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Coler-Reilly A, Pincus Z, Scheller EL, Civitelli R. Six drivers of aging identified among genes differentially expressed with age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606402. [PMID: 39149379 PMCID: PMC11326176 DOI: 10.1101/2024.08.02.606402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Many studies have compared gene expression in young and old samples to gain insights on aging, the primary risk factor for most major chronic diseases. However, these studies only describe associations, failing to distinguish drivers of aging from compensatory geroprotective responses and incidental downstream effects. Here, we introduce a workflow to characterize the causal effects of differentially expressed genes on lifespan. First, we performed a meta-analysis of 25 gene expression datasets comprising samples of various tissues from healthy, untreated adult mammals (humans, dogs, and rodents) at two distinct ages. We ranked each gene according to the number of distinct datasets in which the gene was differentially expressed with age in a consistent direction. The top age-upregulated genes were TMEM176A, EFEMP1, CP, and HLA-A; the top age-downregulated genes were CA4, SIAH, SPARC, and UQCR10. Second, the effects of the top ranked genes on lifespan were measured by applying post-developmental RNA interference of the corresponding ortholog in the nematode C. elegans (two trials, with roughly 100 animals per genotype per trial). Out of 10 age-upregulated and 9 age-downregulated genes that were tested, two age-upregulated genes (csp-3/CASP1 and spch-2/RSRC1) and four age-downregulated genes (C42C1.8/DIRC2, ost-1/SPARC, fzy-1/CDC20, and cah-3/CA4) produced significant and reproducible lifespan extension. Notably, the data do not suggest that the direction of differential expression with age is predictive of the effect on lifespan. Our study provides novel insight into the relationship between differential gene expression and aging phenotypes, pilots an unbiased workflow that can be easily repeated and expanded, and pinpoints six genes with evolutionarily conserved, causal roles in the aging process for further study.
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Affiliation(s)
- Ariella Coler-Reilly
- Division of Bone and Mineral Diseases, Musculoskeletal Research Center
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA
| | - Zachary Pincus
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Erica L. Scheller
- Division of Bone and Mineral Diseases, Musculoskeletal Research Center
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology; Washington University School of Medicine, St. Louis, MO, USA
| | - Roberto Civitelli
- Division of Bone and Mineral Diseases, Musculoskeletal Research Center
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology; Washington University School of Medicine, St. Louis, MO, USA
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2
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Turner CD, Stuhr NL, Ramos CM, Van Camp BT, Curran SP. A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons. Proc Natl Acad Sci U S A 2023; 120:e2308565120. [PMID: 38113255 PMCID: PMC10756303 DOI: 10.1073/pnas.2308565120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/02/2023] [Indexed: 12/21/2023] Open
Abstract
Coordination of cellular responses to stress is essential for health across the lifespan. The transcription factor SKN-1 is an essential homeostat that mediates survival in stress-inducing environments and cellular dysfunction, but constitutive activation of SKN-1 drives premature aging thus revealing the importance of turning off cytoprotective pathways. Here, we identify how SKN-1 activation in two ciliated ASI neurons in Caenorhabditis elegans results in an increase in organismal transcriptional capacity that drives pleiotropic outcomes in peripheral tissues. An increase in the expression of established SKN-1 stress response and lipid metabolism gene classes of RNA in the ASI neurons, in addition to the increased expression of several classes of noncoding RNA, define a molecular signature of animals with constitutive SKN-1 activation and diminished healthspan. We reveal neddylation as a unique regulator of the SKN-1 homeostat that mediates SKN-1 abundance within intestinal cells. Moreover, RNAi-independent activity of the dicer-related DExD/H-box helicase, drh-1, in the intestine, can oppose the effects of aberrant SKN-1 transcriptional activation and delays age-dependent decline in health. Taken together, our results uncover a cell nonautonomous circuit to maintain organism-level homeostasis in response to excessive SKN-1 transcriptional activity in the sensory nervous system.
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Affiliation(s)
- Chris D. Turner
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Nicole L. Stuhr
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Carmen M. Ramos
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Bennett T. Van Camp
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Sean P. Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
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3
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Turner CD, Stuhr NL, Ramos CM, Van Camp BT, Curran SP. A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.01.560409. [PMID: 37873147 PMCID: PMC10592859 DOI: 10.1101/2023.10.01.560409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Coordination of cellular responses to stress are essential for health across the lifespan. The transcription factor SKN-1 is an essential homeostat that mediates survival in stress-inducing environments and cellular dysfunction, but constitutive activation of SKN-1 drives premature aging thus revealing the importance of turning off cytoprotective pathways. Here we identify how SKN-1 activation in two ciliated ASI neurons in C. elegans results in an increase in organismal transcriptional capacity that drives pleiotropic outcomes in peripheral tissues. An increase in the expression of established SKN-1 stress response and lipid metabolism gene classes of RNA in the ASI neurons, in addition to the increased expression of several classes of non-coding RNA, define a molecular signature of animals with constitutive SKN-1 activation and diminished healthspan. We reveal neddylation as a novel regulator of the SKN-1 homeostat that mediates SKN-1 abundance within intestinal cells. Moreover, RNAi-independent activity of the dicer-related DExD/H-box helicase, drh-1 , in the intestine, can oppose the e2ffects of aberrant SKN-1 transcriptional activation and delays age-dependent decline in health. Taken together, our results uncover a cell non-autonomous circuit to maintain organism-level homeostasis in response to excessive SKN-1 transcriptional activity in the sensory nervous system. SIGNIFICANCE STATEMENT Unlike activation, an understudied fundamental question across biological systems is how to deactivate a pathway, process, or enzyme after it has been turned on. The irony that the activation of a transcription factor that is meant to be protective can diminish health was first documented by us at the organismal level over a decade ago, but it has long been appreciated that chronic activation of the human ortholog of SKN-1, NRF2, could lead to chemo- and radiation resistance in cancer cells. A colloquial analogy to this biological idea is a sink faucet that has an on valve without a mechanism to shut the water off, which will cause the sink to overflow. Here, we define this off valve.
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4
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Roux AE, Yuan H, Podshivalova K, Hendrickson D, Kerr R, Kenyon C, Kelley D. Individual cell types in C. elegans age differently and activate distinct cell-protective responses. Cell Rep 2023; 42:112902. [PMID: 37531250 DOI: 10.1016/j.celrep.2023.112902] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/17/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023] Open
Abstract
Aging is characterized by a global decline in physiological function. However, by constructing a complete single-cell gene expression atlas, we find that Caenorhabditis elegans aging is not random in nature but instead is characterized by coordinated changes in functionally related metabolic, proteostasis, and stress-response genes in a cell-type-specific fashion, with downregulation of energy metabolism being the only nearly universal change. Similarly, the rates at which cells age differ significantly between cell types. In some cell types, aging is characterized by an increase in cell-to-cell variance, whereas in others, variance actually decreases. Remarkably, multiple resilience-enhancing transcription factors known to extend lifespan are activated across many cell types with age; we discovered new longevity candidates, such as GEI-3, among these. Together, our findings suggest that cells do not age passively but instead react strongly, and individualistically, to events that occur during aging. This atlas can be queried through a public interface.
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Affiliation(s)
| | - Han Yuan
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | | | - Rex Kerr
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Cynthia Kenyon
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
| | - David Kelley
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
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5
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Bapteste E, Huneman P, Keller L, Teulière J, Lopez P, Teeling EC, Lindner AB, Baudisch A, Ludington WB, Franceschi C. Expanding evolutionary theories of ageing to better account for symbioses and interactions throughout the Web of Life. Ageing Res Rev 2023; 89:101982. [PMID: 37321383 PMCID: PMC10771319 DOI: 10.1016/j.arr.2023.101982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/26/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023]
Abstract
How, when, and why organisms age are fascinating issues that can only be fully addressed by adopting an evolutionary perspective. Consistently, the main evolutionary theories of ageing, namely the Mutation Accumulation theory, the Antagonistic Pleiotropy theory, and the Disposable Soma theory, have formulated stimulating hypotheses that structure current debates on both the proximal and ultimate causes of organismal ageing. However, all these theories leave a common area of biology relatively under-explored. The Mutation Accumulation theory and the Antagonistic Pleiotropy theory were developed under the traditional framework of population genetics, and therefore are logically centred on the ageing of individuals within a population. The Disposable Soma theory, based on principles of optimising physiology, mainly explains ageing within a species. Consequently, current leading evolutionary theories of ageing do not explicitly model the countless interspecific and ecological interactions, such as symbioses and host-microbiomes associations, increasingly recognized to shape organismal evolution across the Web of Life. Moreover, the development of network modelling supporting a deeper understanding on the molecular interactions associated with ageing within and between organisms is also bringing forward new questions regarding how and why molecular pathways associated with ageing evolved. Here, we take an evolutionary perspective to examine the effects of organismal interactions on ageing across different levels of biological organisation, and consider the impact of surrounding and nested systems on organismal ageing. We also apply this perspective to suggest open issues with potential to expand the standard evolutionary theories of ageing.
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Affiliation(s)
- Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
| | - Philippe Huneman
- Institut d'Histoire et de Philosophie des Sciences et des Techniques (CNRS/ Université Paris I Sorbonne), Paris, France
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
| | - Annette Baudisch
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, 5230 Odense M, Denmark
| | - William B Ludington
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; Department of Applied Mathematics and Laboratory of Systems Medicine of Aging, Lobachevsky University, Nizhny Novgorod 603950, Russia
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6
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Lazaro-Pena MI, Cornwell AB, Diaz-Balzac CA, Das R, Macoretta N, Thakar J, Samuelson AV. Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal Caenorhabditis elegans aging and systemically regulates longevity from serotonergic and GABAergic neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523661. [PMID: 36711523 PMCID: PMC9882034 DOI: 10.1101/2023.01.11.523661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Aging and the age-associated decline of the proteome is determined in part through neuronal control of evolutionarily conserved transcriptional effectors, which safeguard homeostasis under fluctuating metabolic and stress conditions by regulating an expansive proteostatic network. We have discovered the Caenorhabditis elegans h omeodomain-interacting p rotein k inase (HPK-1) acts as a key transcriptional effector to preserve neuronal integrity, function, and proteostasis during aging. Loss of hpk-1 results in drastic dysregulation in expression of neuronal genes, including genes associated with neuronal aging. During normal aging hpk-1 expression increases throughout the nervous system more broadly than any other kinase. Within the aging nervous system, hpk-1 is co-expressed with key longevity transcription factors, including daf-16 (FOXO), hlh-30 (TFEB), skn-1 (Nrf2), and hif-1 , which suggests hpk-1 expression mitigates natural age-associated physiological decline. Consistently, pan-neuronal overexpression of hpk-1 extends longevity, preserves proteostasis both within and outside of the nervous system, and improves stress resistance. Neuronal HPK-1 improves proteostasis through kinase activity. HPK-1 functions cell non-autonomously within serotonergic and GABAergic neurons to improve proteostasis in distal tissues by specifically regulating distinct components of the proteostatic network. Increased serotonergic HPK-1 enhances the heat shock response and survival to acute stress. In contrast, GABAergic HPK-1 induces basal autophagy and extends longevity. Our work establishes hpk-1 as a key neuronal transcriptional regulator critical for preservation of neuronal function during aging. Further, these data provide novel insight as to how the nervous system partitions acute and chronic adaptive response pathways to delay aging by maintaining organismal homeostasis.
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7
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Teulière J, Bernard C, Corel E, Lapointe FJ, Martens J, Lopez P, Bapteste E. Network analyses unveil ageing-associated pathways evolutionarily conserved from fungi to animals. GeroScience 2022; 45:1059-1080. [PMID: 36508078 PMCID: PMC9886728 DOI: 10.1007/s11357-022-00704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
The genetic roots of the diverse paces and shapes of ageing and of the large variations in longevity observed across the tree of life are poorly understood. Indeed, pathways associated with ageing/longevity are incompletely known, both in terms of their constitutive genes/proteins and of their molecular interactions. Moreover, there is limited overlap between the genes constituting these pathways across mammals. Yet, dedicated comparative analyses might still unravel evolutionarily conserved, important pathways associated with longevity or ageing. Here, we used an original strategy with a double evolutionary and systemic focus to analyse protein interactions associated with ageing or longevity during the evolution of five species of Opisthokonta. We ranked these proteins and interactions based on their evolutionary conservation and centrality in past and present protein-protein interaction (PPI) networks, providing a big systemic picture of the evolution of ageing and longevity pathways that identified which pathways emerged in which Opisthokonta lineages, were conserved, and/or central. We confirmed that longevity/ageing-associated proteins (LAPs), be they pro- or anti-longevity, are highly central in extant PPI, consistently with the antagonistic pleiotropy theory of ageing, and identified key antagonistic regulators of ageing/longevity, 52 of which with homologues in humans. While some highly central LAPs were evolutionarily conserved for over a billion years, we report a clear transition in the functionally important components of ageing/longevity within bilaterians. We also predicted 487 novel evolutionarily conserved LAPs in humans, 54% of which are more central than mTOR, and 138 of which are druggable, defining new potential targets for anti-ageing treatments in humans.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eduardo Corel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - François-Joseph Lapointe
- grid.14848.310000 0001 2292 3357Département de Sciences Biologiques, Complexe Des Sciences, Université de Montréal, Montréal, QC Canada
| | - Johannes Martens
- Sciences, Normes, Démocratie (SND), Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France.
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8
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Oz N, Vayndorf EM, Tsuchiya M, McLean S, Turcios-Hernandez L, Pitt JN, Blue BW, Muir M, Kiflezghi MG, Tyshkovskiy A, Mendenhall A, Kaeberlein M, Kaya A. Evidence that conserved essential genes are enriched for pro-longevity factors. GeroScience 2022; 44:1995-2006. [PMID: 35695982 PMCID: PMC9616985 DOI: 10.1007/s11357-022-00604-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/03/2022] [Indexed: 02/02/2023] Open
Abstract
At the cellular level, many aspects of aging are conserved across species. This has been demonstrated by numerous studies in simple model organisms like Saccharomyces cerevisiae, Caenorhabdits elegans, and Drosophila melanogaster. Because most genetic screens examine loss of function mutations or decreased expression of genes through reverse genetics, essential genes have often been overlooked as potential modulators of the aging process. By taking the approach of increasing the expression level of a subset of conserved essential genes, we found that 21% of these genes resulted in increased replicative lifespan in S. cerevisiae. This is greater than the ~ 3.5% of genes found to affect lifespan upon deletion, suggesting that activation of essential genes may have a relatively disproportionate effect on increasing lifespan. The results of our experiments demonstrate that essential gene overexpression is a rich, relatively unexplored means of increasing eukaryotic lifespan.
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Affiliation(s)
- Naci Oz
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Elena M Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Mitsuhiro Tsuchiya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Samantha McLean
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | - Jason N Pitt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin W Blue
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael Muir
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael G Kiflezghi
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander Mendenhall
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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9
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Curran SP, Lithgow GJ, Verdin E, P C. University of Southern California and buck institute nathan shock center: multidimensional models of aging. GeroScience 2021; 43:2119-2127. [PMID: 34269983 PMCID: PMC8599784 DOI: 10.1007/s11357-021-00416-z] [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: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022] Open
Abstract
The USC-Buck Nathan Shock Center of Excellence in the Biology of Aging is a new and fully integrated multi-institutional center focused on training the next generation of geroscientists and providing access to cutting-edge geroscience technologies to investigators across the nation. The USC-Buck NSC is devoted to forging a deeper understanding of how and why aging processes cause disease in order to advance the translation of basic research on aging into effective preventions and therapies. Including more than 61 NIA-supported investigators, six NIA-funded research centers, four NIA T32s, and several additional aging research centers of excellence, the USC-Buck NSC constitutes one of the largest collections of leaders in geroscience research within the USA; the unique nature of the USC-Buck NSC research infrastructure ensures an integrated organization that is representative of the wide breadth of topics encompassed by the biology of aging field. By leveraging the 25-year-long relationship, current collaborations and joint administrational activities of the University of Southern California and the Buck Institute for Aging Research, the USC-Buck NSC aims to enhance and expand promising research in the biology of aging at both at the and to make a positive impact across California, the nation and throughout the world. Specialized cores provide services to all Shock Center members, as well as provide support for services to the community at large.
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Affiliation(s)
- Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, USA.
| | | | - Eric Verdin
- Buck Institute for Research On Aging, Novato, CA, USA
- UCSF Department of Medicine, San Francisco, CA, USA
| | - Cohen P
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, USA
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10
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Matei IV, Samukange VNC, Bunu G, Toren D, Ghenea S, Tacutu R. Knock-down of odr-3 and ife-2 additively extends lifespan and healthspan in C. elegans. Aging (Albany NY) 2021; 13:21040-21065. [PMID: 34506301 PMCID: PMC8457566 DOI: 10.18632/aging.203518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023]
Abstract
Genetic manipulations can ameliorate the aging process and extend the lifespan of model organisms. The aim of this research was to identify novel genetic interventions that promote both lifespan and healthspan, by combining the effects of multiple longevity-associated gene inactivations in C. elegans. For this, the individual and combined effects of the odr-3 mutation and of ife-2 and cku-70 knock-downs were studied, both in the wild type and daf-16 mutant backgrounds. We found that besides increasing the lifespan of wild type animals, the knock-down of ife-2 (starting at L4) also extends the lifespan and healthspan of long-lived odr-3 mutants. In the daf-16 background, ife-2 and odr-3 impairment exert opposing effects individually, while the daf-16; odr-3; ife-2 deficient animals show a similar lifespan and healthspan as daf-16, suggesting that the odr-3 and ife-2 effector outcomes converge downstream of DAF-16. By contrast, cku-70 knock-down did not extend the lifespan of single or double odr-3; ife-2 inactivated animals, and was slightly deleterious to healthspan. In conclusion, we report that impairment of odr-3 and ife-2 increases lifespan and healthspan in an additive and synergistic manner, respectively, and that this result is not improved by further knocking-down cku-70.
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Affiliation(s)
- Ioan Valentin Matei
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | | | - Gabriela Bunu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Dmitri Toren
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Simona Ghenea
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Robi Tacutu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
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11
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Podder A, Raju A, Schork NJ. Cross-Species and Human Inter-Tissue Network Analysis of Genes Implicated in Longevity and Aging Reveal Strong Support for Nutrient Sensing. Front Genet 2021; 12:719713. [PMID: 34512728 PMCID: PMC8430347 DOI: 10.3389/fgene.2021.719713] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/10/2021] [Indexed: 12/22/2022] Open
Abstract
Intensive research efforts have been undertaken to slow human aging and therefore potentially delay the onset of age-related diseases. These efforts have generated an enormous amount of high-throughput data covering different levels in the physiologic hierarchy, e.g., genetic, epigenetic, transcriptomic, proteomic, and metabolomic, etc. We gathered 15 independent sources of information about genes potentially involved in human longevity and lifespan (N = 5836) and subjected them to various integrated analyses. Many of these genes were initially identified in non-human species, and we investigated their orthologs in three non-human species [i.e., mice (N = 967), fruit fly (N = 449), and worm (N = 411)] for further analysis. We characterized experimentally determined protein-protein interaction networks (PPIN) involving each species' genes from 9 known protein databases and studied the enriched biological pathways among the individually constructed PPINs. We observed three important signaling pathways: FoxO signaling, mTOR signaling, and autophagy to be common and highly enriched in all four species (p-value ≤ 0.001). Our study implies that the interaction of proteins involved in the mechanistic target of rapamycin (mTOR) signaling pathway is somewhat limited to each species or that a "rewiring" of specific networks has taken place over time. To corroborate our findings, we repeated our analysis in 43 different human tissues. We investigated conserved modules in various tissue-specific PPINs of the longevity-associated genes based upon their protein expression. This analysis also revealed mTOR signaling as shared biological processes across four different human tissue-specific PPINs for liver, heart, skeletal muscle, and adipose tissue. Further, we explored our results' translational potential by assessing the protein interactions with all the reported drugs and compounds that have been experimentally verified to promote longevity in the three-comparator species. We observed that the target proteins of the FDA-approved drug rapamycin (a known inhibitor of mTOR) were conserved across all four species. Drugs like melatonin and metformin exhibited shared targets with rapamycin in the human PPIN. The detailed information about the curated gene list, cross-species orthologs, PPIN, and pathways was assembled in an interactive data visualization portal using RStudio's Shiny framework (https://agingnetwork.shinyapps.io/frontiers/).
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Affiliation(s)
- Avijit Podder
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Anish Raju
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Nicholas J. Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
- Department of Population Sciences and Molecular and Cell Biology, The City of Hope National Medical Center, Duarte, CA, United States
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12
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Analysis of aging-related protein interactome and cross-network module comparisons across tissues provide new insights into aging. Comput Biol Chem 2021; 92:107506. [PMID: 34020164 DOI: 10.1016/j.compbiolchem.2021.107506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/09/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022]
Abstract
Delaying the human aging process and thus eliminating the risk factors for age-related diseases is one of the prime objectives. While various aging-associated genes and proteins have been characterized, which provide a significant understanding of the human aging process, a significant success in regulating aging is not achieved yet. Understanding how aging proteins interact with each other and also with other proteins could provide important insights into the underlying mechanisms governing the aging process. Therefore, in this work, information of gene expression was included to the static aging-related protein interactome to understand the network-based relationships among aging-related essential (AE) proteins, aging-related non-essential (ANE) proteins, and housekeeping-proteins that could regulate or influence aging. Comprehensive analyses provided various systems-level insights into the regulatory characteristics of aging; for example, (i) network-based correlation analysis predicted functional relationships among AE proteins and ANE proteins; (ii) network variability analysis predicted aging to affect different tissues in strikingly different ways by differentially regulating various regulatory interactions; (iii) cross-network comparisons identified two aging-related modules to be significantly conserved across most of the tissues. Overall, the findings obtained during this study could be helpful for researchers to delay, prevent, or even reverse various aspects of the aging.
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13
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Network analysis in aged C. elegans reveals candidate regulatory genes of ageing. Biogerontology 2021; 22:345-367. [PMID: 33871732 DOI: 10.1007/s10522-021-09920-3] [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: 12/17/2020] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Ageing is a biological process guided by genetic and environmental factors that ultimately lead to adverse outcomes for organismal lifespan and healthspan. Determination of molecular pathways that are affected with age and increase disease susceptibility is crucial. The gene expression profile of the ideal ageing model, namely the nematode Caenorhabditis elegans mapped with the microarray technology initially led to the identification of age-dependent gene expression alterations that characterize the nematode's ageing process. The list of differentially expressed genes was then utilized to construct a network of molecular interactions with their first neighbors/interactors using the interactions listed in the WormBase database. The subsequent network analysis resulted in the unbiased selection of 110 candidate genes, among which well-known ageing regulators appeared. More importantly, our approach revealed candidates that have never been linked to ageing before, thus suggesting promising potential targets/ageing regulators.
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14
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Stuhr NL, Curran SP. Bacterial diets differentially alter lifespan and healthspan trajectories in C. elegans. Commun Biol 2020; 3:653. [PMID: 33159120 PMCID: PMC7648844 DOI: 10.1038/s42003-020-01379-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/14/2020] [Indexed: 01/21/2023] Open
Abstract
Diet is one of the more variable aspects in life due to the variety of options that organisms are exposed to in their natural habitats. In the laboratory, C. elegans are raised on bacterial monocultures, traditionally the E. coli B strain OP50, and spontaneously occurring microbial contaminants are removed to limit experimental variability because diet-including the presence of contaminants-can exert a potent influence over animal physiology. In order to diversify the menu available to culture C. elegans in the lab, we have isolated and cultured three such microbes: Methylobacterium, Xanthomonas, and Sphingomonas. The nutritional composition of these bacterial foods is unique, and when fed to C. elegans, can differentially alter multiple life history traits including development, reproduction, and metabolism. In light of the influence each food source has on specific physiological attributes, we comprehensively assessed the impact of these bacteria on animal health and devised a blueprint for utilizing different food combinations over the lifespan, in order to promote longevity. The expansion of the bacterial food options to use in the laboratory will provide a critical tool to better understand the complexities of bacterial diets and subsequent changes in physiology and gene expression.
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Affiliation(s)
- Nicole L Stuhr
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
- Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA.
- Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
- Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Ave, Los Angeles, CA, 90033, USA.
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15
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Bunu G, Toren D, Ion CF, Barardo D, Sârghie L, Grigore LG, de Magalhães JP, Fraifeld VE, Tacutu R. SynergyAge, a curated database for synergistic and antagonistic interactions of longevity-associated genes. Sci Data 2020; 7:366. [PMID: 33106474 PMCID: PMC7589469 DOI: 10.1038/s41597-020-00710-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
Interventional studies on genetic modulators of longevity have significantly changed gerontology. While available lifespan data are continually accumulating, further understanding of the aging process is still limited by the poor understanding of epistasis and of the non-linear interactions between multiple longevity-associated genes. Unfortunately, based on observations so far, there is no simple method to predict the cumulative impact of genes on lifespan. As a step towards applying predictive methods, but also to provide information for a guided design of epistasis lifespan experiments, we developed SynergyAge - a database containing genetic and lifespan data for animal models obtained through multiple longevity-modulating interventions. The studies included in SynergyAge focus on the lifespan of animal strains which are modified by at least two genetic interventions, with single gene mutants included as reference. SynergyAge, which is publicly available at www.synergyage.info , provides an easy to use web-platform for browsing, searching and filtering through the data, as well as a network-based interactive module for visualization and analysis.
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Affiliation(s)
- Gabriela Bunu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Dmitri Toren
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Catalin-Florentin Ion
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Diogo Barardo
- Science Divisions, Yale, NUS College, Singapore, Singapore
| | - Larisa Sârghie
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | | | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Vadim E Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Robi Tacutu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania.
- Chronos Biosystems SRL, Bucharest, Romania.
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16
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Ye Y, Gu Q, Sun X. Potential of Caenorhabditis elegans as an antiaging evaluation model for dietary phytochemicals: A review. Compr Rev Food Sci Food Saf 2020; 19:3084-3105. [PMID: 33337057 DOI: 10.1111/1541-4337.12654] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/02/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022]
Abstract
Aging is an inevitable process characterized by the accumulation of degenerative damage, leading to serious diseases that affect human health. Studies on aging aim to develop pre-protection or therapies to delay aging and age-related diseases. A preventive approach is preferable to clinical treatment not only to reduce investment but also to alleviate pain in patients. Adjusting daily diet habits to improve the aging condition is a potentially attractive strategy. Fruits and vegetables containing active compounds that can effectively delay the aging process and reduce or inhibit age-related degenerative diseases have been identified. The signaling pathways related to aging in Caenorhabditis elegans are evolutionarily conserved; thus, studying antiaging components by intervening senescence process may contribute to the prevention and treatment of age-related diseases in humans. This review focuses on the effects of food-derived extracts or purified substance on antiaging in nematodes, as well as the underlying mechanisms, on the basis of several major signaling pathways and key regulatory factors in aging. The aim is to provide references for a healthy diet guidance and the development of antiaging nutritional supplements. Finally, challenges in the use of C. elegans as the antiaging evaluation model are discussed, together with the development that potentially inspire novel strategies and research tools.
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Affiliation(s)
- Yongli Ye
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, P. R. China
| | - Qingyin Gu
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, P. R. China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, P. R. China
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17
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Toren D, Kulaga A, Jethva M, Rubin E, Snezhkina AV, Kudryavtseva AV, Nowicki D, Tacutu R, Moskalev AA, Fraifeld VE. Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. Aging Cell 2020; 19:e13158. [PMID: 32515539 PMCID: PMC7433004 DOI: 10.1111/acel.13158] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/16/2020] [Accepted: 04/09/2020] [Indexed: 12/29/2022] Open
Abstract
One important question in aging research is how differences in genomics and transcriptomics determine the maximum lifespan in various species. Despite recent progress, much is still unclear on the topic, partly due to the lack of samples in nonmodel organisms and due to challenges in direct comparisons of transcriptomes from different species. The novel ranking‐based method that we employ here is used to analyze gene expression in the gray whale and compare its de novo assembled transcriptome with that of other long‐ and short‐lived mammals. Gray whales are among the top 1% longest‐lived mammals. Despite the extreme environment, or maybe due to a remarkable adaptation to its habitat (intermittent hypoxia, Arctic water, and high pressure), gray whales reach at least the age of 77 years. In this work, we show that long‐lived mammals share common gene expression patterns between themselves, including high expression of DNA maintenance and repair, ubiquitination, apoptosis, and immune responses. Additionally, the level of expression for gray whale orthologs of pro‐ and anti‐longevity genes found in model organisms is in support of their alleged role and direction in lifespan determination. Remarkably, among highly expressed pro‐longevity genes many are stress‐related, reflecting an adaptation to extreme environmental conditions. The conducted analysis suggests that the gray whale potentially possesses high resistance to cancer and stress, at least in part ensuring its longevity. This new transcriptome assembly also provides important resources to support the efforts of maintaining the endangered population of gray whales.
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Affiliation(s)
- Dmitri Toren
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
| | - Anton Kulaga
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
- Humenhance OÜ Tallinn Estonia
| | - Mineshbhai Jethva
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Dmitry Nowicki
- Center for Cybernetics Institute of MMS of NASU Kiev Ukraine
| | - Robi Tacutu
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
- Chronos Biosystems SRL Bucharest Romania
| | - Alexey A. Moskalev
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
- Institute of Biology of Komi Science Center of Ural Branch of RAS Syktyvkar Russia
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
- 8IVAO LLC Saint Petersburg Russia
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18
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Abstract
Using neXtProt release 2019-01-11, we manually curated a list of 1837 functionally uncharacterized human proteins. Using OrthoList 2, we found that 270 of them have homologues in Caenorhabditis elegans, including 60 with a one-to-one orthology relationship. According to annotations extracted from WormBase, the vast majority of these 60 worm genes have RNAi experimental data or mutant alleles, but manual inspection shows that only 15% have phenotypes that could be interpreted in terms of a specific function. One third of the worm orthologs have protein-protein interaction data, and two of these interactions are conserved in humans. The combination of phenotypic, protein-protein interaction, and gene expression data provides functional hypotheses for 8 uncharacterized human proteins. Experimental validation in human or orthologs is necessary before they can be considered for annotation.
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Affiliation(s)
- Paula Duek
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland
| | - Lydie Lane
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland
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19
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Abstract
Despite tremendous progress in recent years, our understanding of the evolution of ageing is still incomplete. A dominant paradigm maintains that ageing evolves due to the competing energy demands of reproduction and somatic maintenance leading to slow accumulation of unrepaired cellular damage with age. However, the centrality of energy trade-offs in ageing has been increasingly challenged as studies in different organisms have uncoupled the trade-off between reproduction and longevity. An emerging theory is that ageing instead is caused by biological processes that are optimized for early-life function but become harmful when they continue to run-on unabated in late life. This idea builds on the realization that early-life regulation of gene expression can break down in late life because natural selection is too weak to optimize it. Empirical evidence increasingly supports the hypothesis that suboptimal gene expression in adulthood can result in physiological malfunction leading to organismal senescence. We argue that the current state of the art in the study of ageing contradicts the widely held view that energy trade-offs between growth, reproduction, and longevity are the universal underpinning of senescence. Future research should focus on understanding the relative contribution of energy and function trade-offs to the evolution and expression of ageing.
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Affiliation(s)
- Alexei A Maklakov
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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20
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Freund A. Untangling Aging Using Dynamic, Organism-Level Phenotypic Networks. Cell Syst 2019; 8:172-181. [PMID: 30878357 DOI: 10.1016/j.cels.2019.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/14/2018] [Accepted: 02/13/2019] [Indexed: 12/15/2022]
Abstract
Research on aging requires the ability to measure aging, and therein lies a challenge: it is impossible to measure every molecular, cellular, and physiological change that develops over time, but it is difficult to prioritize phenotypes for measurement because it is unclear which biological changes should be considered aspects of aging and, further, which species and environments exhibit "real aging." Here, I propose a strategy to address this challenge: rather than classify phenotypes as "real aging" or not, conceptualize aging as the set of all age-dependent phenotypes and appreciate that this set and its underlying mechanisms may vary by population. Use automated phenotyping technologies to measure as many age-dependent phenotypes as possible within individuals over time, prioritizing organism-level (i.e., physiological) phenotypes in order to enrich for health relevance. Use those high-dimensional phenotypic data to construct dynamic networks that allow aging to be studied with unprecedented sophistication and rigor.
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Affiliation(s)
- Adam Freund
- Calico Life Sciences, LLC, South San Francisco, CA 94080, USA.
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21
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Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN. Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity. Aging Cell 2018; 17:e12740. [PMID: 29671950 PMCID: PMC6052463 DOI: 10.1111/acel.12740] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2018] [Indexed: 12/14/2022] Open
Abstract
Lifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life-history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer-lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing. Interestingly, these gene expression patterns resembled those of flies under dietary restriction and several other lifespan-extending interventions, although on the individual gene level, there was no significant overlap with genes previously reported to have lifespan-extension effects. We experimentally tested the lifespan regulation potential of several candidate genes and found no consistent effects, suggesting that individual genes generally do not explain the observed longevity patterns. Instead, it appears that lifespan regulation across species is modulated by complex relationships at the system level represented by global gene expression.
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Affiliation(s)
- Siming Ma
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Genome Institute of SingaporeA*STARSingapore CitySingapore
| | - Andrei S. Avanesov
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Emily Porter
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Byung Cheon Lee
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- College of Life Sciences and BiotechnologyKorea UniversitySeoulSouth Korea
| | - Marco Mariotti
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Bioinformatics and Genomics ProgramCentre for Genomic Regulation and Universitat Pompeu FabraBarcelonaSpain
| | - Nadezhda Zemskaya
- Institute of BiologyKomi Science CenterRussian Academy of SciencesSyktyvkarRussia
| | - Roderic Guigo
- Bioinformatics and Genomics ProgramCentre for Genomic Regulation and Universitat Pompeu FabraBarcelonaSpain
| | - Alexey A. Moskalev
- Institute of BiologyKomi Science CenterRussian Academy of SciencesSyktyvkarRussia
- Moscow Institute of Physics and TechnologyDolgoprudny, Moscow RegionRussia
- Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia
| | - Vadim N. Gladyshev
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Belozersky Institute of Physico‐Chemical BiologyMoscow State UniversityMoscowRussia
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22
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Chaudhari SN, Kipreos ET. The Energy Maintenance Theory of Aging: Maintaining Energy Metabolism to Allow Longevity. Bioessays 2018; 40:e1800005. [PMID: 29901833 PMCID: PMC6314662 DOI: 10.1002/bies.201800005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 04/28/2018] [Indexed: 12/17/2022]
Abstract
Fused, elongated mitochondria are more efficient in generating ATP than fragmented mitochondria. In diverse C. elegans longevity pathways, increased levels of fused mitochondria are associated with lifespan extension. Blocking mitochondrial fusion in these animals abolishes their extended longevity. The long-lived C. elegans vhl-1 mutant is an exception that does not have increased fused mitochondria, and is not dependent on fusion for longevity. Loss of mammalian VHL upregulates alternate energy generating pathways. This suggests that mitochondrial fusion facilitates longevity in C. elegans by increasing energy metabolism. In diverse animals, ATP levels broadly decreases with age. Substantial evidence supports the theory that increasing or maintaining energy metabolism promotes the survival of older animals. Increased ATP levels in older animals allow energy-intensive repair and homeostatic mechanisms such as proteostasis that act to prevent cellular aging. These observations support the emerging paradigm that maintaining energy metabolism promotes the survival of older animals.
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Affiliation(s)
- Snehal N. Chaudhari
- Department of Cellular Biology University of Georgia Athens, GA 30602
- Present address: Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston, MA 02115
| | - Edward T. Kipreos
- Department of Cellular Biology University of Georgia Athens, GA 30602
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23
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Fernandes M, Wan C, Tacutu R, Barardo D, Rajput A, Wang J, Thoppil H, Thornton D, Yang C, Freitas A, de Magalhães JP. Systematic analysis of the gerontome reveals links between aging and age-related diseases. Hum Mol Genet 2018; 25:4804-4818. [PMID: 28175300 PMCID: PMC5418736 DOI: 10.1093/hmg/ddw307] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/05/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022] Open
Abstract
In model organisms, over 2,000 genes have been shown to modulate aging, the collection of which we call the ‘gerontome’. Although some individual aging-related genes have been the subject of intense scrutiny, their analysis as a whole has been limited. In particular, the genetic interaction of aging and age-related pathologies remain a subject of debate. In this work, we perform a systematic analysis of the gerontome across species, including human aging-related genes. First, by classifying aging-related genes as pro- or anti-longevity, we define distinct pathways and genes that modulate aging in different ways. Our subsequent comparison of aging-related genes with age-related disease genes reveals species-specific effects with strong overlaps between aging and age-related diseases in mice, yet surprisingly few overlaps in lower model organisms. We discover that genetic links between aging and age-related diseases are due to a small fraction of aging-related genes which also tend to have a high network connectivity. Other insights from our systematic analysis include assessing how using datasets with genes more or less studied than average may result in biases, showing that age-related disease genes have faster molecular evolution rates and predicting new aging-related drugs based on drug-gene interaction data. Overall, this is the largest systems-level analysis of the genetics of aging to date and the first to discriminate anti- and pro-longevity genes, revealing new insights on aging-related genes as a whole and their interactions with age-related diseases.
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Affiliation(s)
- Maria Fernandes
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.,LaSIGE - Large-Scale Informatics Systems Laboratory, Faculty of Sciences, University of Lisbon, Portugal
| | - Cen Wan
- School of Computing, University of Kent, Canterbury, UK.,Department of Computer Science, University College London, London, UK
| | - Robi Tacutu
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Diogo Barardo
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Ashish Rajput
- Research Group for Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Jingwei Wang
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Harikrishnan Thoppil
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Chenhao Yang
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Alex Freitas
- School of Computing, University of Kent, Canterbury, UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
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24
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Yanai H, Budovsky A, Tacutu R, Barzilay T, Abramovich A, Ziesche R, Fraifeld VE. Tissue repair genes: the TiRe database and its implication for skin wound healing. Oncotarget 2018; 7:21145-55. [PMID: 27049721 PMCID: PMC5008274 DOI: 10.18632/oncotarget.8501] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/18/2016] [Indexed: 12/20/2022] Open
Abstract
Wound healing is an inherent feature of any multicellular organism and recent years have brought about a huge amount of data regarding regular and abnormal tissue repair. Despite the accumulated knowledge, modulation of wound healing is still a major biomedical challenge, especially in advanced ages. In order to collect and systematically organize what we know about the key players in wound healing, we created the TiRe (Tissue Repair) database, an online collection of genes and proteins that were shown to directly affect skin wound healing. To date, TiRe contains 397 entries for four organisms: Mus musculus, Rattus norvegicus, Sus domesticus, and Homo sapiens. Analysis of the TiRe dataset of skin wound healing-associated genes showed that skin wound healing genes are (i) over-conserved among vertebrates, but are under-conserved in invertebrates; (ii) enriched in extracellular and immuno-inflammatory genes; and display (iii) high interconnectivity and connectivity to other proteins. The latter may provide potential therapeutic targets. In addition, a slower or faster skin wound healing is indicative of an aging or longevity phenotype only when assessed in advanced ages, but not in the young. In the long run, we aim for TiRe to be a one-station resource that provides researchers and clinicians with the essential data needed for a better understanding of the mechanisms of wound healing, designing new experiments, and the development of new therapeutic strategies. TiRe is freely available online at http://www.tiredb.org.
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Affiliation(s)
- Hagai Yanai
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Arie Budovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer Sheva, Israel.,Judea Regional Research & Development Center, Carmel, Israel
| | - Robi Tacutu
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Thomer Barzilay
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Amir Abramovich
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Rolf Ziesche
- Division of Pulmonary Medicine, Department of Internal Medicine II, Medical University of Vienna, Waehringer Guertel, Vienna, Austria
| | - Vadim E Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer Sheva, Israel
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25
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Matsumura A, Higuchi J, Watanabe Y, Kato M, Aoki K, Akabane S, Endo T, Oka T. Inactivation of cardiolipin synthase triggers changes in mitochondrial morphology. FEBS Lett 2017; 592:209-218. [DOI: 10.1002/1873-3468.12948] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/01/2017] [Accepted: 12/05/2017] [Indexed: 12/27/2022]
Affiliation(s)
| | - Jun Higuchi
- Department of Life Science Rikkyo University Tokyo Japan
| | - Yasunori Watanabe
- Department of Bioscience Graduate School of Agriculture Ehime University Japan
| | - Masahiro Kato
- Department of Life Science Rikkyo University Tokyo Japan
| | - Keigo Aoki
- Department of Life Science Rikkyo University Tokyo Japan
| | - Shiori Akabane
- Department of Life Science Rikkyo University Tokyo Japan
| | - Toshiya Endo
- Faculty of Life Sciences Kyoto Sangyo University Japan
| | - Toshihiko Oka
- Department of Life Science Rikkyo University Tokyo Japan
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26
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Yanai H, Budovsky A, Barzilay T, Tacutu R, Fraifeld VE. Wide-scale comparative analysis of longevity genes and interventions. Aging Cell 2017; 16:1267-1275. [PMID: 28836369 PMCID: PMC5676071 DOI: 10.1111/acel.12659] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2017] [Indexed: 12/17/2022] Open
Abstract
Hundreds of genes, when manipulated, affect the lifespan of model organisms (yeast, worm, fruit fly, and mouse) and thus can be defined as longevity-associated genes (LAGs). A major challenge is to determine whether these LAGs are model-specific or may play a universal role as longevity regulators across diverse taxa. A wide-scale comparative analysis of the 1805 known LAGs across 205 species revealed that (i) LAG orthologs are substantially overrepresented, from bacteria to mammals, compared to the entire genomes or interactomes, and this was especially noted for essential LAGs; (ii) the effects on lifespan, when manipulating orthologous LAGs in different model organisms, were mostly concordant, despite a high evolutionary distance between them; (iii) LAGs that have orthologs across a high number of phyla were enriched in translational processes, energy metabolism, and DNA repair genes; (iv) LAGs that have no orthologs out of the taxa in which they were discovered were enriched in autophagy (Ascomycota/Fungi), G proteins (Nematodes), and neuroactive ligand-receptor interactions (Chordata). The results also suggest that antagonistic pleiotropy might be a conserved principle of aging and highlight the importance of overexpression studies in the search for longevity regulators.
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Affiliation(s)
- Hagai Yanai
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev POB 653 Beer Sheva 8410501 Israel
| | - Arie Budovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev POB 653 Beer Sheva 8410501 Israel
- Biotechnology Unit Technological Center Beer Sheva 8489101 Israel
| | - Thomer Barzilay
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev POB 653 Beer Sheva 8410501 Israel
| | - Robi Tacutu
- Computational Biology of Aging Group Institute of Biochemistry Romanian Academy Bucharest 060031 Romania
- Chronos Biosystems SRL Bucharest Romania
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev POB 653 Beer Sheva 8410501 Israel
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27
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Sutphin GL, Backer G, Sheehan S, Bean S, Corban C, Liu T, Peters MJ, van Meurs JBJ, Murabito JM, Johnson AD, Korstanje R. Caenorhabditis elegans orthologs of human genes differentially expressed with age are enriched for determinants of longevity. Aging Cell 2017; 16:672-682. [PMID: 28401650 PMCID: PMC5506438 DOI: 10.1111/acel.12595] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2017] [Indexed: 12/21/2022] Open
Abstract
We report a systematic RNAi longevity screen of 82 Caenorhabditis elegans genes selected based on orthology to human genes differentially expressed with age. We find substantial enrichment in genes for which knockdown increased lifespan. This enrichment is markedly higher than published genomewide longevity screens in C. elegans and similar to screens that preselected candidates based on longevity‐correlated metrics (e.g., stress resistance). Of the 50 genes that affected lifespan, 46 were previously unreported. The five genes with the greatest impact on lifespan (>20% extension) encode the enzyme kynureninase (kynu‐1), a neuronal leucine‐rich repeat protein (iglr‐1), a tetraspanin (tsp‐3), a regulator of calcineurin (rcan‐1), and a voltage‐gated calcium channel subunit (unc‐36). Knockdown of each gene extended healthspan without impairing reproduction. kynu‐1(RNAi) alone delayed pathology in C. elegans models of Alzheimer's disease and Huntington's disease. Each gene displayed a distinct pattern of interaction with known aging pathways. In the context of published work, kynu‐1, tsp‐3, and rcan‐1 are of particular interest for immediate follow‐up. kynu‐1 is an understudied member of the kynurenine metabolic pathway with a mechanistically distinct impact on lifespan. Our data suggest that tsp‐3 is a novel modulator of hypoxic signaling and rcan‐1 is a context‐specific calcineurin regulator. Our results validate C. elegans as a comparative tool for prioritizing human candidate aging genes, confirm age‐associated gene expression data as valuable source of novel longevity determinants, and prioritize select genes for mechanistic follow‐up.
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Affiliation(s)
| | - Grant Backer
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Susan Sheehan
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Shannon Bean
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Caroline Corban
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Teresa Liu
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Marjolein J. Peters
- Department of Internal Medicine; Erasmus Medical Center; Postbus 2040 3000 CA Rotterdam The Netherlands
| | - Joyce B. J. van Meurs
- Department of Internal Medicine; Erasmus Medical Center; Postbus 2040 3000 CA Rotterdam The Netherlands
| | - Joanne M. Murabito
- Section of General Internal Medicine; Boston University School of Medicine; 801 Massachusetts Ave, Crosstown Center Boston MA 02118 USA
- The National Heart, Lung, and Blood Institute's Framingham Heart Study; 73 Mt. Wayte Ave, Suite 2 Framingham MA 01702-5827 USA
| | - Andrew D. Johnson
- The National Heart, Lung, and Blood Institute's Framingham Heart Study; 73 Mt. Wayte Ave, Suite 2 Framingham MA 01702-5827 USA
- Population Sciences Branch; National Heart, Lung, and Blood Institute; Building 31, Room 5A52, 31 Center Drive MSC 2486 Bethesda MD 20892 USA
| | - Ron Korstanje
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
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Wang D, Hou L, Nakamura S, Su M, Li F, Chen W, Yan Y, Green CD, Chen D, Zhang H, Antebi A, Han JDJ. LIN-28 balances longevity and germline stem cell number in Caenorhabditis elegans through let-7/AKT/DAF-16 axis. Aging Cell 2017; 16:113-124. [PMID: 27730721 PMCID: PMC5242300 DOI: 10.1111/acel.12539] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 01/23/2023] Open
Abstract
The RNA‐binding protein LIN‐28 was first found to control developmental timing in Caenorhabditis elegans. Later, it was found to play important roles in pluripotency, metabolism, and cancer in mammals. Here we report that a low dosage of lin‐28 enhanced stress tolerance and longevity, and reduced germline stem/progenitor cell number in C. elegans. The germline LIN‐28‐regulated microRNA let‐7 was required for these effects by targeting akt‐1/2 and decreasing their protein levels. AKT‐1/2 and the downstream DAF‐16 transcription factor were both required for the lifespan and germline stem cell effects of lin‐28. The pathway also mediated dietary restriction induced lifespan extension and reduction in germline stem cell number. Thus, the LIN‐28/let‐7/AKT/DAF‐16 axis we delineated here is a program that plays an important role in balancing reproduction and somatic maintenance and their response to the environmental energy level—a central dogma of the ‘evolutionary optimization’ of resource allocation that modulates aging.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
- University of Chinese Academy of Science; Beijing 100049 China
| | - Lei Hou
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Shuhei Nakamura
- Max Planck Institute for Biology of Ageing; Joseph-Stelzmann-Strasse 9b Cologne 50931 Germany
| | - Ming Su
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Fang Li
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Weiyang Chen
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Yizhen Yan
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
- University of Chinese Academy of Science; Beijing 100049 China
| | - Christopher D. Green
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Di Chen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study; Model Animal Research Center; Nanjing University; Nanjing Jiangsu 210061 China
| | - Hong Zhang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing; Joseph-Stelzmann-Strasse 9b Cologne 50931 Germany
| | - Jing-Dong J. Han
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
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29
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Zhang Q, Nogales-Cadenas R, Lin JR, Zhang W, Cai Y, Vijg J, Zhang ZD. Systems-level analysis of human aging genes shed new light on mechanisms of aging. Hum Mol Genet 2016; 25:2934-2947. [PMID: 27179790 DOI: 10.1093/hmg/ddw145] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 04/07/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
Although studies over the last decades have firmly connected a number of genes and molecular pathways to aging, the aging process as a whole still remains poorly understood. To gain novel insights into the mechanisms underlying aging, instead of considering aging genes individually, we studied their characteristics at the systems level in the context of biological networks. We calculated a comprehensive set of network characteristics for human aging-related genes from the GenAge database. By comparing them with other functional groups of genes, we identified a robust group of aging-specific network characteristics. To find the structural basis and the molecular mechanisms underlying this aging-related network specificity, we also analyzed protein domain interactions and gene expression patterns across different tissues. Our study revealed that aging genes not only tend to be network hubs, playing important roles in communication among different functional modules or pathways, but also are more likely to physically interact and be co-expressed with essential genes. The high expression of aging genes across a large number of tissue types also points to a high level of connectivity among aging genes. Unexpectedly, contrary to the depletion of interactions among hub genes in biological networks, we observed close interactions among aging hubs, which renders the aging subnetworks vulnerable to random attacks and thus may contribute to the aging process. Comparison across species reveals the evolution process of the aging subnetwork. As the organisms become more complex, the complexity of its aging mechanisms increases and their aging hub genes are more functionally connected.
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Affiliation(s)
| | | | | | | | | | - Jan Vijg
- Department of Genetics.,Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, USA
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30
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Calvert S, Tacutu R, Sharifi S, Teixeira R, Ghosh P, de Magalhães JP. A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans. Aging Cell 2016; 15:256-66. [PMID: 26676933 PMCID: PMC4783339 DOI: 10.1111/acel.12432] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2015] [Indexed: 01/04/2023] Open
Abstract
Caloric restriction (CR), a reduction in calorie intake without malnutrition, retards aging in several animal models from worms to mammals. Developing CR mimetics, compounds that reproduce the longevity benefits of CR without its side effects, is of widespread interest. Here, we employed the Connectivity Map to identify drugs with overlapping gene expression profiles with CR. Eleven statistically significant compounds were predicted as CR mimetics using this bioinformatics approach. We then tested rapamycin, allantoin, trichostatin A, LY‐294002 and geldanamycin in Caenorhabditis elegans. An increase in lifespan and healthspan was observed for all drugs except geldanamycin when fed to wild‐type worms, but no lifespan effects were observed in eat‐2 mutant worms, a genetic model of CR, suggesting that life‐extending effects may be acting via CR‐related mechanisms. We also treated daf‐16 worms with rapamycin, allantoin or trichostatin A, and a lifespan extension was observed, suggesting that these drugs act via DAF‐16‐independent mechanisms, as would be expected from CR mimetics. Supporting this idea, an analysis of predictive targets of the drugs extending lifespan indicates various genes within CR and longevity networks. We also assessed the transcriptional profile of worms treated with either rapamycin or allantoin and found that both drugs use several specific pathways that do not overlap, indicating different modes of action for each compound. The current work validates the capabilities of this bioinformatic drug repositioning method in the context of longevity and reveals new putative CR mimetics that warrant further studies.
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Affiliation(s)
- Shaun Calvert
- Integrative Genomics of Ageing Group; Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - Robi Tacutu
- Integrative Genomics of Ageing Group; Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - Samim Sharifi
- Integrative Genomics of Ageing Group; Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - Rute Teixeira
- Integrative Genomics of Ageing Group; Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - Pratul Ghosh
- Integrative Genomics of Ageing Group; Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group; Institute of Integrative Biology; University of Liverpool; Liverpool UK
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31
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Zierer J, Menni C, Kastenmüller G, Spector TD. Integration of 'omics' data in aging research: from biomarkers to systems biology. Aging Cell 2015; 14:933-44. [PMID: 26331998 PMCID: PMC4693464 DOI: 10.1111/acel.12386] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2015] [Indexed: 12/16/2022] Open
Abstract
Age is the strongest risk factor for many diseases including neurodegenerative disorders, coronary heart disease, type 2 diabetes and cancer. Due to increasing life expectancy and low birth rates, the incidence of age-related diseases is increasing in industrialized countries. Therefore, understanding the relationship between diseases and aging and facilitating healthy aging are major goals in medical research. In the last decades, the dimension of biological data has drastically increased with high-throughput technologies now measuring thousands of (epi) genetic, expression and metabolic variables. The most common and so far successful approach to the analysis of these data is the so-called reductionist approach. It consists of separately testing each variable for association with the phenotype of interest such as age or age-related disease. However, a large portion of the observed phenotypic variance remains unexplained and a comprehensive understanding of most complex phenotypes is lacking. Systems biology aims to integrate data from different experiments to gain an understanding of the system as a whole rather than focusing on individual factors. It thus allows deeper insights into the mechanisms of complex traits, which are caused by the joint influence of several, interacting changes in the biological system. In this review, we look at the current progress of applying omics technologies to identify biomarkers of aging. We then survey existing systems biology approaches that allow for an integration of different types of data and highlight the need for further developments in this area to improve epidemiologic investigations.
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Affiliation(s)
- Jonas Zierer
- Department of Twins Research and Genetic EpidemiologyKings College LondonLondonUnited Kingdom
- Institute of Bioinformatics and Systems BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Cristina Menni
- Department of Twins Research and Genetic EpidemiologyKings College LondonLondonUnited Kingdom
| | - Gabi Kastenmüller
- Department of Twins Research and Genetic EpidemiologyKings College LondonLondonUnited Kingdom
- Institute of Bioinformatics and Systems BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Tim D. Spector
- Department of Twins Research and Genetic EpidemiologyKings College LondonLondonUnited Kingdom
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32
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Abstract
The theory of medicine and its complement systems biology are intended to explain the workings of the large number of mutually interdependent complex physiologic networks in the human body and to apply that understanding to maintaining the functions for which nature designed them. Therefore, when what had originally been made as a simplifying assumption or a working hypothesis becomes foundational to understanding the operation of physiologic networks it is in the best interests of science to replace or at least update that assumption. The replacement process requires, among other things, an evaluation of how the new hypothesis affects modern day understanding of medical science. This paper identifies linear dynamics and Normal statistics as being such arcane assumptions and explores some implications of their retirement. Specifically we explore replacing Normal with fractal statistics and examine how the latter are related to non-linear dynamics and chaos theory. The observed ubiquity of inverse power laws in physiology entails the need for a new calculus, one that describes the dynamics of fractional phenomena and captures the fractal properties of the statistics of physiological time series. We identify these properties as a necessary consequence of the complexity resulting from the network dynamics and refer to them collectively as The Network Effect.
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Affiliation(s)
- Bruce J. West
- Mathematics and Information Science Directorate, Army Research OfficeResearch Triangle Park, NC, USA
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33
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Demongeot J, Taramasco C. Evolution of social networks: the example of obesity. Biogerontology 2014; 15:611-26. [PMID: 25466389 DOI: 10.1007/s10522-014-9542-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/11/2014] [Indexed: 01/17/2023]
Abstract
The present paper deals with the effect of the social transmission of nutrition habits in a social and biological age-dependent context on obesity, and accordingly on type II diabetes and among its complications, the neurodegenerative diseases. The evolution of social networks and inside a network the healthy weight of a person are depending on the context in which this person has contacts and exchanges concerning his alimentation, physical activity and sedentary habits, inside the dominant social network in which the person lives (e.g., scholar for young, professional for adult, home or institution for elderly people). Three successive steps of evolution will be considered for social networks (like for neural one's): initial random connectivity, destruction and consolidation of links following a new transition rule called homophilic until an asymptotic architectural organization and configuration of states. The application of such a network dynamics concerns the sequence overweight/obesity/type II diabetes and neurodegenerative diseases.
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Affiliation(s)
- Jacques Demongeot
- AGIM FRE CNRS/UJF 3405, Faculty of Medicine, University J. Fourier of Grenoble, La Tronche, 38700, France,
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34
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de Magalhães JP. The scientific quest for lasting youth: prospects for curing aging. Rejuvenation Res 2014; 17:458-67. [PMID: 25132068 PMCID: PMC4203147 DOI: 10.1089/rej.2014.1580] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 08/17/2014] [Indexed: 12/22/2022] Open
Abstract
People have always sought eternal life and everlasting youth. Recent technological breakthroughs and our growing understanding of aging have given strength to the idea that a cure for human aging can eventually be developed. As such, it is crucial to debate the long-term goals and potential impact of the field. Here, I discuss the scientific prospect of eradicating human aging. I argue that curing aging is scientifically possible and not even the most challenging enterprise in the biosciences. Developing the means to abolish aging is also an ethical endeavor because the goal of biomedical research is to allow people to be as healthy as possible for as long as possible. There is no evidence, however, that we are near to developing the technologies permitting radical life extension. One major difficulty in aging research is the time and costs it takes to do experiments and test interventions. I argue that unraveling the functioning of the genome and developing predictive computer models of human biology and disease are essential to increase the accuracy of medical interventions, including in the context of life extension, and exponential growth in informatics and genomics capacity might lead to rapid progress. Nonetheless, developing the tools for significantly modifying human biology is crucial to intervening in a complex process like aging. Yet in spite of advances in areas like regenerative medicine and gene therapy, the development of clinical applications has been slow and this remains a key hurdle for achieving radical life extension in the foreseeable future.
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Affiliation(s)
- João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool , Liverpool, United Kingdom
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35
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Ayyadevara S, Tazearslan C, Alla R, Jiang JC, Jazwinski SM, Shmookler Reis RJ. Rec-8 dimorphism affects longevity, stress resistance and X-chromosome nondisjunction in C. elegans, and replicative lifespan in S. cerevisiae. Front Genet 2014; 5:211. [PMID: 25136348 PMCID: PMC4120681 DOI: 10.3389/fgene.2014.00211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/19/2014] [Indexed: 12/18/2022] Open
Abstract
A quantitative trait locus (QTL) in the nematode C. elegans, “lsq4,” was recently implicated by mapping longevity genes. QTLs for lifespan and three stress-resistance traits coincided within a span of <300 kbp, later narrowed to <200 kbp. A single gene in this interval is now shown to modulate all lsq4-associated traits. Full-genome analysis of transcript levels indicates that lsq4 contains a dimorphic gene governing the expression of many sperm-specific genes, suggesting an effect on spermatogenesis. Quantitative analysis of allele-specific transcripts encoded within the lsq4 interval revealed significant, 2- to 15-fold expression differences for 10 of 33 genes. Fourteen “dual-candidate” genes, implicated by both position and expression, were tested for RNA-interference effects on QTL-linked traits. In a strain carrying the shorter-lived allele, knockdown of rec-8 (encoding a meiotic cohesin) reduced its transcripts 4-fold, to a level similar to the longer-lived strain, while extending lifespan 25–26%, whether begun before fertilization or at maturity. The short-lived lsq4 allele also conferred sensitivity to oxidative and thermal stresses, and lower male frequency (reflecting X-chromosome non-disjunction), traits reversed uniquely by rec-8 knockdown. A strain bearing the longer-lived lsq4 allele, differing from the short-lived strain at <0.3% of its genome, derived no lifespan or stress-survival benefit from rec-8 knockdown. We consider two possible explanations: high rec-8 expression may include increased “leaky” expression in mitotic cells, leading to deleterious destabilization of somatic genomes; or REC-8 may act entirely in germ-line meiotic cells to reduce aberrations such as non-disjunction, thereby blunting a stress-resistance response mediated by innate immunity. Replicative lifespan was extended 20% in haploid S. cerevisiae (BY4741) by deletion of REC8, orthologous to nematode rec-8, implying that REC8 disruption of mitotic-cell survival is widespread, exemplifying antagonistic pleiotropy (opposing effects on lifespan vs. reproduction), and/or balancing selection wherein genomic disruption increases genetic variation under harsh conditions.
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Affiliation(s)
- Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare System, VA Medical Center Little Rock, AR, USA ; Department of Geriatrics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Cagdas Tazearslan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Ramani Alla
- Central Arkansas Veterans Healthcare System, VA Medical Center Little Rock, AR, USA ; Department of Geriatrics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - James C Jiang
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center New Orleans, LA, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center New Orleans, LA, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare System, VA Medical Center Little Rock, AR, USA ; Department of Geriatrics, University of Arkansas for Medical Sciences Little Rock, AR, USA ; Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock, AR, USA
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van den Akker EB, Passtoors WM, Jansen R, van Zwet EW, Goeman JJ, Hulsman M, Emilsson V, Perola M, Willemsen G, Penninx BW, Heijmans BT, Maier AB, Boomsma DI, Kok JN, Slagboom PE, Reinders MJ, Beekman M. Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging. Aging Cell 2014; 13:216-25. [PMID: 24119000 PMCID: PMC4331790 DOI: 10.1111/acel.12160] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2013] [Indexed: 11/30/2022] Open
Abstract
The bodily decline that occurs with advancing age strongly impacts on the prospects for future health and life expectancy. Despite the profound role of age in disease etiology, knowledge about the molecular mechanisms driving the process of aging in humans is limited. Here, we used an integrative network-based approach for combining multiple large-scale expression studies in blood (2539 individuals) with protein–protein Interaction (PPI) data for the detection of consistently coexpressed PPI modules that may reflect key processes that change throughout the course of normative aging. Module detection followed by a meta-analysis on chronological age identified fifteen consistently coexpressed PPI modules associated with chronological age, including a highly significant module (P = 3.5 × 10−38) enriched for ‘T-cell activation’ marking age-associated shifts in lymphocyte blood cell counts (R2 = 0.603; P = 1.9 × 10−10). Adjusting the analysis in the compendium for the ‘T-cell activation’ module showed five consistently coexpressed PPI modules that robustly associated with chronological age and included modules enriched for ‘Translational elongation’, ‘Cytolysis’ and ‘DNA metabolic process’. In an independent study of 3535 individuals, four of five modules consistently associated with chronological age, underpinning the robustness of the approach. We found three of five modules to be significantly enriched with aging-related genes, as defined by the GenAge database, and association with prospective survival at high ages for one of the modules including ASF1A. The hereby-detected age-associated and consistently coexpressed PPI modules therefore may provide a molecular basis for future research into mechanisms underlying human aging.
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Affiliation(s)
- Erik B. van den Akker
- Department of Molecular Epidemiology; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
- The Delft Bioinformatics Lab; Delft University of Technology; PO Box 5031 2600 GA Delft The Netherlands
| | - Willemijn M. Passtoors
- Department of Molecular Epidemiology; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
| | - Rick Jansen
- Department of Psychiatry; VU University Medical Center; Neuroscience Campus Amsterdam; VU University Medical Center; A.J. Ernststraat 1187 1081 HL Amsterdam The Netherlands
- EMGO Institute for Health and Care Research; Neuroscience Campus Amsterdam; Van der Boechorststraat 7 1081 BT Amsterdam The Netherlands
| | - Erik W. van Zwet
- Department of Medical Statistics; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
| | - Jelle J. Goeman
- Department of Medical Statistics; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
| | - Marc Hulsman
- The Delft Bioinformatics Lab; Delft University of Technology; PO Box 5031 2600 GA Delft The Netherlands
| | - Valur Emilsson
- Icelandic Heart Association; Holtasmari 1 IS-201 Kópavogur Iceland
| | - Markus Perola
- National Institute for Health and Welfare; PO Box 30 00271 Helsinki Finland
| | - Gonneke Willemsen
- Department of Biological Psychology; VU University; Van der Boechorststraat 7 1081 BT Amsterdam The Netherlands
| | - Brenda W.J.H. Penninx
- Department of Psychiatry; VU University Medical Center; Neuroscience Campus Amsterdam; VU University Medical Center; A.J. Ernststraat 1187 1081 HL Amsterdam The Netherlands
- EMGO Institute for Health and Care Research; Neuroscience Campus Amsterdam; Van der Boechorststraat 7 1081 BT Amsterdam The Netherlands
| | - Bas T. Heijmans
- Department of Molecular Epidemiology; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
| | - Andrea B. Maier
- Section of Gerontology and Geriatrics; Department of Internal Medicine; VU University Medical Center; De Boelelaan 1117 1007 MB Amsterdam The Netherlands
| | - Dorret I. Boomsma
- EMGO Institute for Health and Care Research; Neuroscience Campus Amsterdam; Van der Boechorststraat 7 1081 BT Amsterdam The Netherlands
- Department of Biological Psychology; VU University; Van der Boechorststraat 7 1081 BT Amsterdam The Netherlands
| | - Joost N. Kok
- Department of Molecular Epidemiology; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
- Department of Algorithms; Leiden Institute of Advanced Computer Science; University of Leiden; Niels Bohrweg 1 2333 CA Leiden The Netherlands
| | - Pieternella E. Slagboom
- Department of Molecular Epidemiology; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
- Netherlands Consortium for Healthy Ageing; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
| | - Marcel J.T. Reinders
- The Delft Bioinformatics Lab; Delft University of Technology; PO Box 5031 2600 GA Delft The Netherlands
| | - Marian Beekman
- Department of Molecular Epidemiology; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
- Netherlands Consortium for Healthy Ageing; Leiden University Medical Center; PO Box 9600 2300 RC Leiden The Netherlands
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Pavlidis P, Gillis J. Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update. F1000Res 2013; 2:230. [PMID: 24715959 PMCID: PMC3962002 DOI: 10.12688/f1000research.2-230.v1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/21/2013] [Indexed: 12/12/2022] Open
Abstract
In an opinion published in 2012, we reviewed and discussed our studies of how gene network-based guilt-by-association (GBA) is impacted by confounds related to gene multifunctionality. We found such confounds account for a significant part of the GBA signal, and as a result meaningfully evaluating and applying computationally-guided GBA is more challenging than generally appreciated. We proposed that effort currently spent on incrementally improving algorithms would be better spent in identifying the features of data that do yield novel functional insights. We also suggested that part of the problem is the reliance by computational biologists on gold standard annotations such as the Gene Ontology. In the year since, there has been continued heavy activity in GBA-based research, including work that contributes to our understanding of the issues we raised. Here we provide a review of some of the most relevant recent work, or which point to new areas of progress and challenges.
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Affiliation(s)
- Paul Pavlidis
- Centre for High-Throughput Biology and Department of Psychiatry, University of British Columbia, Vancouver, V6T1Z4, Canada
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY, 11797, USA
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38
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Developmental drift as a mechanism for aging: lessons from nematodes. Biogerontology 2013; 14:693-701. [DOI: 10.1007/s10522-013-9462-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/30/2013] [Indexed: 01/16/2023]
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39
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Abstracts of Strategies for Engineered Negligible Senescence (SENS), Sixth Conference. Cambridge, United Kingdom. September 3–7, 2013. Rejuvenation Res 2013; 16 Suppl 1:S12-47. [PMID: 23944655 DOI: 10.1089/rej.2013.16.sens6abs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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