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Bonnefous H, Teulière J, Lapointe FJ, Lopez P, Bapteste E. Most genetic roots of fungal and animal aging are hundreds of millions of years old according to phylostratigraphy analyses of aging networks. GeroScience 2024:10.1007/s11357-024-01234-9. [PMID: 38862758 DOI: 10.1007/s11357-024-01234-9] [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: 11/16/2023] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Few studies have systematically analyzed how old aging is. Gaining a more accurate knowledge about the natural history of aging could however have several payoffs. This knowledge could unveil lineages with dated genetic hardware, possibly maladapted to current environmental challenges, and also uncover "phylogenetic modules of aging," i.e., naturally evolved pathways associated with aging or longevity from a single ancestry, with translational interest for anti-aging therapies. Here, we approximated the natural history of the genetic hardware of aging for five model fungal and animal species. We propose a lower-bound estimate of the phylogenetic age of origination for their protein-encoding gene families and protein-protein interactions. Most aging-associated gene families are hundreds of million years old, older than the other gene families from these genomes. Moreover, we observed a form of punctuated evolution of the aging hardware in all species, as aging-associated families born at specific phylogenetic times accumulate preferentially in genomes. Most protein-protein interactions between aging genes are also old, and old aging-associated proteins showed a reduced potential to contribute to novel interactions associated with aging, suggesting that aging networks are at risk of losing in evolvability over long evolutionary periods. Finally, due to reshuffling events, aging networks presented a very limited phylogenetic structure that challenges the detection of "maladaptive" or "adaptative" phylogenetic modules of aging in present-day genomes.
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Affiliation(s)
- Hugo Bonnefous
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - François-Joseph Lapointe
- Département de Sciences Biologiques, Complexe Des Sciences, Université de Montréal, Montréal, QC, Canada
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France.
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2
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Perillo M, Silla A, Punzo A, Caliceti C, Kriete A, Sell C, Lorenzini A. Peto's paradox: Nature has used multiple strategies to keep cancer at bay while evolving long lifespans and large body masses. A systematic review. Biomed J 2024; 47:100654. [PMID: 37604250 PMCID: PMC10973980 DOI: 10.1016/j.bj.2023.100654] [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: 07/02/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Comparative oncology is an understudied field of science. We are far from understanding the key mechanisms behind Peto's paradox, i.e., understanding how long-lived and large animals are not subject to a higher cancer burden despite the longer exposure time to mutations and the larger number of cells exposed. In this work, we investigated the scientific evidence on such mechanisms through a systematic mini-review of the literature about the relation of longevity and/or large body mass with physiological, genetic, or environmental traits among mammalian species. More than forty thousand articles were retrieved from three repositories, and 383 of them were screened using an active-learning-based tool. Of those, 36 articles on longevity and 37 on body mass were selected for the review. Such articles were examined focusing on: number and type of species considered, statistical methods used, traits investigated, and observed relationship with longevity and/or body mass. Where applicable, the traits investigated were matched with one or more hallmarks of cancer. We obtained a list of potential candidate traits to explain Peto's paradox related to replicative immortality, cell senescence, genome instability and mutations, proliferative signaling, growth suppression evasion, and cell resistance to death. Our investigation suggests that different strategies have been followed to prevent cancer in large and long-lived species. The large number of papers retrieved emphasizes that more studies can be launched in the future, using more efficient analytical approaches to comprehensively evaluate the convergent biological mechanisms essential for acquiring longevity and large body mass without increasing cancer risk.
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Affiliation(s)
- Matteo Perillo
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.
| | - Alessia Silla
- Department for Life Quality Studies, University of Bologna, Italy
| | - Angela Punzo
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy; National Institute of Biosystems and Biostructures INBB, Rome, Italy
| | - Cristiana Caliceti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy; National Institute of Biosystems and Biostructures INBB, Rome, Italy
| | - Andres Kriete
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Christian Sell
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Antonello Lorenzini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy; National Institute of Biosystems and Biostructures INBB, Rome, Italy
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Bapteste E, Huneman P, Keller L, Teulière J, Lopez P, Teeling EC, Lindner AB, Baudisch A, Ludington WB, Franceschi C. Expanding evolutionary theories of ageing to better account for symbioses and interactions throughout the Web of Life. Ageing Res Rev 2023; 89:101982. [PMID: 37321383 PMCID: PMC10771319 DOI: 10.1016/j.arr.2023.101982] [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: 04/14/2023] [Revised: 05/26/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023]
Abstract
How, when, and why organisms age are fascinating issues that can only be fully addressed by adopting an evolutionary perspective. Consistently, the main evolutionary theories of ageing, namely the Mutation Accumulation theory, the Antagonistic Pleiotropy theory, and the Disposable Soma theory, have formulated stimulating hypotheses that structure current debates on both the proximal and ultimate causes of organismal ageing. However, all these theories leave a common area of biology relatively under-explored. The Mutation Accumulation theory and the Antagonistic Pleiotropy theory were developed under the traditional framework of population genetics, and therefore are logically centred on the ageing of individuals within a population. The Disposable Soma theory, based on principles of optimising physiology, mainly explains ageing within a species. Consequently, current leading evolutionary theories of ageing do not explicitly model the countless interspecific and ecological interactions, such as symbioses and host-microbiomes associations, increasingly recognized to shape organismal evolution across the Web of Life. Moreover, the development of network modelling supporting a deeper understanding on the molecular interactions associated with ageing within and between organisms is also bringing forward new questions regarding how and why molecular pathways associated with ageing evolved. Here, we take an evolutionary perspective to examine the effects of organismal interactions on ageing across different levels of biological organisation, and consider the impact of surrounding and nested systems on organismal ageing. We also apply this perspective to suggest open issues with potential to expand the standard evolutionary theories of ageing.
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Affiliation(s)
- Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
| | - Philippe Huneman
- Institut d'Histoire et de Philosophie des Sciences et des Techniques (CNRS/ Université Paris I Sorbonne), Paris, France
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
| | - Annette Baudisch
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, 5230 Odense M, Denmark
| | - William B Ludington
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; Department of Applied Mathematics and Laboratory of Systems Medicine of Aging, Lobachevsky University, Nizhny Novgorod 603950, Russia
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Abstract
The proteasome is a multi-subunit proteolytic complex that functions to degrade normal proteins for physiological regulation and to eliminate abnormal proteins for cellular protection. Generally, the proteasome targets substrate proteins that are marked by attachment of multiple ubiquitin molecules. In various types of cells in an organism, damage to proteins occurs both from internal sources such as reactive oxygen species and from external ones such as UV radiation from the sun. The proteasome functions to protect the cells by degrading damaged proteins. With ageing, however, the capacity of the proteasome to degrade damaged proteins is reduced as indicated by evidence gathered by many studies. Studies on ageing in muscle, skin, and brain show that with age catalytic activity of the proteasome is decreased and the expression of proteasome subunits is altered. Age-related accumulation of damaged or misfolded proteins causes further reduction of proteasome activity. Abnormal proteins also accumulate as a result of age-related neurodegenerative diseases. Deficits in proteasome activity might be responsible for accumulation of protein aggregates and thus contribute to the pathology. Results from several studies suggest a link between the proteasome and longevity. This chapter reviews the various ways in which the proteasome is associated with the ageing process and examines evidence gathered from investigations on cultured cells, model organisms, and humans.
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Affiliation(s)
- Ashok N Hegde
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA.
| | - Lindsey M Duke
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA
| | - Logan E Timm
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA
| | - Hannah Nobles
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA
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Teulière J, Bernard C, Corel E, Lapointe FJ, Martens J, Lopez P, Bapteste E. Network analyses unveil ageing-associated pathways evolutionarily conserved from fungi to animals. GeroScience 2022; 45:1059-1080. [PMID: 36508078 PMCID: PMC9886728 DOI: 10.1007/s11357-022-00704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
The genetic roots of the diverse paces and shapes of ageing and of the large variations in longevity observed across the tree of life are poorly understood. Indeed, pathways associated with ageing/longevity are incompletely known, both in terms of their constitutive genes/proteins and of their molecular interactions. Moreover, there is limited overlap between the genes constituting these pathways across mammals. Yet, dedicated comparative analyses might still unravel evolutionarily conserved, important pathways associated with longevity or ageing. Here, we used an original strategy with a double evolutionary and systemic focus to analyse protein interactions associated with ageing or longevity during the evolution of five species of Opisthokonta. We ranked these proteins and interactions based on their evolutionary conservation and centrality in past and present protein-protein interaction (PPI) networks, providing a big systemic picture of the evolution of ageing and longevity pathways that identified which pathways emerged in which Opisthokonta lineages, were conserved, and/or central. We confirmed that longevity/ageing-associated proteins (LAPs), be they pro- or anti-longevity, are highly central in extant PPI, consistently with the antagonistic pleiotropy theory of ageing, and identified key antagonistic regulators of ageing/longevity, 52 of which with homologues in humans. While some highly central LAPs were evolutionarily conserved for over a billion years, we report a clear transition in the functionally important components of ageing/longevity within bilaterians. We also predicted 487 novel evolutionarily conserved LAPs in humans, 54% of which are more central than mTOR, and 138 of which are druggable, defining new potential targets for anti-ageing treatments in humans.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eduardo Corel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - François-Joseph Lapointe
- grid.14848.310000 0001 2292 3357Département de Sciences Biologiques, Complexe Des Sciences, Université de Montréal, Montréal, QC Canada
| | - Johannes Martens
- Sciences, Normes, Démocratie (SND), Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France.
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6
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Intermediate alleles of HTT: A new pathway in longevity. J Neurol Sci 2022; 438:120274. [DOI: 10.1016/j.jns.2022.120274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/22/2022] [Accepted: 04/30/2022] [Indexed: 11/29/2022]
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Tejada-Martinez D, Avelar RA, Lopes I, Zhang B, Novoa G, de Magalhães JP, Trizzino M. Positive selection and enhancer evolution shaped lifespan and body mass in great apes. Mol Biol Evol 2021; 39:6491260. [PMID: 34971383 PMCID: PMC8837823 DOI: 10.1093/molbev/msab369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Within primates, the great apes are outliers both in terms of body size and lifespan, since they include the largest and longest-lived species in the order. Yet, the molecular bases underlying such features are poorly understood. Here, we leveraged an integrated approach to investigate multiple sources of molecular variation across primates, focusing on over ten thousand genes, including ∼1,500 previously associated with lifespan, and additional ∼9,000 for which an association with longevity has never been suggested. We analyzed dN/dS rates, positive selection, gene expression (RNA-seq) and gene regulation (ChIP-seq). By analyzing the correlation between dN/dS, maximum lifespan and body mass we identified 276 genes whose rate of evolution positively correlates with maximum lifespan in primates. Further, we identified 5 genes, important for tumor suppression, adaptive immunity, metastasis and inflammation, under positive selection exclusively in the great ape lineage. RNA-seq data, generated from the liver of six species representing all the primate lineages, revealed that 8% of ∼1,500 genes previously associated with longevity are differentially expressed in apes relative to other primates. Importantly, by integrating RNA-seq with ChIP-seq for H3K27ac (which marks active enhancers), we show that the differentially expressed longevity genes are significantly more likely than expected to be located near a novel "ape-specific" enhancer. Moreover, these particular ape-specific enhancers are enriched for young transposable elements, and specifically SINE-Vntr-Alus (SVAs). In summary, we demonstrate that multiple evolutionary forces have contributed to the evolution of lifespan and body size in primates.
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Affiliation(s)
- Daniela Tejada-Martinez
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.,Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Roberto A Avelar
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Inês Lopes
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Bruce Zhang
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Guy Novoa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
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Zhang Q, Tombline G, Ablaeva J, Zhang L, Zhou X, Smith Z, Zhao Y, Xiaoli AM, Wang Z, Lin JR, Jabalameli MR, Mitra J, Nguyen N, Vijg J, Seluanov A, Gladyshev VN, Gorbunova V, Zhang ZD. Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation. Cell Rep 2021; 37:109965. [PMID: 34758328 PMCID: PMC8656434 DOI: 10.1016/j.celrep.2021.109965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 06/07/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
The North American beaver is an exceptionally long-lived and cancer-resistant rodent species. Here, we report the evolutionary changes in its gene coding sequences, copy numbers, and expression. We identify changes that likely increase its ability to detoxify aldehydes, enhance tumor suppression and DNA repair, and alter lipid metabolism, potentially contributing to its longevity and cancer resistance. Hpgd, a tumor suppressor gene, is uniquely duplicated in beavers among rodents, and several genes associated with tumor suppression and longevity are under positive selection in beavers. Lipid metabolism genes show positive selection signals, changes in copy numbers, or altered gene expression in beavers. Aldh1a1, encoding an enzyme for aldehydes detoxification, is particularly notable due to its massive expansion in beavers, which enhances their cellular resistance to ethanol and capacity to metabolize diverse aldehyde substrates from lipid oxidation and their woody diet. We hypothesize that the amplification of Aldh1a1 may contribute to the longevity of beavers. Zhang et al. examine the genome of North American beavers and find evolutionary changes that could contribute to beavers’ longevity. In particular, Aldh1a1, encoding an enzyme for aldehyde detoxification, is massively expanded in the beaver genome, protecting them against exposure to aldehydes from lipid oxidation and their woody diet.
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Affiliation(s)
- Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zachary Smith
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alus M Xiaoli
- Departments of Medicine and Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhen Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nha Nguyen
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
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9
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Kaya A, Phua CZJ, Lee M, Wang L, Tyshkovskiy A, Ma S, Barre B, Liu W, Harrison BR, Zhao X, Zhou X, Wasko BM, Bammler TK, Promislow DEL, Kaeberlein M, Gladyshev VN. Evolution of natural lifespan variation and molecular strategies of extended lifespan in yeast. eLife 2021; 10:e64860. [PMID: 34751131 PMCID: PMC8612763 DOI: 10.7554/elife.64860] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/04/2021] [Indexed: 01/29/2023] Open
Abstract
To understand the genetic basis and selective forces acting on longevity, it is useful to examine lifespan variation among closely related species, or ecologically diverse isolates of the same species, within a controlled environment. In particular, this approach may lead to understanding mechanisms underlying natural variation in lifespan. Here, we analyzed 76 ecologically diverse wild yeast isolates and discovered a wide diversity of replicative lifespan (RLS). Phylogenetic analyses pointed to genes and environmental factors that strongly interact to modulate the observed aging patterns. We then identified genetic networks causally associated with natural variation in RLS across wild yeast isolates, as well as genes, metabolites, and pathways, many of which have never been associated with yeast lifespan in laboratory settings. In addition, a combined analysis of lifespan-associated metabolic and transcriptomic changes revealed unique adaptations to interconnected amino acid biosynthesis, glutamate metabolism, and mitochondrial function in long-lived strains. Overall, our multiomic and lifespan analyses across diverse isolates of the same species shows how gene-environment interactions shape cellular processes involved in phenotypic variation such as lifespan.
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Affiliation(s)
- Alaattin Kaya
- Department of Biology, Virginia Commonwealth UniversityRichmondUnited States
| | - Cheryl Zi Jin Phua
- Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Mitchell Lee
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of WashingtonSeattleUnited States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
- Belozersky Institute of Physico-Chemical Biology, Moscow State UniversityMoscowRussian Federation
| | - Siming Ma
- Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Benjamin Barre
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Weiqiang Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Institute of ZoologyBeijingChina
| | - Benjamin R Harrison
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Xiaqing Zhao
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
| | - Brian M Wasko
- Department of Biology, University of Houston - Clear LakeHoustonUnited States
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of WashingtonSeattleUnited States
| | - Daniel EL Promislow
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
- Department of Biology, University of WashingtonSeattleUnited States
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical SchoolBostonUnited States
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10
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The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proc Natl Acad Sci U S A 2021; 118:2010632118. [PMID: 33574059 PMCID: PMC7896301 DOI: 10.1073/pnas.2010632118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Surviving challenging environments, living long lives, and engaging in complex cognitive processes are hallmark human characteristics. Similar traits have evolved in parallel in capuchin monkeys, but their genetic underpinnings remain unexplored. We developed and annotated a reference assembly for white-faced capuchin monkeys to explore the evolution of these phenotypes. By comparing populations of capuchins inhabiting rainforest versus dry forests with seasonal droughts, we detected selection in genes associated with kidney function, muscular wasting, and metabolism, suggesting adaptation to periodic resource scarcity. When comparing capuchins to other mammals, we identified evidence of selection in multiple genes implicated in longevity and brain development. Our research was facilitated by our method to generate high- and low-coverage genomes from noninvasive biomaterials. Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator. Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity.
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11
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Tollis M, Schneider-Utaka AK, Maley CC. The Evolution of Human Cancer Gene Duplications across Mammals. Mol Biol Evol 2021; 37:2875-2886. [PMID: 32421773 PMCID: PMC7530603 DOI: 10.1093/molbev/msaa125] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer is caused by genetic alterations that affect cellular fitness, and multicellular organisms have evolved mechanisms to suppress cancer such as cell cycle checkpoints and apoptosis. These pathways may be enhanced by the addition of tumor suppressor gene paralogs or deletion of oncogenes. To provide insights to the evolution of cancer suppression across the mammalian radiation, we estimated copy numbers for 548 human tumor suppressor gene and oncogene homologs in 63 mammalian genome assemblies. The naked mole rat contained the most cancer gene copies, consistent with the extremely low rates of cancer found in this species. We found a positive correlation between a species’ cancer gene copy number and its longevity, but not body size, contrary to predictions from Peto’s Paradox. Extremely long-lived mammals also contained more copies of caretaker genes in their genomes, suggesting that the maintenance of genome integrity is an essential form of cancer prevention in long-lived species. We found the strongest association between longevity and copy numbers of genes that are both germline and somatic tumor suppressor genes, suggesting that selection has acted to suppress both hereditary and sporadic cancers. We also found a strong relationship between the number of tumor suppressor genes and the number of oncogenes in mammalian genomes, suggesting that complex regulatory networks mediate the balance between cell proliferation and checks on tumor progression. This study is the first to investigate cancer gene expansions across the mammalian radiation and provides a springboard for potential human therapies based on evolutionary medicine.
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Affiliation(s)
- Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ.,Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ
| | | | - Carlo C Maley
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ.,School of Life Sciences, Arizona State University, Tempe, AZ
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12
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Tejada-Martinez D, de Magalhães JP, Opazo JC. Positive selection and gene duplications in tumour suppressor genes reveal clues about how cetaceans resist cancer. Proc Biol Sci 2021; 288:20202592. [PMID: 33622125 DOI: 10.1098/rspb.2020.2592] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cetaceans are the longest-living species of mammals and the largest in the history of the planet. They have developed mechanisms against diseases such cancer, although the underlying molecular bases of these remain unknown. The goal of this study was to investigate the role of natural selection in the evolution of 1077 tumour suppressor genes (TSGs) in cetaceans. We used a comparative genomic approach to analyse two sources of molecular variation in the form of dN/dS rates and gene copy number variation. We found a signal of positive selection in the ancestor of cetaceans within the CXCR2 gene, an important regulator of DNA damage, tumour dissemination and immune system. Further, in the ancestor of baleen whales, we found six genes exhibiting positive selection relating to diseases such as breast carcinoma, lung neoplasm (ADAMTS8) and leukaemia (ANXA1). The TSGs turnover rate (gene gain and loss) was almost 2.4-fold higher in cetaceans when compared with other mammals, and notably even faster in baleen whales. The molecular variants in TSGs found in baleen whales, combined with the faster gene turnover rate, could have favoured the evolution of their particular traits of anti-cancer resistance, gigantism and longevity. Additionally, we report 71 genes with duplications, of which 11 genes are linked to longevity (e.g. NOTCH3 and SIK1) and are important regulators of senescence, cell proliferation and metabolism. Overall, these results provide evolutionary evidence that natural selection in TSGs could act on species with large body sizes and extended lifespan, providing novel insights into the genetic basis of disease resistance.
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Affiliation(s)
- Daniela Tejada-Martinez
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.,Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Valdivia, Chile.,Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
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13
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Toren D, Kulaga A, Jethva M, Rubin E, Snezhkina AV, Kudryavtseva AV, Nowicki D, Tacutu R, Moskalev AA, Fraifeld VE. Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. Aging Cell 2020; 19:e13158. [PMID: 32515539 PMCID: PMC7433004 DOI: 10.1111/acel.13158] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/16/2020] [Accepted: 04/09/2020] [Indexed: 12/29/2022] Open
Abstract
One important question in aging research is how differences in genomics and transcriptomics determine the maximum lifespan in various species. Despite recent progress, much is still unclear on the topic, partly due to the lack of samples in nonmodel organisms and due to challenges in direct comparisons of transcriptomes from different species. The novel ranking‐based method that we employ here is used to analyze gene expression in the gray whale and compare its de novo assembled transcriptome with that of other long‐ and short‐lived mammals. Gray whales are among the top 1% longest‐lived mammals. Despite the extreme environment, or maybe due to a remarkable adaptation to its habitat (intermittent hypoxia, Arctic water, and high pressure), gray whales reach at least the age of 77 years. In this work, we show that long‐lived mammals share common gene expression patterns between themselves, including high expression of DNA maintenance and repair, ubiquitination, apoptosis, and immune responses. Additionally, the level of expression for gray whale orthologs of pro‐ and anti‐longevity genes found in model organisms is in support of their alleged role and direction in lifespan determination. Remarkably, among highly expressed pro‐longevity genes many are stress‐related, reflecting an adaptation to extreme environmental conditions. The conducted analysis suggests that the gray whale potentially possesses high resistance to cancer and stress, at least in part ensuring its longevity. This new transcriptome assembly also provides important resources to support the efforts of maintaining the endangered population of gray whales.
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Affiliation(s)
- Dmitri Toren
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
| | - Anton Kulaga
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
- Humenhance OÜ Tallinn Estonia
| | - Mineshbhai Jethva
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Dmitry Nowicki
- Center for Cybernetics Institute of MMS of NASU Kiev Ukraine
| | - Robi Tacutu
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
- Chronos Biosystems SRL Bucharest Romania
| | - Alexey A. Moskalev
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
- Institute of Biology of Komi Science Center of Ural Branch of RAS Syktyvkar Russia
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
- 8IVAO LLC Saint Petersburg Russia
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14
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Johnson AA, Shokhirev MN, Wyss-Coray T, Lehallier B. Systematic review and analysis of human proteomics aging studies unveils a novel proteomic aging clock and identifies key processes that change with age. Ageing Res Rev 2020; 60:101070. [PMID: 32311500 DOI: 10.1016/j.arr.2020.101070] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/23/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022]
Abstract
The development of clinical interventions that significantly improve human healthspan requires robust markers of biological age as well as thoughtful therapeutic targets. To promote these goals, we performed a systematic review and analysis of human aging and proteomics studies. The systematic review includes 36 different proteomics analyses, each of which identified proteins that significantly changed with age. We discovered 1,128 proteins that had been reported by at least two or more analyses and 32 proteins that had been reported by five or more analyses. Each of these 32 proteins has known connections relevant to aging and age-related disease. GDF15, for example, extends both lifespan and healthspan when overexpressed in mice and is additionally required for the anti-diabetic drug metformin to exert beneficial effects on body weight and energy balance. Bioinformatic enrichment analyses of our 1,128 commonly identified proteins heavily implicated processes relevant to inflammation, the extracellular matrix, and gene regulation. We additionally propose a novel proteomic aging clock comprised of proteins that were reported to change with age in plasma in three or more different studies. Using a large patient cohort comprised of 3,301 subjects (aged 18-76 years), we demonstrate that this clock is able to accurately predict human age.
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15
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Jasinska AJ. Resources for functional genomic studies of health and development in nonhuman primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:174-194. [PMID: 32221967 DOI: 10.1002/ajpa.24051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 01/01/2023]
Abstract
Primates display a wide range of phenotypic variation underlaid by complex genetically regulated mechanisms. The links among DNA sequence, gene function, and phenotype have been of interest from an evolutionary perspective, to understand functional genome evolution and its phenotypic consequences, and from a biomedical perspective to understand the shared and human-specific roots of health and disease. Progress in methods for characterizing genetic, transcriptomic, and DNA methylation (DNAm) variation is driving the rapid development of extensive omics resources, which are now increasingly available from humans as well as a growing number of nonhuman primates (NHPs). The fast growth of large-scale genomic data is driving the emergence of integrated tools and databases, thus facilitating studies of gene functionality across primates. This review describes NHP genomic resources that can aid in exploration of how genes shape primate phenotypes. It focuses on the gene expression trajectories across development in different tissues, the identification of functional genetic variation (including variants deleterious for protein function and regulatory variants modulating gene expression), and DNAm profiles as an emerging tool to understand the process of aging. These resources enable comparative functional genomics approaches to identify species-specific and primate-shared gene functionalities associated with health and development.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California, USA.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Eye on Primates, Los Angeles, California, USA
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16
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McLain AT, Faulk C. The evolution of CpG density and lifespan in conserved primate and mammalian promoters. Aging (Albany NY) 2019; 10:561-572. [PMID: 29661983 PMCID: PMC5940106 DOI: 10.18632/aging.101413] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/09/2018] [Indexed: 12/12/2022]
Abstract
Gene promoters are evolutionarily conserved across holozoans and enriched in CpG sites, the target for DNA methylation. As animals age, the epigenetic pattern of DNA methylation degrades, with highly methylated CpG sites gradually becoming demethylated while CpG islands increase in methylation. Across vertebrates, aging is a trait that varies among species. We used this variation to determine whether promoter CpG density correlates with species’ maximum lifespan. Human promoter sequences were used to identify conserved regions in 131 mammals and a subset of 28 primate genomes. We identified approximately 1000 gene promoters (5% of the total), that significantly correlated CpG density with lifespan. The correlations were performed via the phylogenetic least squares method to account for trait similarity by common descent using phylogenetic branch lengths. Gene set enrichment analysis revealed no significantly enriched pathways or processes, consistent with the hypothesis that aging is not under positive selection. However, within both mammals and primates, 95% of the promoters showed a positive correlation between increasing CpG density and species lifespan, and two thirds were shared between the primate subset and mammalian datasets. Thus, these genes may require greater buffering capacity against age-related dysregulation of DNA methylation in longer-lived species.
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Affiliation(s)
- Adam T McLain
- Department of Biology and Chemistry, College of Arts and Sciences, SUNY Polytechnic Institute, Utica, NY 13502, USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN 55108, USA
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17
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Muntané G, Farré X, Rodríguez JA, Pegueroles C, Hughes DA, de Magalhães JP, Gabaldón T, Navarro A. Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis. Mol Biol Evol 2019; 35:1990-2004. [PMID: 29788292 PMCID: PMC6063263 DOI: 10.1093/molbev/msy105] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan across primate species. We used two different approaches. First, we searched for parallel amino-acid mutations that co-occur with increases in longevity across the primate linage. Twenty-five such amino-acid variants were identified, several of which have been previously reported by studies with different experimental setups and in different model organisms. The genes harboring these mutations are mainly enriched in functional categories such as wound healing, blood coagulation, and cardiovascular disorders. We demonstrate that these pathways are highly enriched for pleiotropic effects, as predicted by the antagonistic pleiotropy theory of aging. A second approach was focused on changes in rates of protein evolution across the primate phylogeny. Using the phylogenetic generalized least squares, we show that some genes exhibit strong correlations between their evolutionary rates and longevity-associated traits. These include genes in the Sphingosine 1-phosphate pathway, PI3K signaling, and the Thrombin/protease-activated receptor pathway, among other cardiovascular processes. Together, these results shed light into human senescence patterns and underscore the power of comparative genomics to identify pathways related to aging and longevity.
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Affiliation(s)
- Gerard Muntané
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Biomedical Network Research Centre on Mental Health (CIBERSAM), Reus, Spain
| | - Xavier Farré
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Juan Antonio Rodríguez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cinta Pegueroles
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - David A Hughes
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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18
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Longitudinal comparative transcriptomics reveals unique mechanisms underlying extended healthspan in bats. Nat Ecol Evol 2019; 3:1110-1120. [DOI: 10.1038/s41559-019-0913-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/01/2019] [Indexed: 12/22/2022]
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19
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Sahm A, Almaida-Pagán P, Bens M, Mutalipassi M, Lucas-Sánchez A, de Costa Ruiz J, Görlach M, Cellerino A. Analysis of the coding sequences of clownfish reveals molecular convergence in the evolution of lifespan. BMC Evol Biol 2019; 19:89. [PMID: 30975078 PMCID: PMC6460853 DOI: 10.1186/s12862-019-1409-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 03/10/2019] [Indexed: 01/12/2023] Open
Abstract
Background Standard evolutionary theories of aging postulate that reduced extrinsic mortality leads to evolution of longevity. Clownfishes of the genus Amphiprion live in a symbiotic relationship with sea anemones that provide protection from predators. We performed a survey and identified at least two species with a lifespan of over 20 years. Given their small size and ease of captive reproduction, clownfish lend themselves as experimental models of exceptional longevity. To identify genetic correlates of exceptional longevity, we sequenced the transcriptomes of Amphiprion percula and A. clarkii and performed a scan for positively-selected genes (PSGs). Results The PSGs that we identified in the last common clownfish ancestor were compared with PSGs detected in long-lived mole rats and short-lived killifishes revealing convergent evolution in processes such as mitochondrial biogenesis. Among individual genes, the Mitochondrial Transcription Termination Factor 1 (MTERF1), was positively-selected in all three clades, whereas the Glutathione S-Transferase Kappa 1 (GSTK1) was under positive selection in two independent clades. For the latter, homology modelling strongly suggested that positive selection targeted enzymatically important residues. Conclusions These results indicate that specific pathways were recruited in independent lineages evolving an exceptionally extended or shortened lifespan and point to mito-nuclear balance as a key factor. Electronic supplementary material The online version of this article (10.1186/s12862-019-1409-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arne Sahm
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | | | - Martin Bens
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | | | | | | | - Matthias Görlach
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Alessandro Cellerino
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany. .,Bio@SNS, Scuola Normale Superiore, Pisa, Italy.
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20
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Tian X, Seluanov A, Gorbunova V. Molecular Mechanisms Determining Lifespan in Short- and Long-Lived Species. Trends Endocrinol Metab 2017; 28:722-734. [PMID: 28888702 PMCID: PMC5679293 DOI: 10.1016/j.tem.2017.07.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/16/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022]
Abstract
Aging is a global decline of physiological functions, leading to an increased susceptibility to diseases and ultimately death. Maximum lifespans differ up to 200-fold between mammalian species. Although considerable progress has been achieved in identifying conserved pathways that regulate individual lifespan within model organisms, whether the same pathways are responsible for the interspecies differences in longevity remains to be determined. Recent cross-species studies have begun to identify pathways responsible for interspecies differences in lifespan. Here, we review the evidence supporting the role of anticancer mechanisms, DNA repair machinery, insulin/insulin-like growth factor 1 signaling, and proteostasis in defining species lifespans. Understanding the mechanisms responsible for the dramatic differences in lifespan between species will have a transformative effect on developing interventions to improve human health and longevity.
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Affiliation(s)
- Xiao Tian
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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21
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22
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Sands WA, Page MM, Selman C. Proteostasis and ageing: insights from long-lived mutant mice. J Physiol 2017; 595:6383-6390. [PMID: 28718225 PMCID: PMC5638872 DOI: 10.1113/jp274334] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/03/2017] [Indexed: 12/30/2022] Open
Abstract
The global increase in life expectancy is creating significant medical, social and economic challenges to current and future generations. Consequently, there is a need to identify the fundamental mechanisms underlying the ageing process. This knowledge should help develop realistic interventions capable of combatting age‐related disease, and thus improving late‐life health and vitality. While several mechanisms have been proposed as conserved lifespan determinants, the loss of proteostasis – where proteostasis is defined here as the maintenance of the proteome – appears highly relevant to both ageing and disease. Several studies have shown that multiple proteostatic mechanisms, including the endoplasmic reticulum (ER)‐induced unfolded protein response (UPR), the ubiquitin–proteasome system (UPS) and autophagy, appear indispensable for longevity in many long‐lived invertebrate mutants. Similarly, interspecific comparisons suggest that proteostasis may be an important lifespan determinant in vertebrates. Over the last 20 years a number of long‐lived mouse mutants have been described, many of which carry single‐gene mutations within the growth‐hormone, insulin/IGF‐1 or mTOR signalling pathways. However, we still do not know how these mutations act mechanistically to increase lifespan and healthspan, and accordingly whether mechanistic commonality occurs between different mutants. Recent evidence supports the premise that the successful maintenance of the proteome during ageing may be linked to the increased lifespan and healthspan of long‐lived mouse mutants.
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Affiliation(s)
- William A Sands
- Glasgow Ageing Research Network (GARNER), Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Melissa M Page
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Colin Selman
- Glasgow Ageing Research Network (GARNER), Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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23
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Dammann P. Slow aging in mammals-Lessons from African mole-rats and bats. Semin Cell Dev Biol 2017; 70:154-163. [PMID: 28698112 DOI: 10.1016/j.semcdb.2017.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/30/2022]
Abstract
Traditionally, the main mammalian models used in aging research have been mice and rats, i.e. short-lived species that obviously lack effective maintenance mechanisms to keep their soma in a functional state for prolonged periods of time. It is doubtful that life-extending mechanisms identified only in such short-lived species adequately reflect the diversity of longevity pathways that have naturally evolved in mammals, or that they have much relevance for long-lived species such as humans. Therefore, some complementary, long-lived mammalian models have been introduced to aging research in the past 15-20 years, particularly naked mole-rats (and to a lesser extent also other mole-rats) and bats. Here, I summarize and compare the most important results regarding various aspects of aging - oxidative stress, molecular homeostasis and repair, and endocrinology - that have been obtained from studies using these new mammalian models of high longevity. I argue that the inclusion of these models was an important step forward, because it drew researchers' attention to certain oversimplifications of existing aging theories and to several features that appear to be universal components of enhanced longevity in mammals. However, even among mammals with high longevity, considerable variation exists with respect to other candidate mechanisms that also must be taken into account if inadequate generalizations are to be avoided.
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Affiliation(s)
- Philip Dammann
- Central Animal Laboratory, Faculty of Medicine, University of Duisburg, Essen, Germany.
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24
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Sahm A, Bens M, Platzer M, Cellerino A. Parallel evolution of genes controlling mitonuclear balance in short-lived annual fishes. Aging Cell 2017; 16:488-496. [PMID: 28295945 PMCID: PMC5418189 DOI: 10.1111/acel.12577] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2016] [Indexed: 12/15/2022] Open
Abstract
The current molecular understanding of the aging process derives almost exclusively from the study of random or targeted single‐gene mutations in highly inbred laboratory species, mostly invertebrates. Little information is available as to the genetic mechanisms responsible for natural lifespan variation and the evolution of lifespan, especially in vertebrates. Here, we investigated the pattern of positive selection in annual (i.e., short‐lived) and nonannual (i.e., longer‐lived) African killifishes to identify a genomic substrate for evolution of annual life history (and reduced lifespan). We identified genes under positive selection in all steps of mitochondrial biogenesis: mitochondrial (mt) DNA replication, transcription from mt promoters, processing and stabilization of mt RNAs, mt translation, assembly of respiratory chain complexes, and electron transport chain. Signs of paralleled evolution (i.e., evolution in more than one branch of Nothobranchius phylogeny) are observed in four out of five steps. Moreover, some genes under positive selection in Nothobranchius are under positive selection also in long‐lived mammals such as bats and mole‐rats. Complexes of the respiratory chain are formed in a coordinates multistep process where nuclearly and mitochondrially encoded components are assembled and inserted into the inner mitochondrial membrane. The coordination of this process is named mitonuclear balance, and experimental manipulations of mitonuclear balance can increase longevity of laboratory species. Our data strongly indicate that these genes are also casually linked to evolution lifespan in vertebrates.
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Affiliation(s)
- Arne Sahm
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Martin Bens
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Matthias Platzer
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Alessandro Cellerino
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
- Bio@SNS; Scuola Normale Superiore; Pisa 56124 Italy
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25
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Tollis M, Schiffman JD, Boddy AM. Evolution of cancer suppression as revealed by mammalian comparative genomics. Curr Opin Genet Dev 2017; 42:40-47. [DOI: 10.1016/j.gde.2016.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 02/05/2023]
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26
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Patel SA, Velingkaar N, Makwana K, Chaudhari A, Kondratov R. Calorie restriction regulates circadian clock gene expression through BMAL1 dependent and independent mechanisms. Sci Rep 2016; 6:25970. [PMID: 27170536 PMCID: PMC4864379 DOI: 10.1038/srep25970] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 04/26/2016] [Indexed: 12/19/2022] Open
Abstract
Feeding behavior, metabolism and circadian clocks are interlinked. Calorie restriction (CR) is a feeding paradigm known to extend longevity. We found that CR significantly affected the rhythms in the expression of circadian clock genes in mice on the mRNA and protein levels, suggesting that CR reprograms the clocks both transcriptionally and post-transcriptionally. The effect of CR on gene expression was distinct from the effects of time-restricted feeding or fasting. Furthermore, CR affected the circadian output through up- or down-regulation of the expression of several clock-controlled transcriptional factors and the longevity candidate genes. CR-dependent effects on some clock gene expression were impaired in the liver of mice deficient for BMAL1, suggesting importance of this transcriptional factor for the transcriptional reprogramming of the clock, however, BMAL1- independent mechanisms also exist. We propose that CR recruits biological clocks as a natural mechanism of metabolic optimization under conditions of limited energy resources.
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Affiliation(s)
- Sonal A. Patel
- Department of Biological, Geological, and Environmental Sciences and Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, OH 44115, USA
| | - Nikkhil Velingkaar
- Department of Biological, Geological, and Environmental Sciences and Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, OH 44115, USA
| | - Kuldeep Makwana
- Department of Biological, Geological, and Environmental Sciences and Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, OH 44115, USA
| | - Amol Chaudhari
- Department of Biological, Geological, and Environmental Sciences and Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, OH 44115, USA
| | - Roman Kondratov
- Department of Biological, Geological, and Environmental Sciences and Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, OH 44115, USA
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Lemaître JF, Berger V, Bonenfant C, Douhard M, Gamelon M, Plard F, Gaillard JM. Early-late life trade-offs and the evolution of ageing in the wild. Proc Biol Sci 2016; 282:20150209. [PMID: 25833848 DOI: 10.1098/rspb.2015.0209] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Empirical evidence for declines in fitness components (survival and reproductive performance) with age has recently accumulated in wild populations, highlighting that the process of senescence is nearly ubiquitous in the living world. Senescence patterns are highly variable among species and current evolutionary theories of ageing propose that such variation can be accounted for by differences in allocation to growth and reproduction during early life. Here, we compiled 26 studies of free-ranging vertebrate populations that explicitly tested for a trade-off between performance in early and late life. Our review brings overall support for the presence of early-late life trade-offs, suggesting that the limitation of available resources leads individuals to trade somatic maintenance later in life for high allocation to reproduction early in life. We discuss our results in the light of two closely related theories of ageing-the disposable soma and the antagonistic pleiotropy theories-and propose that the principle of energy allocation roots the ageing process in the evolution of life-history strategies. Finally, we outline research topics that should be investigated in future studies, including the importance of natal environmental conditions in the study of trade-offs between early- and late-life performance and the evolution of sex-differences in ageing patterns.
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Affiliation(s)
- Jean-François Lemaître
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Vérane Berger
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Christophe Bonenfant
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Mathieu Douhard
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Marlène Gamelon
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Floriane Plard
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Jean-Michel Gaillard
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
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28
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Vinogradov AE. Accelerated pathway evolution in mouse-like rodents involves cell cycle control. Mamm Genome 2015; 26:609-18. [PMID: 26424469 DOI: 10.1007/s00335-015-9605-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/23/2015] [Indexed: 10/23/2022]
Abstract
Rodents include both the cancer-susceptible short-lived mouse and the two unrelated cancer-resistant long-lived mole-rats. In this work, their genomes were analyzed with the goal to reveal pathways enriched in genes, which are more similar between the mole-rats than between the mouse and the naked mole-rat. The pathways related to cell cycle control were prominent. They include external signal transduction and all cell cycle stages. There are several stem cell pathways among them. The other enriched pathways involve ubiquitin-dependent protein degradation, immunity, mRNA splicing, and apoptosis. The ubiquitin-dependent protein degradation is a core of network of enriched pathways. However, this phenomenon is not specific for the mouse and the mole-rats. The other muroid species show features similar to the mouse, whereas the non-muroid rodents and the human show features similar to the mole-rats. The higher ratio of non-synonymous to synonymous nucleotide substitutions (dN/dS) indicates the accelerated evolution of revealed pathways in the muroid rodents (except the blind mole-rat). Paradoxically, the dN/dS averaged over the whole genome is lower in the muroids, i.e., the purifying selection is generally stronger in them. In practical sense, these data suggest caveat for using muroid rodents (mouse, rat, and hamsters) as biomedical models of human conditions involving cell cycle and show the network of pathways where muroid genes are most different (compared with non-muroid) from human genes. The guinea pig is emphasized as a more suitable rodent model for biomedical research involving cell cycle.
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29
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Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, Grishin NV, Nielsen NH, Heide-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O'Connell MJ, Bickham JW, Thomsen B, de Magalhães JP. Insights into the evolution of longevity from the bowhead whale genome. Cell Rep 2015; 10:112-22. [PMID: 25565328 PMCID: PMC4536333 DOI: 10.1016/j.celrep.2014.12.008] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 11/21/2014] [Accepted: 12/03/2014] [Indexed: 01/01/2023] Open
Abstract
The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response. Our data are made available online (http://www.bowhead-whale.org) to facilitate research in this long-lived species.
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Affiliation(s)
- Michael Keane
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jeremy Semeiks
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Yang I Li
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Thomas Craig
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Lone Bruhn Madsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Sipko van Dam
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David Brawand
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Patrícia I Marques
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Pawel Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lin Kang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Hyung-Soon Yim
- KIOST, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea
| | - Nick V Grishin
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA
| | | | | | - Elias M Oziolor
- Department of Environmental Science, Center for Reservoir and Aquatic Systems Research (CRASR) and Institute for Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - Cole W Matson
- Department of Environmental Science, Center for Reservoir and Aquatic Systems Research (CRASR) and Institute for Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gary W Stuart
- The Center for Genomic Advocacy (TCGA) and Department of Biology, Indiana State University, Terre Haute, IN 47809, USA
| | - John C Patton
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
| | - J Craig George
- North Slope Borough, Department of Wildlife Management, Barrow, AK 99723, USA
| | - Robert Suydam
- North Slope Borough, Department of Wildlife Management, Barrow, AK 99723, USA
| | - Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - John W Bickham
- Battelle Memorial Institute, Houston, TX 77079, USA; Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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Vlahopoulos SA, Cen O, Hengen N, Agan J, Moschovi M, Critselis E, Adamaki M, Bacopoulou F, Copland JA, Boldogh I, Karin M, Chrousos GP. Dynamic aberrant NF-κB spurs tumorigenesis: a new model encompassing the microenvironment. Cytokine Growth Factor Rev 2015; 26:389-403. [PMID: 26119834 PMCID: PMC4526340 DOI: 10.1016/j.cytogfr.2015.06.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 06/15/2015] [Indexed: 12/15/2022]
Abstract
Recently it was discovered that a transient activation of transcription factor NF-κB can give cells properties essential for invasiveness and cancer initiating potential. In contrast, most oncogenes to date were characterized on the basis of mutations or by their constitutive overexpression. Study of NF-κB actually leads to a far more dynamic perspective on cancer: tumors caused by diverse oncogenes apparently evolve into cancer after loss of feedback regulation for NF-κB. This event alters the cellular phenotype and the expression of hormonal mediators, modifying signals between diverse cell types in a tissue. The result is a disruption of stem cell hierarchy in the tissue, and pervasive changes in the microenvironment and immune response to the malignant cells.
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Affiliation(s)
- Spiros A Vlahopoulos
- First Department of Pediatrics, University of Athens, Horemeio Research Laboratory, Athens, Greece.
| | - Osman Cen
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, United States
| | - Nina Hengen
- Bernard J. Dunn School of Pharmacy, Shenandoah University, United States
| | - James Agan
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, United States
| | - Maria Moschovi
- First Department of Pediatrics, University of Athens, Horemeio Research Laboratory, Athens, Greece
| | - Elena Critselis
- First Department of Pediatrics, University of Athens, Horemeio Research Laboratory, Athens, Greece
| | - Maria Adamaki
- First Department of Pediatrics, University of Athens, Horemeio Research Laboratory, Athens, Greece
| | - Flora Bacopoulou
- First Department of Pediatrics, University of Athens, Horemeio Research Laboratory, Athens, Greece
| | - John A Copland
- Mayo Clinic Comprehensive Cancer Center, Department of Cancer Biology, United States
| | - Istvan Boldogh
- Department of Microbiology and Immunology, School of Medicine, University of Texas Medical Branch at Galveston, United States
| | - Michael Karin
- Department of Pharmacology, University of California, San Diego, United States
| | - George P Chrousos
- First Department of Pediatrics, University of Athens, Horemeio Research Laboratory, Athens, Greece
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31
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Abstract
The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile- and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub- or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades.
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32
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MacRae SL, Zhang Q, Lemetre C, Seim I, Calder RB, Hoeijmakers J, Suh Y, Gladyshev VN, Seluanov A, Gorbunova V, Vijg J, Zhang ZD. Comparative analysis of genome maintenance genes in naked mole rat, mouse, and human. Aging Cell 2015; 14:288-91. [PMID: 25645816 PMCID: PMC4364841 DOI: 10.1111/acel.12314] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2014] [Indexed: 12/21/2022] Open
Abstract
Genome maintenance (GM) is an essential defense system against aging and cancer, as both are characterized by increased genome instability. Here, we compared the copy number variation and mutation rate of 518 GM-associated genes in the naked mole rat (NMR), mouse, and human genomes. GM genes appeared to be strongly conserved, with copy number variation in only four genes. Interestingly, we found NMR to have a higher copy number of CEBPG, a regulator of DNA repair, and TINF2, a protector of telomere integrity. NMR, as well as human, was also found to have a lower rate of germline nucleotide substitution than the mouse. Together, the data suggest that the long-lived NMR, as well as human, has more robust GM than mouse and identifies new targets for the analysis of the exceptional longevity of the NMR.
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Affiliation(s)
- Sheila L. MacRae
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461USA
| | - Quanwei Zhang
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461USA
| | - Christophe Lemetre
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461USA
| | - Inge Seim
- Division of Genetics Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA 02115USA
| | - Robert B. Calder
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461USA
| | - Jan Hoeijmakers
- Department of Genetics Erasmus University Medical Center Rotterdam The Netherlands
| | - Yousin Suh
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461USA
| | - Vadim N. Gladyshev
- Division of Genetics Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA 02115USA
| | - Andrei Seluanov
- Department of Biology University of Rochester Rochester NY 14627USA
| | - Vera Gorbunova
- Department of Biology University of Rochester Rochester NY 14627USA
| | - Jan Vijg
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461USA
| | - Zhengdong D. Zhang
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461USA
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33
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Neill D. Evolution of lifespan. J Theor Biol 2014; 358:232-45. [PMID: 24992233 DOI: 10.1016/j.jtbi.2014.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 11/26/2022]
Abstract
Present-day evolutionary theory, modern synthesis and evo-devo, appear to explain evolution. There remain however several points of contention. These include: biological time, direction, macroevolution verses microevolution, ageing and the extent of internal as opposed to external mediation. A new theoretical model for the control of biological time in vertebrates/bilaterians is introduced. Rather than biological time being controlled solely by a molecular cascade domino effect, it is suggested there is also an intracellular oscillatory clock. This clock (life's timekeeper) is synchronised across all cells in an organism and runs at a constant frequency throughout life. Slower frequencies extend lifespan, increase body/brain size and advance behaviour. They also create a time void which could aid additional evolutionary change. Faster frequencies shorten lifespan, reduce body/brain size and diminish behaviour. They are therefore less likely to mediate evolution in vertebrates/mammals. It is concluded that in vertebrates, especially mammals, there is a direction in evolution towards longer lifespan/advanced behaviour. Lifespan extension could equate with macroevolution and subsequent modifications with microevolution. As life's timekeeper controls the rate of ageing it constitutes a new genetic theory of ageing. Finally, as lifespan extension is internally mediated, this suggests a major role for internal mediation in evolution.
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Affiliation(s)
- David Neill
- University of Newcastle, Wear Base Unit, Monkwearmouth Hospital, Newcastle Road, Sunderland SR5 1NB, UK.
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34
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Comparative genetics of longevity and cancer: insights from long-lived rodents. Nat Rev Genet 2014; 15:531-40. [PMID: 24981598 DOI: 10.1038/nrg3728] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mammals have evolved a remarkable diversity of ageing rates. Within the single order of Rodentia, maximum lifespans range from 4 years in mice to 32 years in naked mole rats. Cancer rates also differ substantially between cancer-prone mice and almost cancer-proof naked mole rats and blind mole rats. Recent progress in rodent comparative biology, together with the emergence of whole-genome sequence information, has opened opportunities for the discovery of genetic factors that control longevity and cancer susceptibility.
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35
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Distinctive topology of age-associated epigenetic drift in the human interactome. Proc Natl Acad Sci U S A 2013; 110:14138-43. [PMID: 23940324 DOI: 10.1073/pnas.1307242110] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recently, it has been demonstrated that DNA methylation, a covalent modification of DNA that can regulate gene expression, is modified as a function of age. However, the biological and clinical significance of this age-associated epigenetic drift is unclear. To shed light on the potential biological significance, we here adopt a systems approach and study the genes undergoing age-associated changes in DNA methylation in the context of a protein interaction network, focusing on their topological properties. In contrast to what has been observed for other age-related gene classes, including longevity- and disease-associated genes, as well as genes undergoing age-associated changes in gene expression, we here demonstrate that age-associated epigenetic drift occurs preferentially in genes that occupy peripheral network positions of exceptionally low connectivity. In addition, we show that these genes synergize topologically with disease and longevity genes, forming unexpectedly large network communities. Thus, these results point toward a potentially distinct mechanistic and biological role of DNA methylation in dictating the complex aging and disease phenotypes.
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36
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Endless paces of degeneration--applying comparative genomics to study evolution's moulding of longevity. EMBO Rep 2013; 14:661-2. [PMID: 23846314 DOI: 10.1038/embor.2013.96] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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37
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Somel M, Wilson Sayres MA, Jordan G, Huerta-Sanchez E, Fumagalli M, Ferrer-Admetlla A, Nielsen R. A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes. Mol Biol Evol 2013; 30:1808-15. [PMID: 23699470 PMCID: PMC3708504 DOI: 10.1093/molbev/mst098] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Environmental or genomic changes during evolution can relax negative selection pressure on specific loci, permitting high frequency polymorphisms at previously conserved sites. Here, we jointly analyze population genomic and comparative genomic data to search for functional processes showing relaxed negative selection specifically in the human lineage, whereas remaining evolutionarily conserved in other mammals. Consistent with previous studies, we find that olfactory receptor genes display such a signature of relaxation in humans. Intriguingly, proteasome genes also show a prominent signal of human-specific relaxation: multiple proteasome subunits, including four members of the catalytic core particle, contain high frequency nonsynonymous polymorphisms at sites conserved across mammals. Chimpanzee proteasome genes do not display a similar trend. Human proteasome genes also bear no evidence of recent positive or balancing selection. These results suggest human-specific relaxation of negative selection in proteasome subunits; the exact biological causes, however, remain unknown.
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Affiliation(s)
- Mehmet Somel
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
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38
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Alcedo J, Flatt T, Pasyukova EG. Neuronal inputs and outputs of aging and longevity. Front Genet 2013; 4:71. [PMID: 23653632 PMCID: PMC3644678 DOI: 10.3389/fgene.2013.00071] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/13/2013] [Indexed: 12/14/2022] Open
Abstract
An animal’s survival strongly depends on its ability to maintain homeostasis in response to the changing quality of its external and internal environment. This is achieved through intracellular and intercellular communication within and among different tissues. One of the organ systems that plays a major role in this communication and the maintenance of homeostasis is the nervous system. Here we highlight different aspects of the neuronal inputs and outputs of pathways that affect aging and longevity. Accordingly, we discuss how sensory inputs influence homeostasis and lifespan through the modulation of different types of neuronal signals, which reflects the complexity of the environmental cues that affect physiology. We also describe feedback, compensatory, and feed-forward mechanisms in these longevity-modulating pathways that are necessary for homeostasis. Finally, we consider the temporal requirements for these neuronal processes and the potential role of natural genetic variation in shaping the neurobiology of aging.
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Affiliation(s)
- Joy Alcedo
- Friedrich Miescher Institute for Biomedical Research Basel, Switzerland ; Department of Biological Sciences, Wayne State University Detroit, MI, USA
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39
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Abstract
The ageing of populations worldwide is leading to an unprecedented increase in cancer cases and fatalities. Understanding the links between cancer and ageing is therefore more important than ever. How the interplay of ageing-associated changes affects cancer initiation and progression is complex, however, and some ageing processes probably foster cancer development whereas others hinder it, possibly in a tissue-specific manner. In the emerging age of cancer, how can our growing understanding of the biology of ageing inform cancer biology?
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40
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Parallel evolution of senescence in annual fishes in response to extrinsic mortality. BMC Evol Biol 2013; 13:77. [PMID: 23551990 PMCID: PMC3623659 DOI: 10.1186/1471-2148-13-77] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 03/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early evolutionary theories of aging predict that populations which experience low extrinsic mortality evolve a retarded onset of senescence. Experimental support for this theory in vertebrates is scarce, in part for the difficulty of quantifying extrinsic mortality and its condition- and density-dependent components that -when considered- can lead to predictions markedly different to those of the "classical" theories. Here, we study annual fish of the genus Nothobranchius whose maximum lifespan is dictated by the duration of the water bodies they inhabit. Different populations of annual fish do not experience different strengths of extrinsic mortality throughout their life span, but are subject to differential timing (and predictability) of a sudden habitat cessation. In this respect, our study allows testing how aging evolves in natural environments when populations vary in the prospect of survival, but condition-dependent survival has a limited effect. We use 10 Nothobranchius populations from seasonal pools that differ in their duration to test how this parameter affects longevity and aging in two independent clades of these annual fishes. RESULTS We found that replicated populations from a dry region showed markedly shorter captive lifespan than populations from a humid region. Shorter lifespan correlated with accelerated accumulation of lipofuscin (an established age marker) in both clades. Analysis of wild individuals confirmed that fish from drier habitats accumulate lipofuscin faster also under natural conditions. This indicates faster physiological deterioration in shorter-lived populations. CONCLUSIONS Our data provide a strong quantitative example of how extrinsic mortality can shape evolution of senescence in a vertebrate clade. Nothobranchius is emerging as a genomic model species. The characterization of pairs of closely related species with different longevities should provide a powerful paradigm for the identification of genetic variations responsible for evolution of senescence in natural populations.
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41
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Kriete A. Robustness and aging--a systems-level perspective. Biosystems 2013; 112:37-48. [PMID: 23562399 DOI: 10.1016/j.biosystems.2013.03.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/11/2013] [Accepted: 03/15/2013] [Indexed: 12/24/2022]
Abstract
The theory of robustness describes a system level property of evolutionary systems, which predicts tradeoffs of great interest for the systems biology of aging, such as accumulation of non-heritable damage, occurrence of fragilities and limitations in performance, optimized allocation of restricted resources and confined redundancies. According to the robustness paradigm cells and organisms evolved into a state of highly optimized tolerance (HOT), which provides robustness to common perturbations, but causes tradeoffs generally characterized as "robust yet fragile". This raises the question whether the ultimate cause of aging is more than a lack of adaptation, but an inherent fragility of complex evolutionary systems. Since robustness connects to evolutionary designs, consideration of this theory provides a deeper connection between evolutionary aspects of aging, mathematical models and experimental data. In this review several mechanisms influential for aging are re-evaluated in support of robustness tradeoffs. This includes asymmetric cell division improving performance and specialization with limited capacities to prevent and repair age-related damage, as well as feedback control mechanisms optimized to respond to acute stressors, but unable to halt nor revert aging. Improvement in robustness by increasing efficiencies through cellular redundancies in larger organisms alleviates some of the damaging effects of cellular specialization, which can be expressed in allometric relationships. The introduction of the robustness paradigm offers unique insights for aging research and provides novel opportunities for systems biology endeavors.
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Affiliation(s)
- Andres Kriete
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Bossone Research Center, 3141 Chestnut St., Philadelphia, PA 19104, USA.
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42
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Neill D. Life's timekeeper. Ageing Res Rev 2013; 12:567-78. [PMID: 23354279 DOI: 10.1016/j.arr.2013.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/08/2013] [Accepted: 01/10/2013] [Indexed: 12/18/2022]
Abstract
Life's timekeeper is a 'free-running' intracellular oscillator synchronised across all cells. It runs throughout life splitting lifespan into equal length phases. During the maturational period it controls the overall rate of progression whereas in the post-maturational period it controls the overall rate of ageing. This includes the rate of senescence and hence time to death. As such life's timekeeper equates maturational and post-maturational time, hence explains the tight correlation between these time periods that has existed throughout mammalian evolution. Life's timekeeper is proposed to have played an important role in vertebrate evolution. A slower oscillatory frequency results in proportional life phase prolongation. This leads to increased body and brain size, together with extended lifespan. Higher brain centres, neocortex in mammals, are disproportionately enlarged. Hence behavioural capacity is increased. The extended post-maturational period ensures that there is enough time in order that the behavioural advantages can be fully manifest in the environment. A faster oscillatory frequency would result in proportional life phase reduction. This process however would lead to reduced behavioural capacity, and is hence unlikely to be positively selected. Therefore throughout evolution life's timekeeper has operated to extend lifespan. It has hence functioned to promote longevity as opposed to ageing.
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Affiliation(s)
- David Neill
- Department of Psychiatry, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
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Fuellen G, Dengjel J, Hoeflich A, Hoeijemakers J, Kestler HA, Kowald A, Priebe S, Rebholz-Schuhmann D, Schmeck B, Schmitz U, Stolzing A, Sühnel J, Wuttke D, Vera J. Systems biology and bioinformatics in aging research: a workshop report. Rejuvenation Res 2012; 15:631-41. [PMID: 22950424 DOI: 10.1089/rej.2012.1360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In an "aging society," health span extension is most important. As in 2010, talks in this series of meetings in Rostock-Warnemünde demonstrated that aging is an apparently very complex process, where computational work is most useful for gaining insights and to find interventions that counter aging and prevent or counteract aging-related diseases. The specific topics of this year's meeting entitled, "RoSyBA: Rostock Symposium on Systems Biology and Bioinformatics in Ageing Research," were primarily related to "Cancer and Aging" and also had a focus on work funded by the German Federal Ministry of Education and Research (BMBF). The next meeting in the series, scheduled for September 20-21, 2013, will focus on the use of ontologies for computational research into aging, stem cells, and cancer. Promoting knowledge formalization is also at the core of the set of proposed action items concluding this report.
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Affiliation(s)
- Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Department of Medicine, Rostock University, Germany.
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Semeiks J, Grishin NV. A method to find longevity-selected positions in the mammalian proteome. PLoS One 2012; 7:e38595. [PMID: 22701678 PMCID: PMC3372525 DOI: 10.1371/journal.pone.0038595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/10/2012] [Indexed: 11/19/2022] Open
Abstract
Evolutionary theory suggests that the force of natural selection decreases with age. To explore the extent to which this prediction directly affects protein structure and function, we used multiple regression to find longevity-selected positions, defined as the columns of a sequence alignment conserved in long-lived but not short-lived mammal species. We analyzed 7,590 orthologous protein families in 33 mammalian species, accounting for body mass, phylogeny, and species-specific mutation rate. Overall, we found that the number of longevity-selected positions in the mammalian proteome is much higher than would be expected by chance. Further, these positions are enriched in domains of several proteins that interact with one another in inflammation and other aging-related processes, as well as in organismal development. We present as an example the kinase domain of anti-müllerian hormone type-2 receptor (AMHR2). AMHR2 inhibits ovarian follicle recruitment and growth, and a homology model of the kinase domain shows that its longevity-selected positions cluster near a SNP associated with delayed human menopause. Distinct from its canonical role in development, this region of AMHR2 may function to regulate the protein's activity in a lifespan-specific manner.
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Affiliation(s)
- Jeremy Semeiks
- Molecular Biophysics Program, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.
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