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Yasuda K, Miyazawa M, Ishii T, Ishii N. The role of nutrition and oxidative stress as aging factors in Caenorhabditis elegans. J Clin Biochem Nutr 2023; 73:173-177. [PMID: 37970544 PMCID: PMC10636583 DOI: 10.3164/jcbn.23-44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 11/17/2023] Open
Abstract
The molecular mechanism of aging, which has been a "black box" for many years, has been elucidated in recent years, and the nematode C. elegans, which is a model animal for aging research, has played a major role in its elucidation. From the analysis of C. elegans longevity-related mutant genes, many signal transduction systems, with the insulin/insulin-like growth factor signal transduction system at the core, have emerged. It has become clear that this signal transduction system is greatly affected by external nutrients and is involved in the downstream regulation of oxidative stress, which is considered to be one of the main causes of aging.
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Affiliation(s)
- Kayo Yasuda
- Department of Health Management, Undergraduate School of Health Studies, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Masaki Miyazawa
- Department of Health Management, Undergraduate School of Health Studies, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Takamasa Ishii
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Naoaki Ishii
- Office of Professor Emeritus, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
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2
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Li X, Wang P, Pan Q, Liu G, Liu W, Omotoso O, Du J, Li Z, Yu Y, Huang Y, Zhu P, Li M, Zhou X. Chromosome-level Asian elephant genome assembly and comparative genomics of long-lived mammals reveal the common substitutions for cancer resistance. Aging Cell 2023; 22:e13917. [PMID: 37395176 PMCID: PMC10497851 DOI: 10.1111/acel.13917] [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: 12/09/2022] [Revised: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 07/04/2023] Open
Abstract
The naked mole rat (Heterocephalus glaber), bats (e.g., genus Myotis), and elephants (family Elephantidae) are known as long-lived mammals and are assumed to be excellent cancer antagonists. However, whether there are common genetic changes underpinning cancer resistance in these long-lived species is yet to be fully established. Here, we newly generated a high-quality chromosome-level Asian elephant (Elephas maximus) genome and identified that the expanded gene families in elephants are involved in Ras-associated and base excision repair pathways. Moreover, we performed comparative genomic analyses of 12 mammals and examined genes with signatures of positive selection in elephants, naked mole rat, and greater horseshoe bat. Residues at positively selected sites of CDR2L and ALDH6A1 in these long-lived mammals enhanced the inhibition of tumor cell migration compared to those in short-lived relatives. Overall, our study provides a new genome resource and a preliminary survey of common genetic changes in long-lived mammals.
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Affiliation(s)
- Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pengcheng Wang
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Qi Pan
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Olatunde Omotoso
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Yu
- Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Yun Huang
- Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
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3
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Igoshin AV, Yudin NS, Romashov GA, Larkin DM. A Multibreed Genome-Wide Association Study for Cattle Leukocyte Telomere Length. Genes (Basel) 2023; 14:1596. [PMID: 37628647 PMCID: PMC10454124 DOI: 10.3390/genes14081596] [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: 06/25/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Telomeres are terminal DNA regions of chromosomes that prevent chromosomal fusion and degradation during cell division. In cattle, leukocyte telomere length (LTL) is associated with longevity, productive lifespan, and disease susceptibility. However, the genetic basis of LTL in this species is less studied than in humans. In this study, we utilized the whole-genome resequencing data of 239 animals from 17 cattle breeds for computational leukocyte telomere length estimation and subsequent genome-wide association study of LTL. As a result, we identified 42 significant SNPs, of which eight were found in seven genes (EXOC6B, PTPRD, RPS6KC1, NSL1, AGBL1, ENSBTAG00000052188, and GPC1) when using covariates for two major breed groups (Turano-Mongolian and European). Association analysis with covariates for breed effect detected 63 SNPs, including 13 in five genes (EXOC6B, PTPRD, RPS6KC1, ENSBTAG00000040318, and NELL1). The PTPRD gene, demonstrating the top signal in analysis with breed effect, was previously associated with leukocyte telomere length in cattle and likely is involved in the mechanism of alternative lengthening of telomeres. The single nucleotide variants found could be tested for marker-assisted selection to improve telomere-length-associated traits.
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Affiliation(s)
- Alexander V. Igoshin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Nikolay S. Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Grigorii A. Romashov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Denis M. Larkin
- Royal Veterinary College, University of London, London NW1 0TU, UK
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4
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Rouan A, Pousse M, Djerbi N, Porro B, Bourdin G, Carradec Q, Hume BC, Poulain J, Lê-Hoang J, Armstrong E, Agostini S, Salazar G, Ruscheweyh HJ, Aury JM, Paz-García DA, McMinds R, Giraud-Panis MJ, Deshuraud R, Ottaviani A, Morini LD, Leone C, Wurzer L, Tran J, Zoccola D, Pey A, Moulin C, Boissin E, Iwankow G, Romac S, de Vargas C, Banaigs B, Boss E, Bowler C, Douville E, Flores M, Reynaud S, Thomas OP, Troublé R, Thurber RV, Planes S, Allemand D, Pesant S, Galand PE, Wincker P, Sunagawa S, Röttinger E, Furla P, Voolstra CR, Forcioli D, Lombard F, Gilson E. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals. Nat Commun 2023; 14:3038. [PMID: 37263999 DOI: 10.1038/s41467-023-38499-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.
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Affiliation(s)
- Alice Rouan
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France.
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France.
| | - Melanie Pousse
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Nadir Djerbi
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Barbara Porro
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | | | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Benjamin Cc Hume
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, La Paz, Baja California Sur, 23096, La Paz, México
| | - Ryan McMinds
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- University of South Florida Center for Global Health and Infectious Diseases Research, Tampa, FL, USA
- Maison de la Modélisation, de la Simulation et des Interactions (MSI),, Université Côte d'Azur, Nice, France
| | - Marie-Josèphe Giraud-Panis
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Romane Deshuraud
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Alexandre Ottaviani
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Lycia Die Morini
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Camille Leone
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Lia Wurzer
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Jessica Tran
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Alexis Pey
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Tara Ocean Foundation, 8 rue de Prague, 75012, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Guillaume Iwankow
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Bernard Banaigs
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth, and Planetary Sciences, 76100, Rehovot, Israel
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, H91TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Tara Ocean Foundation, 8 rue de Prague, 75012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Stephane Pesant
- European Bioinformatics Institute, Wellcome Genome Campus, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge CB10 1SD, UK, UK
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Eric Röttinger
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Paola Furla
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | | | - Didier Forcioli
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
- Institut Universitaire de France, Ministère chargé de l'enseignement supérieur, Paris, France
| | - Eric Gilson
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France.
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France.
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France.
- Department of Medical Genetics, CHU, Nice, France.
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5
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Alternative telomere maintenance mechanism in Alligator sinensis provides insights into aging evolution. iScience 2022; 26:105850. [PMID: 36636341 PMCID: PMC9829719 DOI: 10.1016/j.isci.2022.105850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 11/27/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022] Open
Abstract
Lifespan is a life-history trait that undergoes natural selection. Telomeres are hallmarks of aging, and shortening rate predicts species lifespan, making telomere maintenance mechanisms throughout different lifespans a worthy topic for study. Alligators are suitable for the exploration of anti-aging molecular mechanisms, because they exhibit low or even negligible mortality in adults and no significant telomere shortening. Telomerase reverse transcriptase (TERT) expression is absent in the adult Alligator sinensis, as in humans. Selection analyses on telomere maintenance genes indicated that ATM, FANCE, SAMHD1, HMBOX1, NAT10, and MAP3K4 experienced positive selection on A. sinensis. Repressed pleiotropic ATM kinase in A. sinensis suggests their fitness optimum shift. In ATM downstream, Alternative Lengthening of Telomeres (ALT)-related genes were clustered in a higher expression pattern in A. sinensis, which covers 10-15% of human cancers showing no telomerase activities. In summary, we demonstrated how telomere shortening, telomerase activities, and ALT contributed to anti-aging strategies.
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6
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Power ML, Foley NM, Jones G, Teeling EC. Taking flight: An ecological, evolutionary and genomic perspective on bat telomeres. Mol Ecol 2022; 31:6053-6068. [PMID: 34387012 DOI: 10.1111/mec.16117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 01/31/2023]
Abstract
Over 20% of all living mammals are bats (order Chiroptera). Bats possess extraordinary adaptations including powered flight, laryngeal echolocation and a unique immune system that enables them to tolerate a diversity of viral infections without presenting clinical disease symptoms. They occupy multiple trophic niches and environments globally. Significant physiological and ecological diversity occurs across the order. Bats also exhibit extreme longevity given their body size with many species showing few signs of ageing. The molecular basis of this extended longevity has recently attracted attention. Telomere maintenance potentially underpins bats' extended healthspan, although functional studies are still required to validate the causative mechanisms. In this review, we detail the current knowledge on bat telomeres, telomerase expression, and how these relate to ecology, longevity and life-history strategies. Patterns of telomere shortening and telomerase expression vary across species, and comparative genomic analyses suggest that alternative telomere maintenance mechanisms evolved in the longest-lived bats. We discuss the unique challenges faced when working with populations of wild bats and highlight ways to advance the field including expanding long-term monitoring across species that display contrasting life-histories and occupy different environmental niches. We further review how new high quality, chromosome-level genome assemblies can enable us to uncover the molecular mechanisms governing telomere dynamics and how phylogenomic analyses can reveal the adaptive significance of telomere maintenance and variation in bats.
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Affiliation(s)
- Megan L Power
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Ireland
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Gareth Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Emma C Teeling
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Ireland
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7
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Borges G, Criqui M, Harrington L. Tieing together loose ends: telomere instability in cancer and aging. Mol Oncol 2022; 16:3380-3396. [PMID: 35920280 PMCID: PMC9490142 DOI: 10.1002/1878-0261.13299] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 11/29/2022] Open
Abstract
Telomere maintenance is essential for maintaining genome integrity in both normal and cancer cells. Without functional telomeres, chromosomes lose their protective structure and undergo fusion and breakage events that drive further genome instability, including cell arrest or death. One means by which this loss can be overcome in stem cells and cancer cells is via re‐addition of G‐rich telomeric repeats by the telomerase reverse transcriptase (TERT). During aging of somatic tissues, however, insufficient telomerase expression leads to a proliferative arrest called replicative senescence, which is triggered when telomeres reach a critically short threshold that induces a DNA damage response. Cancer cells express telomerase but do not entirely escape telomere instability as they often possess short telomeres; hence there is often selection for genetic alterations in the TERT promoter that result in increased telomerase expression. In this review, we discuss our current understanding of the consequences of telomere instability in cancer and aging, and outline the opportunities and challenges that lie ahead in exploiting the reliance of cells on telomere maintenance for preserving genome stability.
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Affiliation(s)
- Gustavo Borges
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4
| | - Mélanie Criqui
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4
| | - Lea Harrington
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4.,Departments of Medicine and Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4
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8
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Chattopadhyay B, Garg KM, Ray R, Mendenhall IH, Rheindt FE. Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats. Genome Biol Evol 2021; 12:259-272. [PMID: 32068833 PMCID: PMC7151552 DOI: 10.1093/gbe/evaa030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 12/01/2022] Open
Abstract
Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as compared with other bats (e.g., loss of echolocation, large size, and frugivory), fruit bats have undergone surprisingly limited change in their genic composition, perhaps apart from a potentially novel gene family expansion relating to telomere protection and longevity. In sharp contrast, within fruit bats, the new Cynopterus genome bears the signal of unusual gene loss and gene family contraction, despite its similar morphology and lifestyle to two other major fruit bat lineages. Most missing genes are regulatory, immune-related, and olfactory in nature, illustrating the diversity of genomic strategies employed by bats to contend with responses to viral infection and olfactory requirements. Our results underscore that significant fluctuations in gene family composition are not always associated with obvious examples of novel physiological and phenotypic adaptations but may often relate to less-obvious shifts in immune strategies.
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Affiliation(s)
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rajasri Ray
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India.,Centre for Studies in Ethnobiology, Biodiversity and Sustainability (CEiBa), Mokdumpur, Malda, West Bengal, India
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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9
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Holtze S, Gorshkova E, Braude S, Cellerino A, Dammann P, Hildebrandt TB, Hoeflich A, Hoffmann S, Koch P, Terzibasi Tozzini E, Skulachev M, Skulachev VP, Sahm A. Alternative Animal Models of Aging Research. Front Mol Biosci 2021; 8:660959. [PMID: 34079817 PMCID: PMC8166319 DOI: 10.3389/fmolb.2021.660959] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Most research on mechanisms of aging is being conducted in a very limited number of classical model species, i.e., laboratory mouse (Mus musculus), rat (Rattus norvegicus domestica), the common fruit fly (Drosophila melanogaster) and roundworm (Caenorhabditis elegans). The obvious advantages of using these models are access to resources such as strains with known genetic properties, high-quality genomic and transcriptomic sequencing data, versatile experimental manipulation capabilities including well-established genome editing tools, as well as extensive experience in husbandry. However, this approach may introduce interpretation biases due to the specific characteristics of the investigated species, which may lead to inappropriate, or even false, generalization. For example, it is still unclear to what extent knowledge of aging mechanisms gained in short-lived model organisms is transferable to long-lived species such as humans. In addition, other specific adaptations favoring a long and healthy life from the immense evolutionary toolbox may be entirely missed. In this review, we summarize the specific characteristics of emerging animal models that have attracted the attention of gerontologists, we provide an overview of the available data and resources related to these models, and we summarize important insights gained from them in recent years. The models presented include short-lived ones such as killifish (Nothobranchius furzeri), long-lived ones such as primates (Callithrix jacchus, Cebus imitator, Macaca mulatta), bathyergid mole-rats (Heterocephalus glaber, Fukomys spp.), bats (Myotis spp.), birds, olms (Proteus anguinus), turtles, greenland sharks, bivalves (Arctica islandica), and potentially non-aging ones such as Hydra and Planaria.
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Affiliation(s)
- Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ekaterina Gorshkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Stan Braude
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Alessandro Cellerino
- Biology Laboratory, Scuola Normale Superiore, Pisa, Italy
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Central Animal Laboratory, University Hospital Essen, Essen, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Faculty of Veterinary Medicine, Free University of Berlin, Berlin, Germany
| | - Andreas Hoeflich
- Division Signal Transduction, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Eva Terzibasi Tozzini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maxim Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir P. Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
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10
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Mikuła-Pietrasik J, Pakuła M, Markowska M, Uruski P, Szczepaniak-Chicheł L, Tykarski A, Książek K. Nontraditional systems in aging research: an update. Cell Mol Life Sci 2020; 78:1275-1304. [PMID: 33034696 PMCID: PMC7904725 DOI: 10.1007/s00018-020-03658-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/15/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022]
Abstract
Research on the evolutionary and mechanistic aspects of aging and longevity has a reductionist nature, as the majority of knowledge originates from experiments on a relatively small number of systems and species. Good examples are the studies on the cellular, molecular, and genetic attributes of aging (senescence) that are primarily based on a narrow group of somatic cells, especially fibroblasts. Research on aging and/or longevity at the organismal level is dominated, in turn, by experiments on Drosophila melanogaster, worms (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), and higher organisms such as mice and humans. Other systems of aging, though numerous, constitute the minority. In this review, we collected and discussed a plethora of up-to-date findings about studies of aging, longevity, and sometimes even immortality in several valuable but less frequently used systems, including bacteria (Caulobacter crescentus, Escherichia coli), invertebrates (Turritopsis dohrnii, Hydra sp., Arctica islandica), fishes (Nothobranchius sp., Greenland shark), reptiles (giant tortoise), mammals (blind mole rats, naked mole rats, bats, elephants, killer whale), and even 3D organoids, to prove that they offer biogerontologists as much as the more conventional tools. At the same time, the diversified knowledge gained owing to research on those species may help to reconsider aging from a broader perspective, which should translate into a better understanding of this tremendously complex and clearly system-specific phenomenon.
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Affiliation(s)
- Justyna Mikuła-Pietrasik
- Department of Pathophysiology of Ageing and Civilization Diseases, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | - Martyna Pakuła
- Department of Hypertensiology, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | - Małgorzata Markowska
- Department of Hypertensiology, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | - Paweł Uruski
- Department of Hypertensiology, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | | | - Andrzej Tykarski
- Department of Hypertensiology, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
| | - Krzysztof Książek
- Department of Pathophysiology of Ageing and Civilization Diseases, Poznań University of Medical Sciences, Długa 1/2 Str., 61-848 Poznań, Poland
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11
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Ineson KM, O’Shea TJ, Kilpatrick CW, Parise KL, Foster JT. Ambiguities in using telomere length for age determination in two North American bat species. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AbstractThe age of an animal, determined by time (chronological age) as well as genetic and environmental factors (biological age), influences the likelihood of mortality and reproduction and thus the animal’s contribution to population growth. For many long-lived species, such as bats, a lack of external and morphological indicators has made determining age a challenge, leading researchers to examine genetic markers of age for application to demographic studies. One widely studied biomarker of age is telomere length, which has been related both to chronological and biological age across taxa, but only recently has begun to be studied in bats. We assessed telomere length from the DNA of known-age and minimum known-age individuals of two bat species using a quantitative PCR assay. We determined that telomere length was quadratically related to chronological age in big brown bats (Eptesicus fuscus), although it had little predictive power for accurate age determination of unknown-age individuals. The relationship was different in little brown bats (Myotis lucifugus), where telomere length instead was correlated with biological age, apparently due to infection and wing damage associated with white-nose syndrome. Furthermore, we showed that wing biopsies currently are a better tissue source for studying telomere length in bats than guano and buccal swabs; the results from the latter group were more variable and potentially influenced by storage time. Refinement of collection and assessment methods for different non-lethally collected tissues will be important for longitudinal sampling to better understand telomere dynamics in these long-lived species. Although further work is needed to develop a biomarker capable of determining chronological age in bats, our results suggest that biological age, as reflected in telomere length, may be influenced by extrinsic stressors such as disease.
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Affiliation(s)
- Katherine M Ineson
- Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Thomas J O’Shea
- United States Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | | | - Katy L Parise
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jeffrey T Foster
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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12
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Shepard A, Kissil JL. The use of non-traditional models in the study of cancer resistance-the case of the naked mole rat. Oncogene 2020; 39:5083-5097. [PMID: 32535616 DOI: 10.1038/s41388-020-1355-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Non-traditional model organisms are typically defined as any model the deviates from the typical laboratory animals, such as mouse, rat, and worm. These models are becoming increasingly important in human disease research, such as cancer, as they often display unusual biological features. Naked mole rats (NMRs) are currently one of the most popular non-traditional model, particularly in the longevity and cancer research fields. NMRs display an exceptionally long lifespan (~30 years), yet have been observed to display a low incidence of cancer, making them excellent candidates for understanding endogenous cancer resistance mechanisms. Over the past decade, many potential resistance mechanisms have been characterized. These include unique biological mechanisms involved in genome stability, protein stability, oxidative metabolism, and other cellular mechanisms such as cell cycle regulation and senescence. This review aims to summarize the many identified cancer resistance mechanisms to understand some of the main hypotheses that have thus far been generated. Many of these proposed mechanisms remain to be fully characterized or confirmed in vivo, giving the field a direction to grow and further understand the complex biology displayed by the NMR.
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Affiliation(s)
- Alyssa Shepard
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Joseph L Kissil
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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13
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Saint-Leandre B, Levine MT. The Telomere Paradox: Stable Genome Preservation with Rapidly Evolving Proteins. Trends Genet 2020; 36:232-242. [PMID: 32155445 DOI: 10.1016/j.tig.2020.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 01/08/2023]
Abstract
Telomeres ensure chromosome length homeostasis and protection from catastrophic end-to-end chromosome fusions. All eukaryotes require this essential, strictly conserved telomere-dependent genome preservation. However, recent evolutionary analyses of mammals, plants, and flies report pervasive rapid evolution of telomere proteins. The causes of this paradoxical observation - that unconserved machinery underlies an essential, conserved function - remain enigmatic. Indeed, these fast-evolving telomere proteins bind, extend, and protect telomeric DNA, which itself evolves slowly in most systems. We hypothesize that the universally fast-evolving subtelomere - the telomere-adjacent, repetitive sequence - is a primary driver of the 'telomere paradox'. Under this model, radical sequence changes in the subtelomere perturb subtelomere-dependent, telomere functions. Compromised telomere function then spurs adaptation of telomere proteins to maintain telomere length homeostasis and protection. We propose an experimental framework that leverages both protein divergence and subtelomeric sequence divergence to test the hypothesis that subtelomere sequence evolution shapes recurrent innovation of telomere machinery.
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Affiliation(s)
- Bastien Saint-Leandre
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Mia T Levine
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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14
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Rubanov LI, Zaraisky AG, Shilovsky GA, Seliverstov AV, Zverkov OA, Lyubetsky VA. Screening for mouse genes lost in mammals with long lifespans. BioData Min 2019; 12:20. [PMID: 31728160 PMCID: PMC6842137 DOI: 10.1186/s13040-019-0208-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/25/2019] [Indexed: 12/23/2022] Open
Abstract
Background Gerontogenes include those that modulate life expectancy in various species and may be the actual longevity genes. We believe that a long (relative to body weight) lifespan in individual rodent and primate species can be due, among other things, to the loss of particular genes that are present in short-lived species of the same orders. These genes can also explain the widely different rates of aging among diverse species as well as why similarly sized rodents or primates sometimes have anomalous life expectancies (e.g., naked mole-rats and humans). Here, we consider the gene loss in the context of the prediction of Williams’ theory that concerns the reallocation of physiological resources of an organism between active reproduction (r-strategy) and self-maintenance (K-strategy). We have identified such lost genes using an original computer-aided approach; the software considers the loss of a gene as disruptions in gene orthology, local gene synteny or both. Results A method and software identifying the genes that are absent from a predefined set of species but present in another predefined set of species are suggested. Examples of such pairs of sets include long-lived vs short-lived, homeothermic vs poikilothermic, amniotic vs anamniotic, aquatic vs terrestrial, and neotenic vs nonneotenic species, among others. Species are included in one of two sets according to the property of interest, such as longevity or homeothermy. The program is universal towards these pairs, i.e., towards the underlying property, although the sets should include species with quality genome assemblies. Here, the proposed method was applied to study the longevity of Euarchontoglires species. It largely predicted genes that are highly expressed in the testis, epididymis, uterus, mammary glands, and the vomeronasal and other reproduction-related organs. This agrees with Williams’ theory that hypothesizes a species transition from r-strategy to K-strategy. For instance, the method predicts the mouse gene Smpd5, which has an expression level 20 times greater in the testis than in organs unrelated to reproduction as experimentally demonstrated elsewhere. At the same time, its paralog Smpd3 is not predicted by the program and is widely expressed in many organs not specifically related to reproduction. Conclusions The method and program, which were applied here to screen for gene losses that can accompany increased lifespan, were also applied to study reduced regenerative capacity and development of the telencephalon, neoteny, etc. Some of these results have been carefully tested experimentally. Therefore, we assume that the method is widely applicable.
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Affiliation(s)
- Lev I Rubanov
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
| | - Andrey G Zaraisky
- 2Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS) 16/10, Miklukho-Maklaya str., Moscow, 117997 Russia
| | - Gregory A Shilovsky
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
| | - Alexandr V Seliverstov
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
| | - Oleg A Zverkov
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
| | - Vassily A Lyubetsky
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
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15
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Shilovsky GA, Putyatina TS, Ashapkin VV, Rozina AA, Lyubetsky VA, Minina EP, Bychkovskaia IB, Markov AV, Skulachev VP. Ants as Object of Gerontological Research. BIOCHEMISTRY (MOSCOW) 2019; 83:1489-1503. [PMID: 30878024 DOI: 10.1134/s0006297918120076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Social insects with identical genotype that form castes with radically different lifespans are a promising model system for studying the mechanisms underlying longevity. The main direction of progressive evolution of social insects, in particular, ants, is the development of the social way of life inextricably linked with the increase in the colony size. Only in a large colony, it is possible to have a developed polyethism, create large food reserves, and actively regulate the nest microclimate. The lifespan of ants hugely varies among genetically similar queens, workers (unproductive females), and males. The main advantage of studies on insects is the determinism of ontogenetic processes, with a single genome leading to completely different lifespans in different castes. This high degree of determinacy is precisely the reason why some researchers (incorrectly) call a colony of ants the "superorganism", emphasizing the fact that during the development, depending on the community needs, ants can switch their ontogenetic programs, which influences their social roles, ability to learn (i.e., the brain [mushroom-like body] plasticity), and, respectively, the spectrum of tasks performed by a given individual. It has been shown that in many types of food behavior, older ants surpass young ones in both performing the tasks and transferring the experience. The balance between the need to reduce the "cost" of non-breeding individuals (short lifespan and small size of workers) and the benefit from experienced long-lived workers possessing useful skills (large size and "non-aging") apparently determines the differences in the lifespan and aging rate of workers in different species of ants. A large spectrum of rigidly determined ontogenetic trajectories in different castes with identical genomes and the possibility of comparison between "evolutionarily advanced" and "primitive" subfamilies (e.g., Formicinae and Ponerinae) make ants an attractive object in the studies of both normal aging and effects of anti-aging drugs.
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Affiliation(s)
- G A Shilovsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia. .,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia.,Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - T S Putyatina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - V V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A A Rozina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - V A Lyubetsky
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - E P Minina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - I B Bychkovskaia
- Nikiforov Center of Emergency and Radiation Medicine of the Russian Ministry of Emergency Control, St. Petersburg, 194044, Russia
| | - A V Markov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - V P Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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16
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Singh PP, Demmitt BA, Nath RD, Brunet A. The Genetics of Aging: A Vertebrate Perspective. Cell 2019; 177:200-220. [PMID: 30901541 PMCID: PMC7592626 DOI: 10.1016/j.cell.2019.02.038] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
Abstract
Aging negatively impacts vitality and health. Many genetic pathways that regulate aging were discovered in invertebrates. However, the genetics of aging is more complex in vertebrates because of their specialized systems. This Review discusses advances in the genetic regulation of aging in vertebrates from work in mice, humans, and organisms with exceptional lifespans. We highlight challenges for the future, including sex-dependent differences in lifespan and the interplay between genes and environment. We also discuss how the identification of reliable biomarkers of age and development of new vertebrate models can be leveraged for personalized interventions to counter aging and age-related diseases.
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Affiliation(s)
- Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Ravi D Nath
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford, CA 94305, USA.
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17
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Shultz AJ, Sackton TB. Immune genes are hotspots of shared positive selection across birds and mammals. eLife 2019; 8:e41815. [PMID: 30620335 PMCID: PMC6338464 DOI: 10.7554/elife.41815] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/08/2019] [Indexed: 12/16/2022] Open
Abstract
Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.
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Affiliation(s)
- Allison J Shultz
- Informatics GroupHarvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
- Museum of Comparative ZoologyHarvard UniversityCambridgeUnited States
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18
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Abstract
All people want to age "successfully," maintaining functional capacity and quality of life as they reach advanced age. Achieving this goal depends on preserving optimal cognitive and brain functioning. Yet, significant individual differences exist in this regard. Some older adults continue to retain most cognitive abilities throughout their lifetime. Others experience declines in cognitive and functional capacity that range from mild decrements in certain cognitive functions over time to severe dementia among those with neurodegenerative diseases. Even among relatively healthy "successful agers," certain cognitive functions are reduced from earlier levels. This is particularly true for cognitive functions that are dependent on cognitive processing speed and efficiency. Working memory and executive and attentional functions tend to be most vulnerable. Learning and memory functions are also usually reduced, although in the absence of neurodegenerative disease learning and retrieval efficiency rather than memory storage are affected. Other functions, such as visual perception, language, semantics, and knowledge, are often well preserved. Structural, functional, and physiologic/metabolic brain changes correspond with age-associated cognitive decline. Physiologic and metabolic mechanisms, such as oxidative stress and neuroinflammation, may contribute to these changes, along with the contribution of comorbidities that secondarily affect the brain of older adults. Cognitive frailty often corresponds with physical frailty, both affected by multiple exogenous and endogenous factors. Neuropsychologic assessment provides a way of measuring the cognitive and functional status of older adults, which is useful for monitoring changes that may be occurring. Neuroimaging is also useful for characterizing age-associated structural, functional, physiologic, and metabolic brain changes, including alterations in cerebral blood flow and metabolite concentrations. Some interventions that may enhance cognitive function, such as cognitive training, neuromodulation, and pharmacologic approaches, exist or are being developed. Yet, preventing, slowing, and reversing the adverse effects of cognitive aging remains a challenge.
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Affiliation(s)
- Ronald A Cohen
- Center for Cognitive Aging and Memory, McKnight Brain Institute, University of Florida, Gainesville, FL, United States; Department of Clinical and Health Psychology, University of Florida, Gainesville, FL, United States.
| | - Michael M Marsiske
- Center for Cognitive Aging and Memory, McKnight Brain Institute, University of Florida, Gainesville, FL, United States; Department of Clinical and Health Psychology, University of Florida, Gainesville, FL, United States
| | - Glenn E Smith
- Center for Cognitive Aging and Memory, McKnight Brain Institute, University of Florida, Gainesville, FL, United States; Department of Clinical and Health Psychology, University of Florida, Gainesville, FL, United States
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19
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Vicens A, Posada D. Selective Pressures on Human Cancer Genes along the Evolution of Mammals. Genes (Basel) 2018; 9:genes9120582. [PMID: 30487452 PMCID: PMC6316132 DOI: 10.3390/genes9120582] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 01/01/2023] Open
Abstract
Cancer is a disease driven by both somatic mutations that increase survival and proliferation of cell lineages and the evolution of genes associated with cancer risk in populations. Several genes associated with cancer in humans, hereafter cancer genes, show evidence of germline positive selection among species. Taking advantage of a large collection of mammalian genomes, we systematically looked for signatures of germline positive selection in 430 cancer genes available in COSMIC. We identified 40 cancer genes with a robust signal of positive selection in mammals. We found evidence for fewer selective constraints—higher number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site (dN/dS)—and higher incidence of positive selection—more positively selected sites—in cancer genes bearing germline and recessive mutations that predispose to cancer. This finding suggests a potential association between relaxed selection, positive selection, and risk of hereditary cancer. On the other hand, we did not find significant differences in terms of tissue or gene type. Human cancer genes under germline positive selection in mammals are significantly enriched in the processes of DNA repair, with high presence of Fanconi anaemia/Breast Cancer A (FA/BRCA) pathway components and T cell proliferation genes. We also show that the inferred positively selected sites in the two genes with the strongest signal of positive selection, i.e., BRCA2 and PTPRC, are in regions of functional relevance, which could be relevant to cancer susceptibility.
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Affiliation(s)
- Alberto Vicens
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
- Galicia Sur Health Research Institute, 36310 Vigo, Spain.
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Jebb D, Foley NM, Whelan CV, Touzalin F, Puechmaille SJ, Teeling EC. Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing. Sci Rep 2018; 8:13634. [PMID: 30206380 PMCID: PMC6134106 DOI: 10.1038/s41598-018-31093-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022] Open
Abstract
Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The "Free Radical Theory of Ageing" (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria deep-sequenced, with a subset sampled over multiple years. The majority of heteroplasmies were at a low frequency and were transitions. Oxidative mutations were present in only a small number of individuals, suggesting local oxidative stress events. Cohort data showed no significant increase in heteroplasmy with age, while longitudinal data from recaptured individuals showed heteroplasmy is dynamic, and does not increase uniformly over time. We show that bats do not suffer from the predicted, inevitable increase in heteroplasmy as posited by the FRTA, instead heteroplasmy was found to be dynamic, questioning its presumed role as a primary driver of ageing.
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Affiliation(s)
- David Jebb
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nicole M Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor V Whelan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Frédéric Touzalin
- Laboratoire Evolution et Diversité Biologique, Université Toulouse 3, Paul Sabatier, 31062, Toulouse Cedex 09, France
| | - Sebastien J Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Applied Zoology and Conservation, Zoological Institute, Greifswald University, Greifswald, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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21
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Foley NM, Hughes GM, Huang Z, Clarke M, Jebb D, Whelan CV, Petit EJ, Touzalin F, Farcy O, Jones G, Ransome RD, Kacprzyk J, O’Connell MJ, Kerth G, Rebelo H, Rodrigues L, Puechmaille SJ, Teeling EC. Growing old, yet staying young: The role of telomeres in bats' exceptional longevity. SCIENCE ADVANCES 2018; 4:eaao0926. [PMID: 29441358 PMCID: PMC5810611 DOI: 10.1126/sciadv.aao0926] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 01/10/2018] [Indexed: 05/02/2023]
Abstract
Understanding aging is a grand challenge in biology. Exceptionally long-lived animals have mechanisms that underpin extreme longevity. Telomeres are protective nucleotide repeats on chromosome tips that shorten with cell division, potentially limiting life span. Bats are the longest-lived mammals for their size, but it is unknown whether their telomeres shorten. Using >60 years of cumulative mark-recapture field data, we show that telomeres shorten with age in Rhinolophus ferrumequinum and Miniopterus schreibersii, but not in the bat genus with greatest longevity, Myotis. As in humans, telomerase is not expressed in Myotis myotis blood or fibroblasts. Selection tests on telomere maintenance genes show that ATM and SETX, which repair and prevent DNA damage, potentially mediate telomere dynamics in Myotis bats. Twenty-one telomere maintenance genes are differentially expressed in Myotis, of which 14 are enriched for DNA repair, and 5 for alternative telomere-lengthening mechanisms. We demonstrate how telomeres, telomerase, and DNA repair genes have contributed to the evolution of exceptional longevity in Myotis bats, advancing our understanding of healthy aging.
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Affiliation(s)
- Nicole M. Foley
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Graham M. Hughes
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Clarke
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Jebb
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor V. Whelan
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eric J. Petit
- Ecologie et Santé des Ecosystèmes (ESE), Ecology and Ecosystem Health, Agrocampus Ouest, INRA, 35042 Rennes, France
| | - Frédéric Touzalin
- Laboratoire Évolution et Diversité Biologique, UMR 5174: Université Toulouse III, CNRS, ENFA, 118 Route de Narbonne, 31062 Toulouse cedex 9, France
| | - Olivier Farcy
- Le Groupe Chiroptères de Bretagne Vivante/SEPNB, 19 rue Gouesnou BP 62132, 29221 Brest cedex 2, France
| | - Gareth Jones
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
| | - Roger D. Ransome
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mary J. O’Connell
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Gerald Kerth
- University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
| | - Hugo Rebelo
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
- CIBIO-InBIO, Universidade do Porto, Campus de Agrário Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
- CEABN-InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-015 Lisboa, Portugal
| | - Luísa Rodrigues
- Instituto da Conservação da Natureza e das Florestas, Avenida da República 16-16B, 1050-191 Lisboa, Portugal
| | - Sébastien J. Puechmaille
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
- University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
| | - Emma C. Teeling
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
- Corresponding author.
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22
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Lagunas-Rangel FA, Chávez-Valencia V. Learning of nature: The curious case of the naked mole rat. Mech Ageing Dev 2017; 164:76-81. [DOI: 10.1016/j.mad.2017.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/24/2017] [Accepted: 04/28/2017] [Indexed: 02/06/2023]
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23
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Limborg MT, Seeb LW, Seeb JE. Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing. Mol Ecol 2016; 25:2117-29. [PMID: 26939067 DOI: 10.1111/mec.13601] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 02/19/2016] [Accepted: 02/24/2016] [Indexed: 01/04/2023]
Abstract
Many plants and animals of polyploid origin are currently enjoying a genomics explosion enabled by modern sequencing and genotyping technologies. However, routine filtering of duplicated loci in most studies using genotyping by sequencing introduces an unacceptable, but often overlooked, bias when detecting selection. Retained duplicates from ancient whole-genome duplications (WGDs) may be found throughout genomes, whereas retained duplicates from recent WGDs are concentrated at distal ends of some chromosome arms. Additionally, segmental duplicates can be found at distal ends or nearly anywhere in a genome. Evidence shows that these duplications facilitate adaptation through one of two pathways: neo-functionalization or increased gene expression. Filtering duplicates removes distal ends of some chromosomes, and distal ends are especially known to harbour adaptively important genes. Thus, filtering of duplicated loci impoverishes the interpretation of genomic data as signals from contiguous duplicated genes are ignored. We review existing strategies to genotype and map duplicated loci; we focus in detail on an overlooked strategy of using gynogenetic haploids (1N) as a part of new genotyping by sequencing studies. We provide guidelines on how to use this haploid strategy for studies on polyploid-origin vertebrates including how it can be used to screen duplicated loci in natural populations. We conclude by discussing areas of research that will benefit from better inclusion of polyploid loci; we particularly stress the sometimes overlooked fact that basing genomic studies on dense maps provides value added in the form of locating and annotating outlier loci or colocating outliers into islands of divergence.
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Affiliation(s)
- Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA.,National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
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24
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Triplett JC, Swomley AM, Kirk J, Grimes KM, Lewis KN, Orr ME, Rodriguez KA, Cai J, Klein JB, Buffenstein R, Butterfield DA. Reaching Out to Send a Message: Proteins Associated with Neurite Outgrowth and Neurotransmission are Altered with Age in the Long-Lived Naked Mole-Rat. Neurochem Res 2016; 41:1625-34. [DOI: 10.1007/s11064-016-1877-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 02/06/2016] [Accepted: 02/18/2016] [Indexed: 10/22/2022]
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25
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Comparative sequence analyses of rhodopsin and RPE65 reveal patterns of selective constraint across hereditary retinal disease mutations. Vis Neurosci 2016; 33:e002. [DOI: 10.1017/s0952523815000322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractRetinitis pigmentosa (RP) comprises several heritable diseases that involve photoreceptor, and ultimately retinal, degeneration. Currently, mutations in over 50 genes have known links to RP. Despite advances in clinical characterization, molecular characterization of RP remains challenging due to the heterogeneous nature of causal genes, mutations, and clinical phenotypes. In this study, we compiled large datasets of two important visual genes associated with RP: rhodopsin, which initiates the phototransduction cascade, and the retinoid isomerase RPE65, which regenerates the visual cycle. We used a comparative evolutionary approach to investigate the relationship between interspecific sequence variation and pathogenic mutations that lead to degenerative retinal disease. Using codon-based likelihood methods, we estimated evolutionary rates (dN/dS) across both genes in a phylogenetic context to investigate differences between pathogenic and nonpathogenic amino acid sites. In both genes, disease-associated sites showed significantly lower evolutionary rates compared to nondisease sites, and were more likely to occur in functionally critical areas of the proteins. The nature of the dataset (e.g., vertebrate or mammalian sequences), as well as selection of pathogenic sites, affected the differences observed between pathogenic and nonpathogenic sites. Our results illustrate that these methods can serve as an intermediate step in understanding protein structure and function in a clinical context, particularly in predicting the relative pathogenicity (i.e., functional impact) of point mutations and their downstream phenotypic effects. Extensions of this approach may also contribute to current methods for predicting the deleterious effects of candidate mutations and to the identification of protein regions under strong constraint where we expect pathogenic mutations to occur.
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26
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Polettini J, Behnia F, Taylor BD, Saade GR, Taylor RN, Menon R. Telomere Fragment Induced Amnion Cell Senescence: A Contributor to Parturition? PLoS One 2015; 10:e0137188. [PMID: 26397719 PMCID: PMC4580414 DOI: 10.1371/journal.pone.0137188] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/13/2015] [Indexed: 01/08/2023] Open
Abstract
Oxidative stress (OS)-induced senescence of the amniochorion has been associated with parturition at term. We investigated whether telomere fragments shed into the amniotic fluid (AF) correlated with labor status and tested if exogenous telomere fragments (T-oligos) could induce human and murine amnion cell senescence. In a cross-sectional clinical study, AF telomere fragment concentrations quantitated by a validated real-time PCR assay were higher in women in labor at term compared to those not in labor. In vitro treatment of primary human amnion epithelial cells with 40 μM T-oligos ([TTAGGG]2) that mimic telomere fragments, activated p38MAPK, produced senescence-associated (SA) β-gal staining and increased interleukin (IL)-6 and IL-8 production compared to cells treated with complementary DNA sequences (Cont-oligos, [AATCCC]2). T-oligos injected into the uteri of pregnant CD1 mice on day 14 of gestation, led to increased p38MAPK, SA-β-gal (SA β-gal) staining in murine amniotic sacs and higher AF IL-8 levels on day 18, compared to saline treated controls. In summary, term labor AF samples had higher telomere fragments than term not in labor AF. In vitro and in situ telomere fragments increased human and murine amnion p38MAPK, senescence and inflammatory cytokines. We propose that telomere fragments released from senescent fetal cells are indicative of fetal cell aging. Based on our data, these telomere fragments cause oxidative stress associated damages to the term amniotic sac and force them to release other DAMPS, which, in turn, provide a sterile immune response that may be one of the many inflammatory signals required to initiate parturition at term.
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Affiliation(s)
- Jossimara Polettini
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- Department of Pathology, Botucatu Medical School, UNESP–Univ. Estadual Paulista, Botucatu, Sao Paulo, Brazil
| | - Faranak Behnia
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Brandie D. Taylor
- Department of Epidemiology & Biostatistics, Texas A&M University System Health Science Center, College Station, Texas, United States of America
| | - George R. Saade
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Robert N. Taylor
- Department of Obstetrics and Gynecology, Wake Forest University, Winston Salem, North Carolina, United States of America
| | - Ramkumar Menon
- Division of Maternal-Fetal Medicine and Perinatal Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- * E-mail:
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Davies KTJ, Bennett NC, Tsagkogeorga G, Rossiter SJ, Faulkes CG. Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis. Mol Biol Evol 2015; 32:3089-107. [PMID: 26318402 PMCID: PMC4652621 DOI: 10.1093/molbev/msv175] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein–protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group.
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Affiliation(s)
- Kalina T J Davies
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Nigel C Bennett
- Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Georgia Tsagkogeorga
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Stephen J Rossiter
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Christopher G Faulkes
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
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Allendorf FW, Bassham S, Cresko WA, Limborg MT, Seeb LW, Seeb JE. Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes. J Hered 2015; 106:217-27. [PMID: 25838153 DOI: 10.1093/jhered/esv015] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 02/19/2015] [Indexed: 01/24/2023] Open
Abstract
A whole genome duplication occurred in the ancestor of all salmonid fishes some 50-100 million years ago. Early inheritance studies with allozymes indicated that loci in the salmonid genome are inherited disomically in females. However, some pairs of duplicated loci showed patterns of inheritance in males indicating pairing and recombination between homeologous chromosomes. Nearly 20% of loci in the salmonid genome are duplicated and share the same alleles (isoloci), apparently due to homeologous recombination. Half-tetrad analysis revealed that isoloci tend to be telomeric. These results suggested that residual tetrasomic inheritance of isoloci results from homeologous recombination near chromosome ends and that continued disomic inheritance resulted from homologous pairing of centromeric regions. Many current genetic maps of salmonids are based on single nucleotide polymorphisms and microsatellites that are no longer duplicated. Therefore, long sections of chromosomes on these maps are poorly represented, especially telomeric regions. In addition, preferential multivalent pairing of homeologs from the same species in F1 hybrids results in an excess of nonparental gametes (so-called pseudolinkage). We consider how not including duplicated loci has affected our understanding of population and evolutionary genetics of salmonids, and we discuss how incorporating these loci will benefit our understanding of population genomics.
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Affiliation(s)
- Fred W Allendorf
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb).
| | - Susan Bassham
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - William A Cresko
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - Morten T Limborg
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - Lisa W Seeb
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - James E Seeb
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
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29
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Davies KT, Tsagkogeorga G, Bennett NC, Dávalos LM, Faulkes CG, Rossiter SJ. Molecular evolution of growth hormone and insulin-like growth factor 1 receptors in long-lived, small-bodied mammals. Gene 2014; 549:228-36. [DOI: 10.1016/j.gene.2014.07.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/16/2014] [Accepted: 07/23/2014] [Indexed: 10/25/2022]
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