1
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Perna S, Tang W, Blimbaum S, Li A, Zhou L. Shared Transcriptomic Signatures of Inflammaging Among Diverse Strains of Drosophila melanogaster. RESEARCH SQUARE 2024:rs.3.rs-4146509. [PMID: 38645033 PMCID: PMC11030547 DOI: 10.21203/rs.3.rs-4146509/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background A prominent hallmark of aging is inflammaging-the increased expression of innate immune genes without identifiable infection. Model organisms with shorter lifespans, such as the fruit fly, provide an essential platform for probing the mechanisms of inflammaging. Multiple groups have reported that, like mammalian models, old flies have significantly higher levels of expression of anti-microbial peptide genes. However, whether some of these genes-or any others-can serve as reliable markers for assessing and comparing inflammaging in different strains remains unclear. Methods and Results We compared RNA-Seq datasets generated by different groups. Although the fly strains used in these studies differ significantly, we found that they share a core group of genes with strong aging-associated expression. In addition to anti-microbial peptide genes, we identified other genes that have prominently increased expression in old flies, especially SPH93. We further showed that machine learning models can be used to predict the "inflammatory age" of the fruit y. Conclusion A core group of genes may serve as markers for studying inflammaging in Drosophila. RNA-Seq profiles, in combination with machine-learning models, can be applied to measure the acceleration or deceleration of inflammaging.
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2
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Yu Z, Dong Y, Chen Y, Aleya L, Zhao Y, Yao L, Gu W. It is time to explore the impact of length of gestation and fetal health on the human lifespan. Aging Cell 2024; 23:e14157. [PMID: 38558485 PMCID: PMC11019132 DOI: 10.1111/acel.14157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/20/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
A recently proposed principal law of lifespan (PLOSP) proposes to extend the whole human lifespan by elongating different life stages. As the preborn stage of a human being, gestation is the foundation for the healthy development of the human body. The antagonistic pleiotropy (AP) theory of aging states that there is a trade-off between early life fitness and late-life mortality. The question is whether slower development during the gestation period would be associated with a longer lifespan. Among all living creatures, the length of the gestation period is highly positively correlated to the length of the lifespan, although such a correlation is thought to be influenced by the body sizes of different species. While examining the relationship between lifespan length and body size within the same species, dogs exhibit a negative correlation between lifespans and body sizes, while there is no such correlation among domestic cats. For humans, most adverse gestational environments shorten the period of gestation, and their impacts are long-term. While many issues remain unsolved, various developmental features have been linked to the conditions during the gestation period. Given that the length of human pregnancies can vary randomly by as long as 5 weeks, it is worth investigating whether a slow steady healthy gestation over a longer period will be related to a longer and healthier lifespan. This article discusses the potential benefits, negative impacts, and challenges of the relative elongation of the gestation period.
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Affiliation(s)
- Zhuo Yu
- Heilongjiang Academy of Traditional Chinese MedicineHarbinChina
| | - Yushan Dong
- Graduate School of Heilongjiang University of Chinese MedicineHarbinHeilongjiangChina
| | - Yuhan Chen
- Guang'anmen Hospital, China Academy of Chinese Medical SciencesBeijingChina
| | - Lotfi Aleya
- Chrono‐Environnement Laboratory, UMR CNRS 6249Bourgogne Franche‐Comté UniversityBesançon CedexFrance
| | - Yinhuan Zhao
- Department of Rheumatism, Shanghai Traditional Chinese Medicine Integrated HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Lan Yao
- College of Health Management, Harbin Medical UniversityHarbinHeilongjiangChina
- Department of Orthopedic Surgery and BME‐Campbell ClinicUniversity of Tennessee Health Science CentreMemphisTennesseeUSA
| | - Weikuan Gu
- Department of Orthopedic Surgery and BME‐Campbell ClinicUniversity of Tennessee Health Science CentreMemphisTennesseeUSA
- Research Lt. Col. Luke WeathersJr. VA Medical CenterMemphisTennesseeUSA
- Department of Pharmaceutical SciencesUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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3
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Webster CF, Smotherman M, Pippel M, Brown T, Winkler S, Pieri M, Mai M, Myers EW, Teeling EC, Vernes SC. The genome sequence of Tadarida brasiliensis I. Geoffroy Saint-Hilaire, 1824 [Molossidae; Tadarida]. Wellcome Open Res 2024; 9:98. [PMID: 38800517 PMCID: PMC11128047 DOI: 10.12688/wellcomeopenres.20603.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2024] [Indexed: 05/29/2024] Open
Abstract
We present a genome assembly from an individual male Tadarida brasiliensis (The Brazilian free-tailed bat; Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.28 Gb in span. The majority of the assembly is scaffolded into 25 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.
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Affiliation(s)
- Cara F. Webster
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Michael Smotherman
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
| | - Thomas Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
| | - Myrtani Pieri
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
| | - Meike Mai
- School of Biology, University of St Andrews, St Andrews, UK
| | - Eugene W. Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire, CB10 1SA, UK
| | - Sonja C. Vernes
- School of Biology, University of St Andrews, St Andrews, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - The Bat1K Consortium
- Department of Biology, Texas A&M University, College Station, Texas, USA
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
- School of Biology, University of St Andrews, St Andrews, UK
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire, CB10 1SA, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
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4
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Lázaro J, Sochacki J, Ebisuya M. The stem cell zoo for comparative studies of developmental tempo. Curr Opin Genet Dev 2024; 84:102149. [PMID: 38199063 PMCID: PMC10882223 DOI: 10.1016/j.gde.2023.102149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024]
Abstract
The rate of development is highly variable across animal species. However, the mechanisms regulating developmental tempo have remained elusive due to difficulties in performing direct interspecies comparisons. Here, we discuss how pluripotent stem cell-based models of development can be used to investigate cell- and tissue-autonomous temporal processes. These systems enable quantitative comparisons of different animal species under similar experimental conditions. Moreover, the constantly growing stem cell zoo collection allows the extension of developmental studies to a great number of unconventional species. We argue that the stem cell zoo constitutes a powerful platform to perform comparative studies of developmental tempo, as well as to study other forms of biological time control such as species-specific lifespan, heart rate, and circadian clocks.
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Affiliation(s)
- Jorge Lázaro
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany. https://twitter.com/@JorgeLazaroF
| | - Jaroslaw Sochacki
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany.
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5
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Diaz-Cuadros M, Pourquié O. The Clockwork Embryo: Mechanisms Regulating Developmental Rate. Annu Rev Genet 2023; 57:117-134. [PMID: 38012023 DOI: 10.1146/annurev-genet-022123-104503] [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] [Indexed: 11/29/2023]
Abstract
Organismal development requires the reproducible unfolding of an ordered sequence of discrete steps (cell fate determination, migration, tissue folding, etc.) in both time and space. Here, we review the mechanisms that grant temporal specificity to developmental steps, including molecular clocks and timers. Individual timing mechanisms must be coordinated with each other to maintain the overall developmental sequence. However, phenotypic novelties can also arise through the modification of temporal patterns over the course of evolution. Two main types of variation in temporal patterning characterize interspecies differences in developmental time: allochrony, where the overall developmental sequence is either accelerated or slowed down while maintaining the relative duration of individual steps, and heterochrony, where the duration of specific developmental steps is altered relative to the rest. New advances in in vitro modeling of mammalian development using stem cells have recently enabled the revival of mechanistic studies of allochrony and heterochrony. In both cases, differences in the rate of basic cellular functions such as splicing, translation, protein degradation, and metabolism seem to underlie differences in developmental time. In the coming years, these studies should identify the genetic differences that drive divergence in developmental time between species.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA;
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA;
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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6
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Jové M, Mota-Martorell N, Fernàndez-Bernal A, Portero-Otin M, Barja G, Pamplona R. Phenotypic molecular features of long-lived animal species. Free Radic Biol Med 2023; 208:728-747. [PMID: 37748717 DOI: 10.1016/j.freeradbiomed.2023.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
One of the challenges facing science/biology today is uncovering the molecular bases that support and determine animal and human longevity. Nature, in offering a diversity of animal species that differ in longevity by more than 5 orders of magnitude, is the best 'experimental laboratory' to achieve this aim. Mammals, in particular, can differ by more than 200-fold in longevity. For this reason, most of the available evidence on this topic derives from comparative physiology studies. But why can human beings, for instance, reach 120 years whereas rats only last at best 4 years? How does nature change the longevity of species? Longevity is a species-specific feature resulting from an evolutionary process. Long-lived animal species, including humans, show adaptations at all levels of biological organization, from metabolites to genome, supported by signaling and regulatory networks. The structural and functional features that define a long-lived species may suggest that longevity is a programmed biological property.
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Affiliation(s)
- Mariona Jové
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), E25198, Lleida, Spain
| | - Natàlia Mota-Martorell
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), E25198, Lleida, Spain
| | - Anna Fernàndez-Bernal
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), E25198, Lleida, Spain
| | - Manuel Portero-Otin
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), E25198, Lleida, Spain
| | - Gustavo Barja
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), E28040, Madrid, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), E25198, Lleida, Spain.
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7
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Danis T, Rokas A. The evolution of gestation length in eutherian mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563491. [PMID: 37961105 PMCID: PMC10634735 DOI: 10.1101/2023.10.22.563491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Gestation length, or the duration of pregnancy, is a critical component of mammalian reproductive biology1. Eutherian mammals exhibit striking variation in their gestation lengths2-5, which has traditionally been linked to and allometrically scales with variation in other life history traits, including body mass and lifespan5-8. How the phenotypic landscape of gestation length variation, including its associations with body mass and lifespan variation, changed over mammalian evolution remains unknown. Phylogeny-informed analyses of 845 representative extant eutherian mammals showed that gestation length variation substantially differed in both whether and how strongly it was associated with body mass and lifespan across mammalian clades. For example, gestation length variation in Chiroptera and Cetacea was not associated with lifespan or body mass but was strongly associated only with body mass in Carnivora. We also identified 52 adaptive shifts in gestation length variation across the mammal phylogeny and 14 adaptive shifts when considering all three life history traits; the placements of six adaptive shifts are common in the two analyses. Notably, two of these shifts occurred at the roots of Cetacea and Pinnipedia, respectively, coinciding with the transition of these clades to the marine environment. The varying dynamics of the phenotypic landscape of gestation length, coupled with the varying patterns of associations between gestation length and two other major life history traits, raise the hypothesis that evolutionary constraints on gestation length have varied substantially across mammalian phylogeny. This variation in constraints implies that the genetic architecture of gestation length differs between mammal clades.
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Affiliation(s)
- Thodoris Danis
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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8
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Huang Z, Jiang C, Gu J, Uvizl M, Power S, Douglas D, Kacprzyk J. Duplications of Human Longevity-Associated Genes Across Placental Mammals. Genome Biol Evol 2023; 15:evad186. [PMID: 37831410 PMCID: PMC10588791 DOI: 10.1093/gbe/evad186] [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: 05/02/2023] [Revised: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023] Open
Abstract
Natural selection has shaped a wide range of lifespans across mammals, with a few long-lived species showing negligible signs of ageing. Approaches used to elucidate the genetic mechanisms underlying mammalian longevity usually involve phylogenetic selection tests on candidate genes, detections of convergent amino acid changes in long-lived lineages, analyses of differential gene expression between age cohorts or species, and measurements of age-related epigenetic changes. However, the link between gene duplication and evolution of mammalian longevity has not been widely investigated. Here, we explored the association between gene duplication and mammalian lifespan by analyzing 287 human longevity-associated genes across 37 placental mammals. We estimated that the expansion rate of these genes is eight times higher than their contraction rate across these 37 species. Using phylogenetic approaches, we identified 43 genes whose duplication levels are significantly correlated with longevity quotients (False Discovery Rate (FDR) < 0.05). In particular, the strong correlation observed for four genes (CREBBP, PIK3R1, HELLS, FOXM1) appears to be driven mainly by their high duplication levels in two ageing extremists, the naked mole rat (Heterocephalus glaber) and the greater mouse-eared bat (Myotis myotis). Further sequence and expression analyses suggest that the gene PIK3R1 may have undergone a convergent duplication event, whereby the similar region of its coding sequence was independently duplicated multiple times in both of these long-lived species. Collectively, this study identified several candidate genes whose duplications may underlie the extreme longevity in mammals, and highlighted the potential role of gene duplication in the evolution of mammalian long lifespans.
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Affiliation(s)
- Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Chongyi Jiang
- Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Jiayun Gu
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Marek Uvizl
- Department of Zoology, National Museum, Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Declan Douglas
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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9
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Işıldak U, Dönertaş HM. Evolutionary paths to mammalian longevity through the lens of gene expression. EMBO J 2023; 42:e114879. [PMID: 37519235 PMCID: PMC10476271 DOI: 10.15252/embj.2023114879] [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: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
The natural variation in mammalian longevity and its underlying mechanisms remain an active area of aging research. In the latest issue of The EMBO Journal, Liu et al (2023) analyze gene expression levels in 103 mammalian species across three tissues, revealing tissue-specific associations between gene expression patterns and longevity. Remarkably, the study suggests that methionine restriction, a strategy shown to increase lifespan, may extend beyond artificial interventions and is similarly employed by natural selection.
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Affiliation(s)
- Ulaş Işıldak
- Leibniz Institute on Aging ‐ Fritz Lipmann Institute (FLI)LeibnizGermany
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10
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Liu W, Zhu P, Li M, Li Z, Yu Y, Liu G, Du J, Wang X, Yang J, Tian R, Seim I, Kaya A, Li M, Li M, Gladyshev VN, Zhou X. Large-scale across species transcriptomic analysis identifies genetic selection signatures associated with longevity in mammals. EMBO J 2023; 42:e112740. [PMID: 37427458 PMCID: PMC10476176 DOI: 10.15252/embj.2022112740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
Lifespan varies significantly among mammals, with more than 100-fold difference between the shortest and longest living species. This natural difference may uncover the evolutionary forces and molecular features that define longevity. To understand the relationship between gene expression variation and longevity, we conducted a comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species. We found that few genes exhibit common expression patterns with longevity in the three organs analyzed. However, pathways related to translation fidelity, such as nonsense-mediated decay and eukaryotic translation elongation, correlated with longevity across mammals. Analyses of selection pressure found that selection intensity related to the direction of longevity-correlated genes is inconsistent across organs. Furthermore, expression of methionine restriction-related genes correlated with longevity and was under strong selection in long-lived mammals, suggesting that a common strategy is utilized by natural selection and artificial intervention to control lifespan. Our results indicate that lifespan regulation via gene expression is driven through polygenic and indirect natural selection.
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Affiliation(s)
- Weiqiang Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Zihao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Yu
- School of Life SciencesUniversity of Science and Technology of ChinaAnhuiChina
| | - Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Jing Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ran Tian
- Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Inge Seim
- Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
| | - Alaattin Kaya
- Department of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityChengduChina
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
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11
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Takasugi M, Yoshida Y, Nonaka Y, Ohtani N. Gene expressions associated with longer lifespan and aging exhibit similarity in mammals. Nucleic Acids Res 2023; 51:7205-7219. [PMID: 37351606 PMCID: PMC10415134 DOI: 10.1093/nar/gkad544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Although molecular features underlying aging and species maximum lifespan (MLS) have been comprehensively studied by transcriptome analyses, the actual impact of transcriptome on aging and MLS remains elusive. Here, we found that transcriptional signatures that are associated with mammalian MLS exhibited significant similarity to those of aging. Moreover, transcriptional signatures of longer MLS and aging both exhibited significant similarity to that of longer-lived mouse strains, suggesting that gene expression patterns associated with species MLS contribute to extended lifespan even within a species and that aging-related gene expression changes overall represent adaptations that extend lifespan rather than deterioration. Finally, we found evidence of co-evolution of MLS and promoter sequences of MLS-associated genes, highlighting the evolutionary contribution of specific transcription factor binding motifs such as that of E2F1 in shaping MLS-associated gene expression signature. Our results highlight the importance of focusing on adaptive aspects of aging transcriptome and demonstrate that cross-species genomics can be a powerful approach for understanding adaptive aging transcriptome.
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Affiliation(s)
- Masaki Takasugi
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Yuya Yoshida
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Yoshiki Nonaka
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Naoko Ohtani
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
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12
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Tyshkovskiy A, Ma S, Shindyapina AV, Tikhonov S, Lee SG, Bozaykut P, Castro JP, Seluanov A, Schork NJ, Gorbunova V, Dmitriev SE, Miller RA, Gladyshev VN. Distinct longevity mechanisms across and within species and their association with aging. Cell 2023; 186:2929-2949.e20. [PMID: 37269831 PMCID: PMC11192172 DOI: 10.1016/j.cell.2023.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2022] [Accepted: 05/02/2023] [Indexed: 06/05/2023]
Abstract
Lifespan varies within and across species, but the general principles of its control remain unclear. Here, we conducted multi-tissue RNA-seq analyses across 41 mammalian species, identifying longevity signatures and examining their relationship with transcriptomic biomarkers of aging and established lifespan-extending interventions. An integrative analysis uncovered shared longevity mechanisms within and across species, including downregulated Igf1 and upregulated mitochondrial translation genes, and unique features, such as distinct regulation of the innate immune response and cellular respiration. Signatures of long-lived species were positively correlated with age-related changes and enriched for evolutionarily ancient essential genes, involved in proteolysis and PI3K-Akt signaling. Conversely, lifespan-extending interventions counteracted aging patterns and affected younger, mutable genes enriched for energy metabolism. The identified biomarkers revealed longevity interventions, including KU0063794, which extended mouse lifespan and healthspan. Overall, this study uncovers universal and distinct strategies of lifespan regulation within and across species and provides tools for discovering longevity interventions.
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Affiliation(s)
- Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anastasia V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stanislav Tikhonov
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Perinur Bozaykut
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - José P Castro
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; Aging and Aneuploidy Laboratory, IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Nicholas J Schork
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA, USA.
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13
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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14
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Zhu P, Liu W, Zhang X, Li M, Liu G, Yu Y, Li Z, Li X, Du J, Wang X, Grueter CC, Li M, Zhou X. Correlated evolution of social organization and lifespan in mammals. Nat Commun 2023; 14:372. [PMID: 36720880 PMCID: PMC9889386 DOI: 10.1038/s41467-023-35869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/05/2023] [Indexed: 02/02/2023] Open
Abstract
Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
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Affiliation(s)
- Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Yang Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,International Center of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, 671003, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.
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15
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Diaz-Cuadros M, Miettinen TP, Skinner OS, Sheedy D, Díaz-García CM, Gapon S, Hubaud A, Yellen G, Manalis SR, Oldham WM, Pourquié O. Metabolic regulation of species-specific developmental rates. Nature 2023; 613:550-557. [PMID: 36599986 PMCID: PMC9944513 DOI: 10.1038/s41586-022-05574-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/18/2022] [Indexed: 01/06/2023]
Abstract
Animals display substantial inter-species variation in the rate of embryonic development despite a broad conservation of the overall sequence of developmental events. Differences in biochemical reaction rates, including the rates of protein production and degradation, are thought to be responsible for species-specific rates of development1-3. However, the cause of differential biochemical reaction rates between species remains unknown. Here, using pluripotent stem cells, we have established an in vitro system that recapitulates the twofold difference in developmental rate between mouse and human embryos. This system provides a quantitative measure of developmental speed as revealed by the period of the segmentation clock, a molecular oscillator associated with the rhythmic production of vertebral precursors. Using this system, we show that mass-specific metabolic rates scale with the developmental rate and are therefore higher in mouse cells than in human cells. Reducing these metabolic rates by inhibiting the electron transport chain slowed down the segmentation clock by impairing the cellular NAD+/NADH redox balance and, further downstream, lowering the global rate of protein synthesis. Conversely, increasing the NAD+/NADH ratio in human cells by overexpression of the Lactobacillus brevis NADH oxidase LbNOX increased the translation rate and accelerated the segmentation clock. These findings represent a starting point for the manipulation of developmental rate, with multiple translational applications including accelerating the differentiation of human pluripotent stem cells for disease modelling and cell-based therapies.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
| | - Teemu P Miettinen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Dylan Sheedy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Carlos Manlio Díaz-García
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Svetlana Gapon
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexis Hubaud
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William M Oldham
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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16
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Mota-Martorell N, Jové M, Berdún R, Òbis È, Barja G, Pamplona R. Methionine Metabolism Is Down-Regulated in Heart of Long-Lived Mammals. BIOLOGY 2022; 11:biology11121821. [PMID: 36552330 PMCID: PMC9775425 DOI: 10.3390/biology11121821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Methionine constitutes a central hub of intracellular metabolic adaptations leading to an extended longevity (maximum lifespan). The present study follows a comparative approach analyzing methionine and related metabolite and amino acid profiles using an LC-MS/MS platform in the hearts of seven mammalian species with a longevity ranging from 3.8 to 57 years. Our findings demonstrate the existence of species-specific heart phenotypes associated with high longevity characterized by: (i) low concentration of methionine and its related sulphur-containing metabolites; (ii) low amino acid pool; and (iii) low choline concentration. Our results support the existence of heart metabotypes characterized by a down-regulation in long-lived species, supporting the idea that in longevity, less is more.
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Affiliation(s)
- Natalia Mota-Martorell
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida), 25008 Lleida, Spain
| | - Mariona Jové
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida), 25008 Lleida, Spain
| | - Rebeca Berdún
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida), 25008 Lleida, Spain
| | - Èlia Òbis
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida), 25008 Lleida, Spain
| | - Gustavo Barja
- Department of Genetics, Physiology and Microbiology, Complutense University, 28040 Madrid, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida), 25008 Lleida, Spain
- Correspondence:
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17
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Li J, Sun K, Dai W, Leng H, Feng J. Divergence in interspecific and intersubspecific gene expression between two closely related horseshoe bats ( Rhinolophus). J Mammal 2022. [DOI: 10.1093/jmammal/gyac103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Closely related species have been used as representative systems to investigate the genetic mechanisms involved in the early stages of species differentiation. Previous studies have indicated that variation in gene expression might be a sensitive indicator of initial species divergence, although the role of expression divergence, and especially that associated with phenotypic variation remained relatively undefined. For three organs (cochlea, brain, and liver) from two closely related bat species (Rhinolophus siamensis and R. episcopus), the interspecific and intersubspecific gene expression profiles were compared using transcriptomics in this study. Striking organ specificity of expression was observed, and expression profiles exhibited similarities between cochlea and brain tissues. Numerous differentially expressed genes (DEGs) were identified for each organ in the interspecific comparison (cochlea/brain/liver: 1,069/647/692) and intersubspecific comparison (608/528/368). Functional enrichment analysis indicated vital variation in expression related to the immune system, ion activities, neuronal function, and multisensory system regulation in both comparisons. DEGs relevant to the variation in echolocation calls (RF) were found, and some of them were involved in the pivotal patterns of expression variation. The regulation of immune, ion channel, neural activity, and sophisticated sensory functions at the expression level might be key mechanisms in the early species divergence of bats, and the expression variation related to acoustical signal could have played a crucial part. This study expands our knowledge of gene expression and patterns of variation for three key organs to echolocation at both the interspecific and intersubspecific levels. Further, the framework described here provides insight into the genetic basis of phenotypic variation during the incipient stage of species differentiation.
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Affiliation(s)
- Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- College of Life Science, Jilin Agricultural University , Changchun 130118 , China
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18
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Li J, Sun K, Dai W, Leng H, Li A, Feng J. Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs. Animals (Basel) 2022; 12:ani12233432. [PMID: 36496954 PMCID: PMC9741297 DOI: 10.3390/ani12233432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level.
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Affiliation(s)
- Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
- Correspondence: (K.S.); (J.F.)
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.S.); (J.F.)
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19
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Branicky R, Wang Y, Khaki A, Liu JL, Kramer-Drauberg M, Hekimi S. Stimulation of RAS-dependent ROS signaling extends longevity by modulating a developmental program of global gene expression. SCIENCE ADVANCES 2022; 8:eadc9851. [PMID: 36449615 PMCID: PMC9710873 DOI: 10.1126/sciadv.adc9851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
We show that elevation of mitochondrial superoxide generation increases Caenorhabditis elegans life span by enhancing a RAS-dependent ROS (reactive oxygen species) signaling pathway (RDRS) that controls the expression of half of the genome as well as animal composition and physiology. RDRS stimulation mimics a program of change in gene expression that is normally observed at the end of postembryonic development. We further show that RDRS is regulated by negative feedback from the superoxide dismutase 1 (SOD-1)-dependent conversion of superoxide into cytoplasmic hydrogen peroxide, which, in turn, acts on a redox-sensitive cysteine (C118) of RAS. Preventing C118 oxidation by replacement with serine, or mimicking oxidation by replacement with aspartic acid, leads to opposite changes in the expression of the same large set of genes that is affected when RDRS is stimulated by mitochondrial superoxide. The identities of these genes suggest that stimulation of the pathway extends life span by boosting turnover and repair while moderating damage from metabolic activity.
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20
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Lobo D, Linheiro R, Godinho R, Archer JP. On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves. PLoS One 2022; 17:e0274591. [PMID: 36136981 PMCID: PMC9498955 DOI: 10.1371/journal.pone.0274591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
The evolution of RNA-seq technologies has yielded datasets of scientific value that are often generated as condition associated biological replicates within expression studies. With expanding data archives opportunity arises to augment replicate numbers when conditions of interest overlap. Despite correction procedures for estimating transcript abundance, a source of ambiguity is transcript level intra-condition count variation; as indicated by disjointed results between analysis tools. We present TVscript, a tool that removes reference-based transcripts associated with intra-condition count variation above specified thresholds and we explore the effects of such variation on differential expression analysis. Initially iterative differential expression analysis involving simulated counts, where levels of intra-condition variation and sets of over represented transcripts are explicitly specified, was performed. Then counts derived from inter- and intra-study data representing brain samples of dogs, wolves and foxes (wolves vs. dogs and aggressive vs. tame foxes) were used. For simulations, the sensitivity in detecting differentially expressed transcripts increased after removing hyper-variable transcripts, although at levels of intra-condition variation above 5% detection became unreliable. For real data, prior to applying TVscript, ≈20% of the transcripts identified as being differentially expressed were associated with high levels of intra-condition variation, an over representation relative to the reference set. As transcripts harbouring such variation were removed pre-analysis, a discordance from 26 to 40% in the lists of differentially expressed transcripts is observed when compared to those obtained using the non-filtered reference. The removal of transcripts possessing intra-condition variation values within (and above) the 97th and 95th percentiles, for wolves vs. dogs and aggressive vs. tame foxes, maximized the sensitivity in detecting differentially expressed transcripts as a result of alterations within gene-wise dispersion estimates. Through analysis of our real data the support for seven genes with potential for being involved with selection for tameness is provided. TVscript is available at: https://sourceforge.net/projects/tvscript/.
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Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail: (DL); (JPA)
| | - Raquel Linheiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - John Patrick Archer
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- * E-mail: (DL); (JPA)
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21
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Shindyapina AV, Cho Y, Kaya A, Tyshkovskiy A, Castro JP, Deik A, Gordevicius J, Poganik JR, Clish CB, Horvath S, Peshkin L, Gladyshev VN. Rapamycin treatment during development extends life span and health span of male mice and Daphnia magna. SCIENCE ADVANCES 2022; 8:eabo5482. [PMID: 36112674 PMCID: PMC9481125 DOI: 10.1126/sciadv.abo5482] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/26/2022] [Indexed: 05/22/2023]
Abstract
Development is tightly connected to aging, but whether pharmacologically targeting development can extend life remains unknown. Here, we subjected genetically diverse UMHET3 mice to rapamycin for the first 45 days of life. The mice grew slower and remained smaller than controls for their entire lives. Their reproductive age was delayed without affecting offspring numbers. The treatment was sufficient to extend the median life span by 10%, with the strongest effect in males, and helped to preserve health as measured by frailty index scores, gait speed, and glucose and insulin tolerance tests. Mechanistically, the liver transcriptome and epigenome of treated mice were younger at the completion of treatment. Analogous to mice, rapamycin exposure during development robustly extended the life span of Daphnia magna and reduced its body size. Overall, the results demonstrate that short-term rapamycin treatment during development is a novel longevity intervention that acts by slowing down development and aging, suggesting that aging may be targeted already early in life.
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Affiliation(s)
| | - Yongmin Cho
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Alexander Tyshkovskiy
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - José P. Castro
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jesse R. Poganik
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Vadim N. Gladyshev
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Corresponding author.
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22
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Vays V, Vangeli I, Eldarov C, Popkov V, Holtze S, Hildebrandt T, Averina O, Zorov D, Bakeeva L. Unique Features of the Tissue Structure in the Naked Mole Rat ( Heterocephalus glaber): Hypertrophy of the Endoplasmic Reticulum and Spatial Mitochondrial Rearrangements in Hepatocytes. Int J Mol Sci 2022; 23:ijms23169067. [PMID: 36012332 PMCID: PMC9409344 DOI: 10.3390/ijms23169067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
The reason for the exceptional longevity of the naked mole rat (Heterocephalus glaber) remains a mystery to researchers. We assumed that evolutionarily, H. glaber acquired the ability to quickly stabilize the functioning of mitochondria and endoplasmic reticulum (ER) to adjust metabolism to external challenges. To test this, a comparison of the hepatic mitochondria and ER of H. glaber and C57BL/6 mice was done. Electron microscopy showed that 2-months-old mice have more developed rough ER (RER) than smooth ER (SER), occupying ~17 and 2.5% of the hepatocytic area correspondingly, and these values do not change with age. On the other hand, in 1-week-old H. glaber, RER occupies only 13% constantly decreasing with age, while SER occupies 35% in a 1-week-old animal, constantly rising with age. The different localization of mitochondria in H. glaber and mouse hepatocytes was confirmed by confocal and electron microscopy: while in H. glaber, mitochondria were mainly clustered around the nucleus and on the periphery of the cell, in mouse hepatocytes they were evenly distributed throughout the cell. We suggest that the noted structural and spatial features of ER and mitochondria in H. glaber reflect adaptive rearrangements aimed at greater tolerance of the cellular system to challenges, primarily hypoxia and endogenous and exogenous toxins. Different mechanisms of adaptive changes including an activated hepatic detoxification system as a hormetic response, are discussed considering the specific metabolic features of the naked mole rat.
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Affiliation(s)
- Valeriya Vays
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Irina Vangeli
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Chupalav Eldarov
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vasily Popkov
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Susanne Holtze
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Thomas Hildebrandt
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Olga Averina
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitry Zorov
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (D.Z.); (L.B.); Tel.: +7-4959395944 (D.Z. & L.B.)
| | - Lora Bakeeva
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (D.Z.); (L.B.); Tel.: +7-4959395944 (D.Z. & L.B.)
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23
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Islam M, Strawn M, Behura SK. Fetal origin of sex‐bias brain aging. FASEB J 2022; 36:e22463. [DOI: 10.1096/fj.202200255rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Maliha Islam
- Division of Animal Sciences University of Missouri Columbia Missouri USA
| | - Monica Strawn
- Division of Animal Sciences University of Missouri Columbia Missouri USA
| | - Susanta K. Behura
- Division of Animal Sciences University of Missouri Columbia Missouri USA
- MU Institute for Data Science and Informatics University of Missouri Columbia Missouri USA
- Interdisciplinary Neuroscience Program University of Missouri Columbia Missouri USA
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24
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Premont A, Saadeh K, Edling C, Lewis R, Marr CM, Jeevaratnam K. Cardiac ion channel expression in the equine model - In-silico prediction utilising RNA sequencing data from mixed tissue samples. Physiol Rep 2022; 10:e15273. [PMID: 35880716 PMCID: PMC9316921 DOI: 10.14814/phy2.15273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/19/2022] [Accepted: 04/03/2022] [Indexed: 06/15/2023] Open
Abstract
Understanding cardiomyocyte ion channel expression is crucial to understanding normal cardiac electrophysiology and underlying mechanisms of cardiac pathologies particularly arrhythmias. Hitherto, equine cardiac ion channel expression has rarely been investigated. Therefore, we aim to predict equine cardiac ion channel gene expression. Raw RNAseq data from normal horses from 9 datasets was retrieved from ArrayExpress and European Nucleotide Archive and reanalysed. The normalised (FPKM) read counts for a gene in a mix of tissue were hypothesised to be the average of the expected expression in each tissue weighted by the proportion of the tissue in the mix. The cardiac-specific expression was predicted by estimating the mean expression in each other tissues. To evaluate the performance of the model, predicted gene expression values were compared to the human cardiac gene expression. Cardiac-specific expression could be predicted for 91 ion channels including most expressed Na+ channels, K+ channels and Ca2+ -handling proteins. These revealed interesting differences from what would be expected based on human studies. These differences included predominance of NaV 1.4 rather than NaV 1.5 channel, and RYR1, SERCA1 and CASQ1 rather than RYR2, SERCA2, CASQ2 Ca2+ -handling proteins. Differences in channel expression not only implicate potentially different regulatory mechanisms but also pathological mechanisms of arrhythmogenesis.
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Affiliation(s)
- Antoine Premont
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
| | - Khalil Saadeh
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
| | - Charlotte Edling
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
| | - Rebecca Lewis
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
| | - Celia M. Marr
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
- Rossdales Equine Hospital and Diagnostic CentreExningSuffolkUK
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25
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Lu JY, Simon M, Zhao Y, Ablaeva J, Corson N, Choi Y, Yamada KYH, Schork NJ, Hood WR, Hill GE, Miller RA, Seluanov A, Gorbunova V. Comparative transcriptomics reveals circadian and pluripotency networks as two pillars of longevity regulation. Cell Metab 2022; 34:836-856.e5. [PMID: 35580607 PMCID: PMC9364679 DOI: 10.1016/j.cmet.2022.04.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/24/2022] [Accepted: 04/22/2022] [Indexed: 01/24/2023]
Abstract
Mammals differ more than 100-fold in maximum lifespan. Here, we conducted comparative transcriptomics on 26 species with diverse lifespans. We identified thousands of genes with expression levels negatively or positively correlated with a species' maximum lifespan (Neg- or Pos-MLS genes). Neg-MLS genes are primarily involved in energy metabolism and inflammation. Pos-MLS genes show enrichment in DNA repair, microtubule organization, and RNA transport. Expression of Neg- and Pos-MLS genes is modulated by interventions, including mTOR and PI3K inhibition. Regulatory networks analysis showed that Neg-MLS genes are under circadian regulation possibly to avoid persistent high expression, whereas Pos-MLS genes are targets of master pluripotency regulators OCT4 and NANOG and are upregulated during somatic cell reprogramming. Pos-MLS genes are highly expressed during embryogenesis but significantly downregulated after birth. This work provides targets for anti-aging interventions by defining pathways correlating with longevity across mammals and uncovering circadian and pluripotency networks as central regulators of longevity.
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Affiliation(s)
- J Yuyang Lu
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Nancy Corson
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yongwook Choi
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - KayLene Y H Yamada
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Nicholas J Schork
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Wendy R Hood
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, 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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26
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Ba H, Chen M, Li C. Cross-Species Analysis Reveals Co-Expressed Genes Regulating Antler Development in Cervidae. Front Genet 2022; 13:878078. [PMID: 35664330 PMCID: PMC9157503 DOI: 10.3389/fgene.2022.878078] [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: 02/17/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Antlers constitute an interesting model for basic research in regenerative biology. Despite decades of being studied, much is still unknown about the genes related to antler development. Here, we utilized both the genome and antlerogenic periosteum (AP) transcriptome data of four deer species to reveal antler-related genes through cross-species comparative analysis. The results showed that the global gene expression pattern matches the status of antler phenotypes, supporting the fact that the genes expressed in the AP may be related to antler phenotypes. The upregulated genes of the AP in three-antlered deer showed evidence of co-expression, and their protein sequences were highly conserved. These genes were growth related and likely participated in antler development. In contrast, the upregulated genes in antler-less deer (Chinese water deer) were involved mainly in organismal death and growth failure, possibly related to the loss of antlers during evolution. Overall, this study demonstrates that the co-expressed genes in antlered deer may regulate antler development.
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Affiliation(s)
- Hengxing Ba
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China.,Jilin Provincial Key Laboratory of Deer Antler Biology, Changchun, China
| | - Min Chen
- School of Life Sciences, Institute of Eco-Chongming (IEC), East China Normal University, Shanghai, China.,Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai Science and Technology Committee, Shanghai, China
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China.,College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China.,Jilin Provincial Key Laboratory of Deer Antler Biology, Changchun, China
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27
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Dickson ZW, Golding GB. Low complexity regions in mammalian proteins are associated with low protein abundance and high transcript abundance. Mol Biol Evol 2022; 39:6575407. [PMID: 35482425 PMCID: PMC9070799 DOI: 10.1093/molbev/msac087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Low Complexity Regions (LCRs) are present in a surprisingly large number of eukaryotic proteins. These highly repetitive and compositionally biased sequences are often structurally disordered, bind promiscuously, and evolve rapidly. Frequently studied in terms of evolutionary dynamics, little is known about how LCRs affect the expression of the proteins which contain them. It would be expected that rapidly evolving LCRs are unlikely to be tolerated in strongly conserved, highly abundant proteins, leading to lower overall abundance in proteins which contain LCRs. To test this hypothesis and examine the associations of protein abundance and transcript abundance with the presence of LCRs, we have integrated high-throughput data from across mammals. We have found that LCRs are indeed associated with reduced protein abundance, but are also associated with elevated transcript abundance. These associations are qualitatively consistent across 12 human tissues and nine mammalian species. The differential impacts of LCRs on abundance at the protein and transcript level are not explained by differences in either protein degradation rates or the inefficiency of translation for LCR containing proteins. We suggest that rapidly evolving LCRs are a source of selective pressure on the regulatory mechanisms which maintain steady-state protein abundance levels.
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Affiliation(s)
- Zachery W Dickson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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28
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Kaplow IM, Schäffer DE, Wirthlin ME, Lawler AJ, Brown AR, Kleyman M, Pfenning AR. Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin. BMC Genomics 2022; 23:291. [PMID: 35410163 PMCID: PMC8996547 DOI: 10.1186/s12864-022-08450-7] [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: 08/17/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Evolutionary conservation is an invaluable tool for inferring functional significance in the genome, including regions that are crucial across many species and those that have undergone convergent evolution. Computational methods to test for sequence conservation are dominated by algorithms that examine the ability of one or more nucleotides to align across large evolutionary distances. While these nucleotide alignment-based approaches have proven powerful for protein-coding genes and some non-coding elements, they fail to capture conservation of many enhancers, distal regulatory elements that control spatial and temporal patterns of gene expression. The function of enhancers is governed by a complex, often tissue- and cell type-specific code that links combinations of transcription factor binding sites and other regulation-related sequence patterns to regulatory activity. Thus, function of orthologous enhancer regions can be conserved across large evolutionary distances, even when nucleotide turnover is high. RESULTS We present a new machine learning-based approach for evaluating enhancer conservation that leverages the combinatorial sequence code of enhancer activity rather than relying on the alignment of individual nucleotides. We first train a convolutional neural network model that can predict tissue-specific open chromatin, a proxy for enhancer activity, across mammals. Next, we apply that model to distinguish instances where the genome sequence would predict conserved function versus a loss of regulatory activity in that tissue. We present criteria for systematically evaluating model performance for this task and use them to demonstrate that our models accurately predict tissue-specific conservation and divergence in open chromatin between primate and rodent species, vastly out-performing leading nucleotide alignment-based approaches. We then apply our models to predict open chromatin at orthologs of brain and liver open chromatin regions across hundreds of mammals and find that brain enhancers associated with neuron activity have a stronger tendency than the general population to have predicted lineage-specific open chromatin. CONCLUSION The framework presented here provides a mechanism to annotate tissue-specific regulatory function across hundreds of genomes and to study enhancer evolution using predicted regulatory differences rather than nucleotide-level conservation measurements.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA. .,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.,Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Michael Kleyman
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA. .,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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29
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Neuronal Phenotype of col4a1 and col25a1: An Intriguing Hypothesis in Vertebrates Brain Aging. Int J Mol Sci 2022; 23:ijms23031778. [PMID: 35163698 PMCID: PMC8836537 DOI: 10.3390/ijms23031778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022] Open
Abstract
Collagens are the most abundant proteins in vertebrates and constitute the major components of the extracellular matrix. Collagens play an important and multifaceted role in the development and functioning of the nervous system and undergo structural remodeling and quantitative modifications during aging. Here, we investigated the age-dependent regulation of col4a1 and col25a1 in the brain of the short-lived vertebrate Nothobranchius furzeri, a powerful model organism for aging research due to its natural fast-aging process and further characterized typical hallmarks of brain aging in this species. We showed that col4a1 and col25a1 are relatively well conserved during vertebrate evolution, and their expression significantly increases in the brain of N. furzeri upon aging. Noteworthy, we report that both col4a1 and col25a1 are expressed in cells with a neuronal phenotype, unlike what has already been documented in mammalian brain, in which only col25a1 is considered a neuronal marker, whereas col4a1 seems to be expressed only in endothelial cells. Overall, our findings encourage further investigation on the role of col4a1 and col25a1 in the biology of the vertebrate brain as well as the onset of aging and neurodegenerative diseases.
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30
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Besse S, Poujol R, Hussin JG. OUP accepted manuscript. Genome Biol Evol 2022; 14:6575329. [PMID: 35482036 PMCID: PMC9086952 DOI: 10.1093/gbe/evac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
The molecular mechanisms of aging and life expectancy have been studied in model organisms with short lifespans. However, long-lived species may provide insights into successful strategies for healthy aging, potentially opening the door for novel therapeutic interventions in age-related diseases. Notably, naked mole-rats, the longest-lived rodent, present attenuated aging phenotypes compared with mice. Their resistance toward oxidative stress has been proposed as one hallmark of their healthy aging, suggesting their ability to maintain cell homeostasis, specifically their protein homeostasis. To identify the general principles behind their protein homeostasis robustness, we compared the aggregation propensity and mutation tolerance of naked mole-rat and mouse orthologous proteins. Our analysis showed no proteome-wide differential effects in aggregation propensity and mutation tolerance between these species, but several subsets of proteins with a significant difference in aggregation propensity. We found an enrichment of proteins with higher aggregation propensity in naked mole-rat, and these are functionally involved in the inflammasome complex and nucleic acid binding. On the other hand, proteins with lower aggregation propensity in naked mole-rat have a significantly higher mutation tolerance compared with the rest of the proteins. Among them, we identified proteins known to be associated with neurodegenerative and age-related diseases. These findings highlight the intriguing hypothesis about the capacity of the naked mole-rat proteome to delay aging through its proteomic intrinsic architecture.
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Affiliation(s)
| | | | - Julie G. Hussin
- Institut de Cardiologie de Montréal, Québec, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, Québec, Canada
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31
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Lagunas-Rangel FA. G protein-coupled receptors that influence lifespan of human and animal models. Biogerontology 2021; 23:1-19. [PMID: 34860303 PMCID: PMC8888397 DOI: 10.1007/s10522-021-09945-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022]
Abstract
Humanity has always sought to live longer and for this, multiple strategies have been tried with varying results. In this sense, G protein-coupled receptors (GPCRs) may be a good option to try to prolong our life while maintaining good health since they have a substantial participation in a wide variety of processes of human pathophysiology and are one of the main therapeutic targets. In this way, we present the analysis of a series of GPCRs whose activity has been shown to affect the lifespan of animal and human models, and in which we put a special interest in describing the molecular mechanisms involved. Our compilation of data revealed that the mechanisms most involved in the role of GPCRs in lifespan are those that mimic dietary restriction, those related to insulin signaling and the AMPK and TOR pathways, and those that alter oxidative homeostasis and severe and/or chronic inflammation. We also discuss the possibility of using agonist or antagonist drugs, depending on the beneficial or harmful effects of each GPCR, in order to prolong people's lifespan and healthspan.
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32
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Endogenous Feline Leukemia Virus (FeLV) siRNA Transcription May Interfere with Exogenous FeLV Infection. J Virol 2021; 95:e0007021. [PMID: 34495702 DOI: 10.1128/jvi.00070-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endogenous retroviruses (ERVs) are increasingly recognized for biological impacts on host cell function and susceptibility to infectious agents, particularly in relation to interactions with exogenous retroviral progenitors (XRVs). ERVs can simultaneously promote and restrict XRV infections using mechanisms that are virus and host specific. The majority of endogenous-exogenous retroviral interactions have been evaluated in experimental mouse or chicken systems, which are limited in their ability to extend findings to naturally infected outbred animals. Feline leukemia virus (FeLV) has a relatively well-characterized endogenous retrovirus with a coexisting virulent exogenous counterpart and is endemic worldwide in domestic cats. We have previously documented an association between endogenous FeLV (enFeLV) long terminal repeat (LTR) copy number and abrogated exogenous FeLV in naturally infected cats and experimental infections in tissue culture. Analyses described here examine limited FeLV replication in experimentally infected peripheral blood mononuclear cells, which correlates with higher enFeLV transcripts in these cells compared to fibroblasts. We further examine NCBI Sequence Read Archive RNA transcripts to evaluate enFeLV transcripts and RNA interference (RNAi) precursors. We find that lymphoid-derived tissues, which are experimentally less permissive to exogenous FeLV infection, transcribe higher levels of enFeLV under basal conditions. Transcription of enFeLV-LTR segments is significantly greater than that of other enFeLV genes. We documented transcription of a 21-nucleotide (nt) microRNA (miRNA) just 3' to the enFeLV 5'-LTR in the feline miRNAome of all data sets evaluated (n = 27). Our findings point to important biological functions of enFeLV transcription linked to solo LTRs distributed within the domestic cat genome, with potential impacts on domestic cat exogenous FeLV susceptibility and pathogenesis. IMPORTANCE Endogenous retroviruses (ERVs) are increasingly implicated in host cellular processes and susceptibility to infectious agents, specifically regarding interactions with exogenous retroviral progenitors (XRVs). Exogenous feline leukemia virus (FeLV) and its endogenous counterpart (enFeLV) represent a well-characterized, naturally occurring XRV-ERV dyad. We have previously documented an abrogated FeLV infection in both naturally infected cats and experimental fibroblast infections that harbor higher enFeLV proviral loads. Using an in silico approach, we provide evidence of miRNA transcription that is produced in tissues that are most important for FeLV infection, replication, and transmission. Our findings point to important biological functions of enFeLV transcription linked to solo-LTRs distributed within the feline genome, with potential impacts on domestic cat exogenous FeLV susceptibility and pathogenesis. This body of work provides additional evidence of RNA interference (RNAi) as a mechanism of viral interference and is a demonstration of ERV exaptation by the host to defend against related XRVs.
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33
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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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Ahn E, Lee J, Han J, Lee SM, Kwon KS, Hwang GS. Glutathione is an aging-related metabolic signature in the mouse kidney. Aging (Albany NY) 2021; 13:21009-21028. [PMID: 34492635 PMCID: PMC8457589 DOI: 10.18632/aging.203509] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022]
Abstract
The ability to maintain systemic metabolic homeostasis through various mechanisms represents a crucial strength of kidneys in the study of metabolic syndrome or aging. Moreover, age-associated kidney failure has been widely accepted. However, efforts to demonstrate aging-dependent renal metabolic rewiring have been limited. In the present study, we investigated aging-related renal metabolic determinants by integrating metabolomic and transcriptomic data sets from kidneys of young (3 months, n = 7 and 3 for respectively) and old (24 months, n = 8 and 3 for respectively) naive C57BL/6 male mice. Metabolite profiling analysis was conducted, followed by data processing via network and pathway analyses, to identify differential metabolites. In the aged group, the levels of glutathione and oxidized glutathione were significantly increased, but the levels of gamma-glutamyl amino acids, amino acids combined with the gamma-glutamyl moiety from glutathione by membrane transpeptidases, and circulating glutathione levels were decreased. In transcriptomic analysis, differential expression of metabolic enzymes is consistent with the hypothesis of aging-dependent rewiring in renal glutathione metabolism; pathway and network analyses further revealed the increased expression of immune-related genes in the aged group. Collectively, our integrative analysis results revealed that defective renal glutathione metabolism is a signature of renal aging. Therefore, we hypothesize that restraining renal glutathione metabolism might alleviate or delay age-associated renal metabolic deterioration, and aberrant activation of the renal immune system.
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Affiliation(s)
- Eunyong Ahn
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seodaemun-Gu, Seoul 03759, Korea
| | - Jueun Lee
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seodaemun-Gu, Seoul 03759, Korea
| | - Jisu Han
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seodaemun-Gu, Seoul 03759, Korea
| | - Seung-Min Lee
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-Gu, Daejeon 34141, Korea
| | - Ki-Sun Kwon
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-Gu, Daejeon 34141, Korea
- Aventi Inc., Yuseong-Gu, Daejeon 34141, Korea
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seodaemun-Gu, Seoul 03759, Korea
- Department of Chemistry and Nano Science, Ewha Womans University, Seodaemun-Gu, Seoul 03760, Korea
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35
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Iwata R. Temporal differences of neurodevelopment processes between species. Neurosci Res 2021; 177:8-15. [PMID: 34419562 DOI: 10.1016/j.neures.2021.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/08/2021] [Accepted: 08/17/2021] [Indexed: 02/06/2023]
Abstract
The ontogeny programs are highly conserved across all vertebrates, although there are significant temporal variations in interspecies developmental processes. Changing the timing and rate of developmental processes could affect subsequent organogenesis profoundly and may also have been critical factors in evolutionary diversity. However, despite their potential importance, the cellular and molecular mechanisms that control interspecies differences in developmental timescale remain unclear. This review highlights recent advances in the experimental models to compare interspecies differences in neurodevelopmental processes, neurogenesis, and neuronal maturation and discusses the possible mechanisms that could generate species-specific timescales.
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Affiliation(s)
- Ryohei Iwata
- VIB KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium; Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium.
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36
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Lomas-Soria C, Cox LA, Nathanielsz PW, Zambrano E. Sexual dimorphism in liver cell cycle and senescence signalling pathways in young and old rats. J Physiol 2021; 599:4309-4320. [PMID: 34387378 DOI: 10.1113/jp281822] [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: 04/23/2021] [Accepted: 08/06/2021] [Indexed: 11/08/2022] Open
Abstract
At the molecular level, cellular ageing involves changes in multiple gene pathways. Cellular senescence is both an important initiator and a consequence of natural ageing. Senescence results in changes in multiple cellular mechanisms that result in a natural decrease in cell cycle activity. Liver senescence changes impair hepatic function. Given the well-established sexual dimorphism in ageing, we hypothesized that the natural hepatic ageing process is driven by sex-dependent gene mechanisms. We studied our well-characterized normal, chow-fed rat ageing model, lifespan ∼850 days, in which we have reported ageing of metabolism, reproduction and endocrine function. We performed liver RNA-seq on males and females at 110 and 650 days to determine changes in the cell cycle and cellular senescence signalling pathways. We found that natural liver ageing shows sexual dimorphism in these pathways. RNA-seq revealed more male (3967) than female (283) differentially expressed genes between 110 and 650 days. Cell cycle pathway signalling changes in males showed decreased protein and expression of key genes (Cdk2, Cdk4, Cycd and PCNA) and increased expression ofp57 at 650 vs 110 days. In females, protein and gene expression of cell growth regulators, e.g. p15 and p21, which inhibit cell cycle G1 progression, were increased. The cell senescence pathway also showed sexual dimorphism. Igfbp3, mTOR and p62 gene and protein expression decreased in males while those ofTgfb3 increased in females. Understanding the involvement of cell cycling and cellular senescence pathways in natural ageing will advance evaluation of mechanisms associated with altered ageing and frailty trajectories. KEY POINTS: In rats RNA-seq analysis showed sexual dimorphism in gene expression across the life-course between 110 and 650 days of life. Fourteen times more liver transcriptome and six times more pathway changes were observed in males compared with females. Significant changes were observed in several signalling pathways during ageing. Bioinformatic analysis were focused on changes in genes and protein products related to cell cycle and cellular senescence pathways. Males showed decreased protein product and expression of the key genes Cdk2 and Cdk4 responsible for cell cycle progression while females increased protein product and expression of p21 and p15, key genes responsible for cell cycle arrest. In conclusion, normative rat hepatic ageing involves changes in cellular pathways that control cell cycle arrest but through changes in different genes in males and females. These findings identify mechanisms that underlie the well-established sexual dimorphism in ageing.
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Affiliation(s)
- Consuelo Lomas-Soria
- Departamento de Biología de la Reproducción, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez, Tlalpan, Mexico, 14080, Mexico.,CONACyT-Cátedras, Departamento de Biología de la Reproducción, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez, Tlalpan, Mexico, 14080, Mexico
| | - Laura A Cox
- Department of Internal Medicine, Section on Molecular Medicine, Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Peter W Nathanielsz
- Department of Animal Science, University of Wyoming, Laramie, WY, USA.,Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Elena Zambrano
- Departamento de Biología de la Reproducción, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez, Tlalpan, Mexico, 14080, Mexico
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Ni X, Wang Z, Gao D, Yuan H, Sun L, Zhu X, Zhou Q, Yang Z. A description of the relationship in healthy longevity and aging-related disease: from gene to protein. Immun Ageing 2021; 18:30. [PMID: 34172062 PMCID: PMC8229348 DOI: 10.1186/s12979-021-00241-0] [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: 02/01/2021] [Accepted: 06/14/2021] [Indexed: 11/22/2022]
Abstract
Human longevity is a complex phenotype influenced by both genetic and environmental factors. It is also known to be associated with various types of age-related diseases, such as Alzheimer's disease (AD) and cardiovascular disease (CVD). The central dogma of molecular biology demonstrates the conversion of DNA to RNA to the encoded protein. These proteins interact to form complex cell signaling pathways, which perform various biological functions. With prolonged exposure to the environment, the in vivo homeostasis adapts to the changes, and finally, humans adopt the phenotype of longevity or aging-related diseases. In this review, we focus on two different states: longevity and aging-related diseases, including CVD and AD, to discuss the relationship between genetic characteristics, including gene variation, the level of gene expression, regulation of gene expression, the level of protein expression, both genetic and environmental influences and homeostasis based on these phenotypes shown in organisms.
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Affiliation(s)
- Xiaolin Ni
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R. China
| | - Zhaoping Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Danni Gao
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China
| | - Huiping Yuan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Liang Sun
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Xiaoquan Zhu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Qi Zhou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Ze Yang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China.
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R. China.
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38
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Plasma methionine metabolic profile is associated with longevity in mammals. Commun Biol 2021; 4:725. [PMID: 34117367 PMCID: PMC8196171 DOI: 10.1038/s42003-021-02254-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 05/20/2021] [Indexed: 01/28/2023] Open
Abstract
Methionine metabolism arises as a key target to elucidate the molecular adaptations underlying animal longevity due to the negative association between longevity and methionine content. The present study follows a comparative approach to analyse plasma methionine metabolic profile using a LC-MS/MS platform from 11 mammalian species with a longevity ranging from 3.5 to 120 years. Our findings demonstrate the existence of a species-specific plasma profile for methionine metabolism associated with longevity characterised by: i) reduced methionine, cystathionine and choline; ii) increased non-polar amino acids; iii) reduced succinate and malate; and iv) increased carnitine. Our results support the existence of plasma longevity features that might respond to an optimised energetic metabolism and intracellular structures found in long-lived species. Mota-Martorell and colleagues use a comparative metabolomics approach to examine plasma metabolite levels associated with methionine metabolism in 11 mammalian species. They identify species specific plasma profiles indicative of a link between lifetime longevity and methionine metabolism.
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39
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Pabis K, Chiari Y, Sala C, Straka E, Giacconi R, Provinciali M, Li X, Brown-Borg H, Nowikovsky K, Valencak TG, Gundacker C, Garagnani P, Malavolta M. Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging. GeroScience 2021; 43:1975-1993. [PMID: 34117600 DOI: 10.1007/s11357-021-00393-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/24/2021] [Indexed: 11/29/2022] Open
Abstract
Cadmium (Cd) accumulates with aging and is elevated in long-lived species. Metallothioneins (MTs), small cysteine-rich proteins involved in metal homeostasis and Cd detoxification, are known to be related to longevity. However, the relationship between Cd accumulation, the role of MTs, and aging is currently unclear. Specifically, we do not know if long-lived species evolved an efficient metal stress response by upregulating their MT levels to reduce the toxic effects of environmental pollutants, such as Cd, that accumulate over their longer life span. It is also unknown if the number of MT genes, their expression, or both protect the organisms from potentially damaging effects during aging. To address these questions, we reanalyzed several cross-species studies and obtained data on MT expression and Cd accumulation in long-lived mouse models. We confirmed a relationship between species maximum life span in captive mammals and their Cd content in liver and kidney. We found that although the number of MT genes does not affect longevity, gene expression and protein amount of specific MT paralogs are strongly related to life span in mammals. MT expression rather than gene number may influence the high Cd levels and longevity of some species. In support of this, we found that overexpression of MT-1 accelerated Cd accumulation in mice and that tissue Cd was higher in long-lived mouse strains with high MT expression. We conclude that long-lived species have evolved a more efficient stress response by upregulating the expression of MT genes in presence of Cd, which contributes to elevated tissue Cd levels.
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Affiliation(s)
- Kamil Pabis
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, 40126, Bologna, Italy
| | - Elisabeth Straka
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy
| | - Xinna Li
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Holly Brown-Borg
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58203, USA
| | - Karin Nowikovsky
- Department of Internal Medicine I and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Teresa G Valencak
- Department of Animal Science and Technology, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Claudia Gundacker
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), and Interdepartmental Centre "L. Galvani" (CIG), University of Bologna, Bologna, Italy.,Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy.
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40
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Common features of aging fail to occur in Drosophila raised without a bacterial microbiome. iScience 2021; 24:102703. [PMID: 34235409 PMCID: PMC8246586 DOI: 10.1016/j.isci.2021.102703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023] Open
Abstract
Lifespan is limited both by intrinsic decline in vigor with age and by accumulation of external insults. There exists a general picture of the deficits of aging, one that is reflected in a pattern of age-correlated changes in gene expression conserved across species. Here, however, by comparing gene expression profiling of Drosophila raised either conventionally, or free of bacteria, we show that ∼70% of these conserved, age-associated changes in gene expression fail to occur in germ-free flies. Among the processes that fail to show time-dependent change under germ-free conditions are two aging features that are observed across phylogeny, declining expression of stress response genes and increasing expression of innate immune genes. These comprise adaptive strategies the organism uses to respond to bacteria, rather than being inevitable components of age-dependent decline. Changes in other processes are independent of the microbiome and can serve as autonomous markers of aging of the individual.
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41
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Rayon T, Briscoe J. Cross-species comparisons and in vitro models to study tempo in development and homeostasis. Interface Focus 2021; 11:20200069. [PMID: 34055305 PMCID: PMC8086913 DOI: 10.1098/rsfs.2020.0069] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 12/14/2022] Open
Abstract
Time is inherent to biological processes. It determines the order of events and the speed at which they take place. However, we still need to refine approaches to measure the course of time in biological systems and understand what controls the pace of development. Here, we argue that the comparison of biological processes across species provides molecular insight into the timekeeping mechanisms in biology. We discuss recent findings and the open questions in the field and highlight the use of in vitro systems as tools to investigate cell-autonomous control as well as the coordination of temporal mechanisms within tissues. Further, we discuss the relevance of studying tempo for tissue transplantation, homeostasis and lifespan.
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42
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Yu Z, Seim I, Yin M, Tian R, Sun D, Ren W, Yang G, Xu S. Comparative analyses of aging-related genes in long-lived mammals provide insights into natural longevity. Innovation (N Y) 2021; 2:100108. [PMID: 34557758 PMCID: PMC8454735 DOI: 10.1016/j.xinn.2021.100108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Abstract
Extreme longevity has evolved multiple times during the evolution of mammals, yet its underlying molecular mechanisms remain largely underexplored. Here, we compared the evolution of 115 aging-related genes in 11 long-lived species and 25 mammals with non-increased lifespan (control group) in the hopes of better understanding the common molecular mechanisms behind longevity. We identified 16 unique positively selected genes and 23 rapidly evolving genes in long-lived species, which included nine genes involved in regulating lifespan through the insulin/IGF-1 signaling (IIS) pathway and 11 genes highly enriched in immune-response-related pathways, suggesting that the IIS pathway and immune response play a particularly important role in exceptional mammalian longevity. Interestingly, 11 genes related to cancer progression, including four positively selected genes and seven genes with convergent amino acid changes, were shared by two or more long-lived lineages, indicating that long-lived mammals might have evolved convergent or similar mechanisms of cancer resistance that extended their lifespan. This suggestion was further corroborated by our identification of 12 robust candidates for longevity-related genes closely related to cancer. Evolution analyses of 115 aging-related genes exploring natural longevity in mammals Positively selected genes & rapidly evolved genes enriched in IIS and immune pathways Convergent mutations in genes associated with cancer in long-lived species Evolution of longevity through cancer resistance in long-lived mammals
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Affiliation(s)
- Zhenpeng Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Inge Seim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.,Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.,School of Biology and Environmental Science, Faculty of Science and Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mengxin Yin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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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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44
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Sharma V, Hecker N, Walther F, Stuckas H, Hiller M. Convergent Losses of TLR5 Suggest Altered Extracellular Flagellin Detection in Four Mammalian Lineages. Mol Biol Evol 2021; 37:1847-1854. [PMID: 32145026 DOI: 10.1093/molbev/msaa058] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Toll-like receptors (TLRs) play an important role for the innate immune system by detecting pathogen-associated molecular patterns. TLR5 encodes the major extracellular receptor for bacterial flagellin and frequently evolves under positive selection, consistent with coevolutionary arms races between the host and pathogens. Furthermore, TLR5 is inactivated in several vertebrates and a TLR5 stop codon polymorphism is widespread in human populations. Here, we analyzed the genomes of 120 mammals and discovered that TLR5 is convergently lost in four independent lineages, comprising guinea pigs, Yangtze river dolphin, pinnipeds, and pangolins. Validated inactivating mutations, absence of protein-coding transcript expression, and relaxed selection on the TLR5 remnants confirm these losses. PCR analysis further confirmed the loss of TLR5 in the pinniped stem lineage. Finally, we show that TLR11, encoding a second extracellular flagellin receptor, is also absent in these four lineages. Independent losses of TLR5 and TLR11 suggest that a major pathway for detecting flagellated bacteria is not essential for different mammals and predicts an impaired capacity to sense extracellular flagellin.
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Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,CRTD-DFG Center for Regenerative Therapies Dresden, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden; German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Felix Walther
- Senckenberg Natural History Collections Dresden, Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Heiko Stuckas
- Senckenberg Natural History Collections Dresden, Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
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45
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Fuentealba M, Fabian DK, Dönertaş HM, Thornton JM, Partridge L. Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice. Mech Ageing Dev 2021; 194:111437. [PMID: 33454277 PMCID: PMC7895802 DOI: 10.1016/j.mad.2021.111437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/09/2020] [Accepted: 01/11/2021] [Indexed: 12/21/2022]
Abstract
Genetically modified mouse models of ageing are the living proof that lifespan and healthspan can be lengthened or shortened, and provide a powerful context in which to unravel the molecular mechanisms at work. In this study, we analysed and compared gene expression data from 10 long-lived and 8 short-lived mouse models of ageing. Transcriptome-wide correlation analysis revealed that mutations with equivalent effects on lifespan induce more similar transcriptomic changes, especially if they target the same pathway. Using functional enrichment analysis, we identified 58 gene sets with consistent changes in long- and short-lived mice, 55 of which were up-regulated in long-lived mice and down-regulated in short-lived mice. Half of these sets represented genes involved in energy and lipid metabolism, among which Ppargc1a, Mif, Aldh5a1 and Idh1 were frequently observed. Based on the gene sets with consistent changes, and also the whole transcriptome, the gene expression changes during normal ageing resembled the transcriptome of short-lived models, suggesting that accelerated ageing models reproduce partially the molecular changes of ageing. Finally, we identified new genetic interventions that may ameliorate ageing, by comparing the transcriptomes of 51 mouse mutants not previously associated with ageing to expression signatures of long- and short-lived mice and ageing-related changes.
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Affiliation(s)
- Matias Fuentealba
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Daniel K Fabian
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Linda Partridge
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK; Max Planck Institute for Biology of Ageing, Cologne, Germany.
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46
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Augereau A, Mariotti M, Pousse M, Filipponi D, Libert F, Beck B, Gorbunova V, Gilson E, Gladyshev VN. Naked mole rat TRF1 safeguards glycolytic capacity and telomere replication under low oxygen. SCIENCE ADVANCES 2021; 7:eabe0174. [PMID: 33608273 PMCID: PMC7895426 DOI: 10.1126/sciadv.abe0174] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/06/2021] [Indexed: 05/31/2023]
Abstract
The naked mole rat (NMR), a long-lived and cancer-resistant rodent, is highly resistant to hypoxia. Here, using robust cellular models wherein the mouse telomeric protein TRF1 is substituted by NMR TRF1 or its mutant forms, we show that TRF1 supports maximal glycolytic capacity under low oxygen, shows increased nuclear localization and association with telomeres, and protects telomeres from replicative stress. We pinpoint this evolutionary gain of metabolic function to specific amino acid changes in the homodimerization domain of this protein. We further find that NMR TRF1 accelerates telomere shortening. These findings reveal an evolutionary strategy to adapt telomere biology for metabolic control under an extreme environment.
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Affiliation(s)
- Adeline Augereau
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mélanie Pousse
- Université Côte d'Azur, CNRS, Inserm, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Doria Filipponi
- Université Côte d'Azur, CNRS, Inserm, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Frédérick Libert
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | | | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
- Department of Medical Genetics, Archet 2 Hospital, CHU of Nice, FHU Oncoage, 06107 Nice, France
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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47
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Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, de Farias TM, Moretti S, Parmentier G, de Laval VR, Rosikiewicz M, Wollbrett J, Echchiki A, Escoriza A, Gharib WH, Gonzales-Porta M, Jarosz Y, Laurenczy B, Moret P, Person E, Roelli P, Sanjeev K, Seppey M, Robinson-Rechavi M. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Nucleic Acids Res 2021; 49:D831-D847. [PMID: 33037820 PMCID: PMC7778977 DOI: 10.1093/nar/gkaa793] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/24/2020] [Accepted: 09/15/2020] [Indexed: 01/24/2023] Open
Abstract
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as ‘healthy’ or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.
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Affiliation(s)
- Frederic B Bastian
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Julien Roux
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Anne Niknejad
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Aurélie Comte
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Sara S Fonseca Costa
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tarcisio Mendes de Farias
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Sébastien Moretti
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Gilles Parmentier
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Valentine Rech de Laval
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Marta Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Julien Wollbrett
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Amina Echchiki
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Angélique Escoriza
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Walid H Gharib
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Mar Gonzales-Porta
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Yohan Jarosz
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Balazs Laurenczy
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Philippe Moret
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Emilie Person
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Patrick Roelli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Komal Sanjeev
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Mathieu Seppey
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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48
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Kulaga AY, Ursu E, Toren D, Tyshchenko V, Guinea R, Pushkova M, Fraifeld VE, Tacutu R. Machine Learning Analysis of Longevity-Associated Gene Expression Landscapes in Mammals. Int J Mol Sci 2021; 22:1073. [PMID: 33499037 PMCID: PMC7865694 DOI: 10.3390/ijms22031073] [Citation(s) in RCA: 3] [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: 12/15/2020] [Revised: 01/16/2021] [Accepted: 01/20/2021] [Indexed: 12/28/2022] Open
Abstract
One of the important questions in aging research is how differences in transcriptomics are associated with the longevity of various species. Unfortunately, at the level of individual genes, the links between expression in different organs and maximum lifespan (MLS) are yet to be fully understood. Analyses are complicated further by the fact that MLS is highly associated with other confounding factors (metabolic rate, gestation period, body mass, etc.) and that linear models may be limiting. Using gene expression from 41 mammalian species, across five organs, we constructed gene-centric regression models associating gene expression with MLS and other species traits. Additionally, we used SHapley Additive exPlanations and Bayesian networks to investigate the non-linear nature of the interrelations between the genes predicted to be determinants of species MLS. Our results revealed that expression patterns correlate with MLS, some across organs, and others in an organ-specific manner. The combination of methods employed revealed gene signatures formed by only a few genes that are highly predictive towards MLS, which could be used to identify novel longevity regulator candidates in mammals.
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Affiliation(s)
- Anton Y. Kulaga
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
- International Longevity Alliance, 92330 Sceaux, France
- CellFabrik SRL, 060512 Bucharest, Romania
| | - Eugen Ursu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
| | - Dmitri Toren
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel;
| | | | - Rodrigo Guinea
- Escuela de Postgrado, Pontificia Universidad Católica del Perú, 15023 San Miguel, Peru;
| | - Malvina Pushkova
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel;
| | - Robi Tacutu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
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49
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Bonnefont J, Vanderhaeghen P. Neuronal fate acquisition and specification: time for a change. Curr Opin Neurobiol 2021; 66:195-204. [PMID: 33412482 PMCID: PMC8064025 DOI: 10.1016/j.conb.2020.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
During embryonic development, neural stem/progenitor cells generate hundreds of different cell types through the combination of intrinsic and extrinsic cues. Recent data obtained in mouse and human cortical neurogenesis provide novel views about this interplay and how it evolves with time, whether during irreversible cell fate transitions that neural stem cells undergo to become neurons, or through gradual temporal changes of competence that lead to increased neuronal diversity from a common stem cell pool. In each case the temporal changes result from a dynamic balance between intracellular states and extracellular signalling factors. The underlying mechanisms are mostly conserved across species, but some display unique features in human corticogenesis, thereby linking temporal features of neurogenesis and human brain evolution.
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Affiliation(s)
- Jérôme Bonnefont
- Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium; VIB-KULeuven Center for Brain & Disease Research, KULeuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
| | - Pierre Vanderhaeghen
- Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium; VIB-KULeuven Center for Brain & Disease Research, KULeuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
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50
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Sun K, Gu L, Ma L, Duan Y. Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2. Heliyon 2021; 7:e05850. [PMID: 33392409 PMCID: PMC7762714 DOI: 10.1016/j.heliyon.2020.e05850] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/03/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
The recent pandemic, COVID-19, is caused by a novel coronavirus, SARS-CoV-2, with elusive origin. SARS-CoV-2 infects mammalian cells via ACE2, a transmembrane protein. Therefore, the conservation and expression patterns of ACE2 may provide valuable insights into tracing the carriers of SARS-CoV-2. In this work, we analyzed the conservation of ACE2 and its expression pattern among various mammalian species that are close to human beings. We show that mammalian ACE2 gene is deeply conserved at both DNA and peptide levels, suggesting that a broad range of mammals can potentially host SARS-CoV-2. We further report that ACE2 expression in certain human tissues are consistent with clinical symptoms of COVID-19 patients. Furthermore, we have built the first atlas of ACE2 expression in various common mammals, which shows that ACE2 expresses in mammalian tissues in a species-specific manner. Most notably, we observe exceptionally high expression of ACE2 in external body parts of cats and dogs, suggesting that these household pet animals could be vulnerable to viral infections and/or may serve as intermediate hosts, thus yielding novel insights into the transmission of SARS-CoV-2.
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Affiliation(s)
- Kun Sun
- Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Liuqi Gu
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS, 66045, USA
- Beijing Huayuan Academy of Biotechnology, Beijing, 100192, China
| | - Li Ma
- Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Yunfeng Duan
- Beijing Huayuan Academy of Biotechnology, Beijing, 100192, China
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