNA. In contrast, transfer of brown hare mtDNA into cultured mtDNA-less mountain hare cells maintained the original LR number, whereas the reciprocal transfer caused copy number instability, suggesting that cellular environment rather than the nuclear genomic background plays a role in the LR maintenance. Due to their dynamic nature and separation from other known conserved sequence elements on the non-coding region of hare mitochondrial genomes, the tandem repeat elements likely to represent signatures of ancient genetic rearrangements. clarifying the nature and dynamics of these rearrangements may shed light on the possible role of NCR repeated elements in mitochondria and in species evolution.
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Affiliation(s)
- Riikka Tapanainen
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Koit Aasumets
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Zsófia Fekete
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland; Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Steffi Goffart
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
| | - Jaakko L O Pohjoismäki
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland.
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Ren P, Zhang J, Vijg J. Somatic mutations in aging and disease. GeroScience 2024; 46:5171-5189. [PMID: 38488948 PMCID: PMC11336144 DOI: 10.1007/s11357-024-01113-3] [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: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jie Zhang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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3
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Dua N, Badrinarayanan A. Heteroplasmy in action: tracking mtDNA segregation dynamics. EMBO J 2024:10.1038/s44318-024-00226-x. [PMID: 39256559 DOI: 10.1038/s44318-024-00226-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/12/2024] Open
Affiliation(s)
- Nitish Dua
- The Scripps Research Institute, La Jolla, CA, USA.
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences (TIFR), Bengaluru, Karnataka, 560065, India.
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Li J, Wu H, Zhou Y, Liu M, Zhou Y, Chu J, Kamili E, Wang W, Yang J, Lin L, Zhang Q, Yang S, Xu Y. Characterization and trans-generation dynamics of mitogene pool in the silver carp (Hypophthalmichthys molitrix). G3 (BETHESDA, MD.) 2024; 14:jkae101. [PMID: 38922124 DOI: 10.1093/g3journal/jkae101] [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: 12/26/2023] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 06/27/2024]
Abstract
Multicopied mitogenome are prone to mutation during replication often resulting in heteroplasmy. The derived variants in a cell, organ, or an individual animal constitute a mitogene pool. The individual mitogene pool is initiated by a small fraction of the egg mitogene pool. However, the characteristics and relationship between them has not yet been investigated. This study quantitatively analyzed the heteroplasmy landscape, genetic loads, and selection strength of the mitogene pool of egg and hatchling in the silver carp (Hypophthalmichthys molitrix) using high-throughput resequencing. The results showed heteroplasmic sites distribute across the whole mitogenome in both eggs and hatchlings. The dominant substitution was Transversion in eggs and Transition in hatching accounting for 95.23%±2.07% and 85.38%±6.94% of total HP sites, respectively. The total genetic loads were 0.293±0.044 in eggs and 0.228±0.022 in hatchlings (P=0.048). The dN/dS ratio was 58.03±38.98 for eggs and 9.44±3.93 for hatchlings (P=0.037). These results suggest that the mitogenomes were under strong positive selection in eggs with tolerance to variants with deleterious effects, while the selection was positive but much weaker in hatchlings showing marked quality control. Based on these findings, we proposed a trans-generation dynamics model to explain differential development mode of the two mitogene pool between oocyte maturation and ontogenesis of offspring. This study sheds light on significance of mitogene pool for persistence of populations and subsequent integration in ecological studies and conservation practices.
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Affiliation(s)
- Jinlin Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Hengshu Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Yingna Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Manhong Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Yongheng Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Jianing Chu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Elizabeth Kamili
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Wenhui Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Jincheng Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Lijun Lin
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Qi Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Shuhui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
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Sturgis J, Singh R, Caron QR, Samuels IS, Shiju TM, Mukkara A, Freedman P, Bonilha VL. Modeling aging and retinal degeneration with mitochondrial DNA mutation burden. Aging Cell 2024:e14282. [PMID: 39210608 DOI: 10.1111/acel.14282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 09/04/2024] Open
Abstract
Somatic mitochondrial DNA (mtDNA) mutation accumulation has been observed in individuals with retinal degenerative disorders. To study the effects of aging and mtDNA mutation accumulation in the retina, a polymerase gamma (POLG) exonuclease-deficient model, the PolgD257A mutator mice (D257A), was used. POLG is an enzyme responsible for regulating mtDNA replication and repair. Retinas of young and older mice with this mutation were analyzed in vivo and ex vivo to provide new insights into the contribution of age-related mitochondrial (mt) dysfunction due to mtDNA damage. Optical coherence tomography (OCT) image analysis revealed a decrease in retinal and photoreceptor thickness starting at 6 months of age in mice with the D257A mutation compared to wild-type (WT) mice. Electroretinography (ERG) testing showed a significant decrease in all recorded responses at 6 months of age. Sections labeled with markers of different types of retinal cells, including cones, rods, and bipolar cells, exhibited decreased labeling starting at 6 months. However, electron microscopy analysis revealed differences in retinal pigment epithelium (RPE) mt morphology beginning at 3 months. Interestingly, there was no increase in oxidative stress and parkin-mediated mitophagy in the ages analyzed in the retina or RPE of D257A mice. Additionally, D257A RPE exhibited an accelerated rate of autofluorescence cytoplasmic granule formation and accumulation. Mt markers displayed different abundance in protein lysates obtained from retina and RPE samples. These findings suggest that the accumulation of mtDNA mutations leads to impaired mt function and accelerated aging, resulting in retinal degeneration.
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Affiliation(s)
- John Sturgis
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rupesh Singh
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Quinn R Caron
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ivy S Samuels
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Thomas Micheal Shiju
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Aditi Mukkara
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
- College of Arts and Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Paul Freedman
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Vera L Bonilha
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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Liang R, Zhu L, Huang Y, Chen J, Tang Q. Mitochondria: fundamental characteristics, challenges, and impact on aging. Biogerontology 2024:10.1007/s10522-024-10132-8. [PMID: 39196438 DOI: 10.1007/s10522-024-10132-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]
Abstract
As one of the most vital organelles within biological cells, mitochondria hold an irreplaceable status and play crucial roles in various diseases. Research and therapies targeting mitochondria have achieved significant progress in numerous conditions. Throughout an organism's lifespan, mitochondrial dynamics persist continuously, and due to their inherent characteristics and various external factors, mitochondria are highly susceptible to damage. This susceptibility is particularly evident during aging, where the decline in biological function is closely intertwined with mitochondrial dysfunction. Despite being an ancient and enigmatic organelle, much remains unknown about mitochondria. Here, we will explore the past and present knowledge of mitochondria, providing a comprehensive review of their intrinsic properties and interactions with nuclear DNA, as well as the challenges and impacts they face during the aging process.
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Affiliation(s)
- Runyu Liang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Luwen Zhu
- Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yongyin Huang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jia Chen
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Qiang Tang
- Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China.
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Hinton AO, Vue Z, Scudese E, Neikirk K, Kirabo A, Montano M. Mitochondrial heterogeneity and crosstalk in aging: Time for a paradigm shift? Aging Cell 2024:e14296. [PMID: 39188058 DOI: 10.1111/acel.14296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/24/2024] [Accepted: 07/26/2024] [Indexed: 08/28/2024] Open
Abstract
The hallmarks of aging have been influential in guiding the biology of aging research, with more recent and growing recognition of the interdependence of these hallmarks on age-related health outcomes. However, a current challenge is personalizing aging trajectories to promote healthy aging, given the diversity of genotypes and lived experience. We suggest that incorporating heterogeneity-including intrinsic (e.g., genetic and structural) and extrinsic (e.g., environmental and exposome) factors and their interdependence of hallmarks-may move the dial. This editorial perspective will focus on one hallmark, namely mitochondrial dysfunction, to exemplify how consideration of heterogeneity and interdependence or crosstalk may reveal new perspectives and opportunities for personalizing aging research. To this end, we highlight heterogeneity within mitochondria as a model.
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Affiliation(s)
- Antentor O Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Estevão Scudese
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Annet Kirabo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Center for Immunobiology, Nashville, Tennessee, USA
- Immunology and Inflammation, Vanderbilt Institute for Infection, Nashville, Tennessee, USA
- Vanderbilt Institute for Global Health, Nashville, Tennessee, USA
| | - Monty Montano
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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8
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Weng C, Weissman JS, Sankaran VG. Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609473. [PMID: 39229039 PMCID: PMC11370557 DOI: 10.1101/2024.08.23.609473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The detection of mitochondrial DNA (mtDNA) mutations in single cells holds considerable potential to define clonal relationships coupled with information on cell state in humans. Previous methods focused on higher heteroplasmy mutations that are limited in number and can be influenced by functional selection, introducing biases for lineage tracing. Although more challenging to detect, intermediate to low heteroplasmy mtDNA mutations are valuable due to their high diversity, abundance, and lower propensity to selection. To enhance mtDNA mutation detection and facilitate fine-scale lineage tracing, we developed the single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling (ReDeeM) approach, an integrated experimental and computational framework. Recently, some concerns have been raised about the analytical workflow in the ReDeeM framework. Specifically, it was noted that the mutations detected in a single molecule per cell are enriched on edges of mtDNA molecules, suggesting they resemble artifacts reported in other sequencing approaches. It was then proposed that all mutations found in one molecule per cell should be removed. We detail our error correction method, demonstrating that the observed edge mutations are distinct from previously reported sequencing artifacts. We further show that the proposed removal leads to massive elimination of bona fide and informative mutations. Indeed, mutations accumulating on edges impact a minority of all mutation calls (for example, in hematopoietic stem cells, the excess mutations on the edge account for only 4.3%-7.6% of the total). Recognizing the value of addressing edge mutations even after applying consensus correction, we provide an additional filtering option in the ReDeeM-R package. This approach effectively eliminates the position biases, leads to a mutational signature indistinguishable from bona fide mitochondrial mutations, and removes excess low molecule high connectedness mutations. Importantly, this option preserves the large majority of unique mutations identified by ReDeeM, maintaining the ability of ReDeeM to provide a more than 10-fold increase in variant detection compared to previous methods. Additionally, the cells remain well-connected. While there is room for further refinement in mutation calling strategies, the significant advances and biological insights provided by the ReDeeM framework are unique and remain intact. We hope that this detailed discussion and analysis enables the community to employ this approach and contribute to its further development.
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Affiliation(s)
- Chen Weng
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
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9
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Alibhai FJ, Li RK. Rejuvenation of the Aging Heart: Molecular Determinants and Applications. Can J Cardiol 2024; 40:1394-1411. [PMID: 38460612 DOI: 10.1016/j.cjca.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/20/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024] Open
Abstract
In Canada and worldwide, the elderly population (ie, individuals > 65 years of age) is increasing disproportionately relative to the total population. This is expected to have a substantial impact on the health care system, as increased aged is associated with a greater incidence of chronic noncommunicable diseases. Within the elderly population, cardiovascular disease is a leading cause of death, therefore developing therapies that can prevent or slow disease progression in this group is highly desirable. Historically, aging research has focused on the development of anti-aging therapies that are implemented early in life and slow the age-dependent decline in cell and organ function. However, accumulating evidence supports that late-in-life therapies can also benefit the aged cardiovascular system by limiting age-dependent functional decline. Moreover, recent studies have demonstrated that rejuvenation (ie, reverting cellular function to that of a younger phenotype) of the already aged cardiovascular system is possible, opening new avenues to develop therapies for older individuals. In this review, we first provide an overview of the functional changes that occur in the cardiomyocyte with aging and how this contributes to the age-dependent decline in heart function. We then discuss the various anti-aging and rejuvenation strategies that have been pursued to improve the function of the aged cardiomyocyte, with a focus on therapies implemented late in life. These strategies include 1) established systemic approaches (caloric restriction, exercise), 2) pharmacologic approaches (mTOR, AMPK, SIRT1, and autophagy-targeting molecules), and 3) emerging rejuvenation approaches (partial reprogramming, parabiosis/modulation of circulating factors, targeting endogenous stem cell populations, and senotherapeutics). Collectively, these studies demonstrate the exciting potential and limitations of current rejuvenation strategies and highlight future areas of investigation that will contribute to the development of rejuvenation therapies for the aged heart.
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Affiliation(s)
- Faisal J Alibhai
- Toronto General Research Hospital Institute, University Health Network, Toronto, Ontario, Canada
| | - Ren-Ke Li
- Toronto General Research Hospital Institute, University Health Network, Toronto, Ontario, Canada; Department of Surgery, Division of Cardiovascular Surgery, University of Toronto, Toronto, Ontario, Canada.
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Yao X, Luo XY, Tai YH, Wang K, Shang JW. What was the global burden of kidney cancer attributable to high body mass index from 1990 to 2019? There existed some points noteworthy. Front Nutr 2024; 11:1358017. [PMID: 38903629 PMCID: PMC11188334 DOI: 10.3389/fnut.2024.1358017] [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: 12/19/2023] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Purpose With the prevalence of high body mass index (HBMI) increasing over the past 30 years, it is essential to examine the impact of obesity on kidney cancer. This study aims to explore the attributable burden of kidney cancer associated with HBMI and its proportion at different levels. Methods and materials The data used in this research were obtained from the Global Burden of Diseases Study 2019. We utilized DisMod-MR 2.1, a Bayesian meta-regression tool, to estimate the burden of kidney cancer attributable to HBMI, which was measured by age-standardized mortality rate (ASMR) and age-standardized disability-adjusted life years rate (ASDR). Correlation analysis was conducted by the Spearman rank order correlation method. The temporal trends were analyzed by estimating the estimated annual percentage change (EAPC). Results Globally in 2019, there were a total of 31.7 thousand deaths and 751.89 thousand disability-adjusted life years (DALYs) attributable to kidney cancer caused by HBMI, increased by 183.1 and 164%, respectively. Over the period from 1990 to 2019, the burden of kidney cancer attributable to HBMI increased in all regions, with the most significant increases occurring in Low-middle socio-demographic index (SDI) and Low SDI regions. At the national level, countries with lower SDI had lower ASMR and ASDR compared to developed nations. However, the EAPC values, which indicate the rate of increase, were significantly higher in these countries than in developed nations. Furthermore, across all years from 1990 to 2019, males experienced a greater and more rapidly increasing burden of kidney cancer attributable to HBMI than females. Conclusion As the population grows and dietary patterns shift, the burden of kidney cancer attributable to HBMI is expected to become even more severe. Males and developed regions have borne a heavier burden from 1990 to 2019. However, the EAPC values for both ASMR and ASDR were higher in males but not in regions with higher SDI values.
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Affiliation(s)
- Xue Yao
- Department of Ambulance Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiao-yan Luo
- Department of Ambulance Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Yang-hao Tai
- Department of Urology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Kang Wang
- Department of Ambulance Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Ji-wen Shang
- Department of Ambulance Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
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11
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [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: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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12
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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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13
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Minko I, Luzadder M, Vartanian V, Rice SM, Nguyen M, Sanchez-Contreras M, Van P, Kennedy S, McCullough A, Lloyd R. Frequencies and spectra of aflatoxin B 1-induced mutations in liver genomes of NEIL1-deficient mice as revealed by duplex sequencing. NAR MOLECULAR MEDICINE 2024; 1:ugae006. [PMID: 38779538 PMCID: PMC11105970 DOI: 10.1093/narmme/ugae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Increased risk for the development of hepatocellular carcinoma (HCC) is driven by a number of etiological factors including hepatitis viral infection and dietary exposures to foods contaminated with aflatoxin-producing molds. Intracellular metabolic activation of aflatoxin B1 (AFB1) to a reactive epoxide generates highly mutagenic AFB1-Fapy-dG adducts. Previously, we demonstrated that repair of AFB1-Fapy-dG adducts can be initiated by the DNA glycosylase NEIL1 and that male Neil1-/- mice were significantly more susceptible to AFB1-induced HCC relative to wild-type mice. To investigate the mechanisms underlying this enhanced carcinogenesis, WT and Neil1-/- mice were challenged with a single, 4 mg/kg dose of AFB1 and frequencies and spectra of mutations were analyzed in liver DNAs 2.5 months post-injection using duplex sequencing. The analyses of DNAs from AFB1-challenged mice revealed highly elevated mutation frequencies in the nuclear genomes of both males and females, but not the mitochondrial genomes. In both WT and Neil1-/- mice, mutation spectra were highly similar to the AFB1-specific COSMIC signature SBS24. Relative to wild-type, the NEIL1 deficiency increased AFB1-induced mutagenesis with concomitant elevated HCCs in male Neil1-/- mice. Our data establish a critical role of NEIL1 in limiting AFB1-induced mutagenesis and ultimately carcinogenesis.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Michael M Luzadder
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Vladimir L Vartanian
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Sean P M Rice
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- School of Public Health, Oregon Health & Science University - Portland State University, Portland, OR, USA
| | - Megan M Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Phu Van
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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14
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Spinazzola A, Perez-Rodriguez D, Ježek J, Holt IJ. Mitochondrial DNA competition: starving out the mutant genome. Trends Pharmacol Sci 2024; 45:225-242. [PMID: 38402076 DOI: 10.1016/j.tips.2024.01.011] [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: 09/24/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
High levels of pathogenic mitochondrial DNA (mtDNA) variants lead to severe genetic diseases, and the accumulation of such mutants may also contribute to common disorders. Thus, selecting against these mutants is a major goal in mitochondrial medicine. Although mutant mtDNA can drift randomly, mounting evidence indicates that active forces play a role in the selection for and against mtDNA variants. The underlying mechanisms are beginning to be clarified, and recent studies suggest that metabolic cues, including fuel availability, contribute to shaping mtDNA heteroplasmy. In the context of pathological mtDNAs, remodeling of nutrient metabolism supports mitochondria with deleterious mtDNAs and enables them to outcompete functional variants owing to a replicative advantage. The elevated nutrient requirement represents a mutant Achilles' heel because small molecules that restrict nutrient consumption or interfere with nutrient sensing can purge cells of deleterious mtDNAs and restore mitochondrial respiration. These advances herald the dawn of a new era of small-molecule therapies to counteract pathological mtDNAs.
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Affiliation(s)
- Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK.
| | - Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Jan Ježek
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Ian J Holt
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK; Biodonostia Health Research Institute, 20014 San Sebastián, Spain; IKERBASQUE (Basque Foundation for Science), 48013 Bilbao, Spain; CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), 28031 Madrid, Spain; Universidad de País Vasco, Barrio Sarriena s/n, 48940 Leioa, Bilbao, Spain.
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15
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Mertens J, Belva F, van Montfoort APA, Regin M, Zambelli F, Seneca S, Couvreu de Deckersberg E, Bonduelle M, Tournaye H, Stouffs K, Barbé K, Smeets HJM, Van de Velde H, Sermon K, Blockeel C, Spits C. Children born after assisted reproduction more commonly carry a mitochondrial genotype associating with low birthweight. Nat Commun 2024; 15:1232. [PMID: 38336715 PMCID: PMC10858059 DOI: 10.1038/s41467-024-45446-1] [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: 12/10/2022] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Children conceived through assisted reproductive technologies (ART) have an elevated risk of lower birthweight, yet the underlying cause remains unclear. Our study explores mitochondrial DNA (mtDNA) variants as contributors to birthweight differences by impacting mitochondrial function during prenatal development. We deep-sequenced the mtDNA of 451 ART and spontaneously conceived (SC) individuals, 157 mother-child pairs and 113 individual oocytes from either natural menstrual cycles or after ovarian stimulation (OS) and find that ART individuals carried a different mtDNA genotype than SC individuals, with more de novo non-synonymous variants. These variants, along with rRNA variants, correlate with lower birthweight percentiles, independent of conception mode. Their higher occurrence in ART individuals stems from de novo mutagenesis associated with maternal aging and OS-induced oocyte cohort size. Future research will establish the long-term health consequences of these changes and how these findings will impact the clinical practice and patient counselling in the future.
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Affiliation(s)
- Joke Mertens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Florence Belva
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Aafke P A van Montfoort
- Department of Obstetrics & Gynaecology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Sara Seneca
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Herman Tournaye
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Research Group Biology of the Testis, Faculty of Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Katrien Stouffs
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Kurt Barbé
- Interfaculty Center Data Processing & Statistics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hubert J M Smeets
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- MHeNs School Institute for Mental Health and Neuroscience, GROW Institute for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Hilde Van de Velde
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Research Group Reproduction and Immunology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Christophe Blockeel
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Department of Obstetrics and Gynaecology, School of Medicine, University of Zagreb, Šalata 3, Zagreb, 10000, Croatia
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium.
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16
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Serrano MJ, Goudet J, Cumer T. Characterization of the diversity of barn owl's mitochondrial genome reveals high copy number variations in the control region. PLoS One 2024; 19:e0295595. [PMID: 38271341 PMCID: PMC10810427 DOI: 10.1371/journal.pone.0295595] [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: 07/06/2023] [Accepted: 11/24/2023] [Indexed: 01/27/2024] Open
Abstract
Mitochondria are known to play an essential role in the cell. These organelles contain their own DNA, which is divided in a coding and non-coding region (NCR). While much of the NCR's function is unknown, tandem repeats have been observed in several vertebrates, with extreme intra-individual, intraspecific and interspecific variation. Taking advantage of a new complete reference for the mitochondrial genome of the Afro-European Barn Owl (Tyto alba), as well as 172 whole genome-resequencing; we (i) describe the reference mitochondrial genome with a special focus on the repeats in the NCR, (ii) quantify the variation in number of copies between individuals, and (iii) explore the possible factors associated with the variation in the number of repetitions. The reference mitochondrial genome revealed a long (256bp) and a short (80bp) tandem repeat in the NCR region. The re-sequenced genomes showed a great variation in number of copies between individuals, with 4 to 38 copies of the Long and 6 to 135 copies of the short repeat. Among the factors associated with this variation between individuals, the tissue used for extraction was the most significant. The exact mechanisms of the formations of these repeats are still to be discovered and understanding them will help explain the maintenance of the polymorphism in the number of copies, as well as their interactions with the metabolism, the aging and health of the individuals.
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Affiliation(s)
- Marcelo J. Serrano
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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17
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Xie F, Guo W, Wang X, Zhou K, Guo S, Liu Y, Sun T, Li S, Xu Z, Yuan Q, Zhang H, Gu X, Xing J, Liu S. Mutational profiling of mitochondrial DNA reveals an epithelial ovarian cancer-specific evolutionary pattern contributing to high oxidative metabolism. Clin Transl Med 2024; 14:e1523. [PMID: 38193640 PMCID: PMC10775184 DOI: 10.1002/ctm2.1523] [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: 08/14/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Epithelial ovarian cancer (EOC) heavily relies on oxidative phosphorylation (OXPHOS) and exhibits distinct mitochondrial metabolic reprogramming. Up to now, the evolutionary pattern of somatic mitochondrial DNA (mtDNA) mutations in EOC tissues and their potential roles in metabolic remodelling have not been systematically elucidated. METHODS Based on a large somatic mtDNA mutation dataset from private and public EOC cohorts (239 and 118 patients, respectively), we most comprehensively characterised the EOC-specific evolutionary pattern of mtDNA mutations and investigated its biological implication. RESULTS Mutational profiling revealed that the mitochondrial genome of EOC tissues was highly unstable compared with non-cancerous ovary tissues. Furthermore, our data indicated the delayed heteroplasmy accumulation of mtDNA control region (mtCTR) mutations and near-complete absence of mtCTR non-hypervariable segment (non-HVS) mutations in EOC tissues, which is consistent with stringent negative selection against mtCTR mutation. Additionally, we observed a bidirectional and region-specific evolutionary pattern of mtDNA coding region mutations, manifested as significant negative selection against mutations in complex V (ATP6/ATP8) and tRNA loop regions, and potential positive selection on mutations in complex III (MT-CYB). Meanwhile, EOC tissues showed higher mitochondrial biogenesis compared with non-cancerous ovary tissues. Further analysis revealed the significant association between mtDNA mutations and both mitochondrial biogenesis and overall survival of EOC patients. CONCLUSIONS Our study presents a comprehensive delineation of EOC-specific evolutionary patterns of mtDNA mutations that aligned well with the specific mitochondrial metabolic remodelling, conferring novel insights into the functional roles of mtDNA mutations in EOC tumourigenesis and progression.
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Affiliation(s)
- Fanfan Xie
- Department of Obstetrics and GynecologyXijing HospitalFourth Military Medical UniversityXi'anChina
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Wenjie Guo
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Xingguo Wang
- Department of Obstetrics and GynecologyXijing HospitalFourth Military Medical UniversityXi'anChina
| | - Kaixiang Zhou
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Shanshan Guo
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Yang Liu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Tianlei Sun
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Shengjing Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Zhiyang Xu
- Department of Obstetrics and GynecologyXijing HospitalFourth Military Medical UniversityXi'anChina
| | - Qing Yuan
- Institute of Medical ResearchNorthwestern Polytechnical UniversityXi'anChina
| | - Huanqin Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Xiwen Gu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of PathologyXijing Hospital and School of Basic MedicineFourth Military Medical UniversityXi'anChina
| | - Jinliang Xing
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Physiology and PathophysiologyFourth Military Medical UniversityXi'anChina
| | - Shujuan Liu
- Department of Obstetrics and GynecologyXijing HospitalFourth Military Medical UniversityXi'anChina
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18
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Sturgis J, Singh R, Caron Q, Samuels IS, Shiju TM, Mukkara A, Freedman P, Bonilha VL. Modeling aging and retinal degeneration with mitochondrial DNA mutation burden. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569464. [PMID: 38076962 PMCID: PMC10705408 DOI: 10.1101/2023.11.30.569464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Somatic mitochondrial DNA (mtDNA) mutation accumulation has been observed in individuals with retinal degenerative disorders. To study the effects of aging and mtDNA mutation accumulation in the retina, a Polymerase gamma (POLG) deficiency model, the POLGD257A mutator mice (PolgD257A), was used. POLG is an enzyme responsible for regulating mtDNA replication and repair. Retinas of young and older mice with this mutation were analyzed in vivo and ex vivo to provide new insights into the contribution of age-related mitochondrial dysfunction due to mtDNA damage. Optical coherence tomography (OCT) image analysis revealed a decrease in retinal and photoreceptor thickness starting at 6 months of age in mice with the POLGD257A mutation compared to wild-type (WT) mice. Electroretinography (ERG) testing showed a significant decrease in all recorded responses at 6 months of age. Sections labeled with markers of different types of retinal cells, including cones, rods, and bipolar cells, exhibited decreased labeling starting at 6 months. However, electron microscopy analysis revealed differences in retinal pigment epithelium (RPE) mitochondria morphology beginning at 3 months. Interestingly, there was no increase in oxidative stress observed in the retina or RPE of POLGD257A mice. Additionally, POLGD257A RPE exhibited an accelerated rate of autofluorescence cytoplasmic granule formation and accumulation. Mitochondrial markers displayed decreased abundance in protein lysates obtained from retina and RPE samples. These findings suggest that the accumulation of mitochondrial DNA mutations leads to impaired mitochondrial function and accelerated aging, resulting in retinal degeneration.
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Affiliation(s)
- John Sturgis
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Rupesh Singh
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Quinn Caron
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ivy S. Samuels
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH
| | - Thomas Micheal Shiju
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Aditi Mukkara
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- College of Arts and Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Paul Freedman
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- Debusk College of Osteopathic Medicine, Knoxville, TN, USA
| | - Vera L. Bonilha
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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19
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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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20
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Abstract
A large-scale study of mutations in mitochondrial DNA has revealed a subset that do not accumulate with age.
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Affiliation(s)
| | | | - Melissa Franco
- Department of Biology, Northeastern UniversityBostonUnited States
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