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Korneenko TV, Pestov NB. Oncogenic BRCA1,2 Mutations in the Human Lineage-A By-Product of Sexual Selection? Biomedicines 2023; 12:22. [PMID: 38275383 PMCID: PMC10813183 DOI: 10.3390/biomedicines12010022] [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: 10/31/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
In this review, we discuss the long-known problem of tissue-specific carcinogenesis in BRCA1 and BRCA2 mutation carriers: while the genes are expressed ubiquitously, increased cancer risk is observed mostly in the breast and ovaries, and to a much lesser extent, in some other tissues such as the prostate or pancreas. We reevaluate hypotheses on the evolutionary origin of these mutations in humans. Also, we align together the reports that at least some great apes have much lower risks of epithelial cancers in general and breast cancer in particular with the fact that humans have more voluminous breast tissue as compared to their closest extant relatives, particularly chimpanzees and bonobos. We conjecture that this disparity may be a consequence of sexual selection, augmented via selection for enhanced lactation. Further, we argue that there is an organ-specific enigma similar to the Peto paradox: breast cancer risk in humans is only minimally correlated with breast size. These considerations lead to the hypothesis that, along with the evolutionary development of larger breasts in humans, additional changes have played a balancing role in suppressing breast cancer. These yet-to-be-discovered mechanisms, while purely speculative, may be valuable to understanding human breast cancer, though they may not be exclusive to the mammary gland epithelial cells. Combining these themes, we review some anti-carcinogenesis preventive strategies and prospects of new interventions against breast cancer.
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Affiliation(s)
- Tatyana V. Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Nikolay B. Pestov
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Institute of Biomedical Chemistry, Moscow 119121, Russia
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow 108819, Russia
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2
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Zhang L, Park JJ, Dong MB, Arsala D, Xia S, Chen J, Sosa D, Atlas JE, Long M, Chen S. Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system. Genome Biol Evol 2023; 15:evad081. [PMID: 37170918 PMCID: PMC10210621 DOI: 10.1093/gbe/evad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/24/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
T cells are a type of white blood cell that play a critical role in the immune response against foreign pathogens through a process called T Cell Adaptive Immunity (TCAI). However, the evolution of the genes and nucleotide sequences involved in TCAI is not well understood. To investigate this, we performed comparative studies of gene annotations and genome assemblies of 28 vertebrate species and identified sets of human genes that are involved in TCAI, carcinogenesis, and ageing. We found that these gene sets share interaction pathways which may have contributed to the evolution of longevity in the vertebrate lineage leading to humans. Our human gene age dating analyses revealed that there was rapid origination of genes with TCAI-related functions prior to the Cretaceous eutherian radiation and these new genes mainly encode negative regulators. We identified no new TCAI-related genes after the divergence of placental mammals, but we did detect an extensive number of amino acid substitutions under strong positive selection in recently evolved human immunity genes suggesting they are co-evolving with adaptive immunity. More specifically, we observed that antigen processing and presentation and checkpoint genes are significantly enriched among new genes evolving under positive selection. These observations reveal an evolutionary process of T Cell Adaptive Immunity that were associated with rapid gene duplication in the early stages of vertebrates and subsequent sequence changes in TCAI-related genes. These processes together suggest an early genetic construction of the vertebrate immune system and subsequent molecular adaptation to diverse antigens.
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Affiliation(s)
- Li Zhang
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
| | - Jonathan J Park
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
| | - Matthew B Dong
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
- Immunobiology Program, The Anlyan Center, New Haven, Connecticut, USA
- Department of Immunobiology, The Anlyan Center, New Haven, Connecticut, USA
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Jared E Atlas
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Sidi Chen
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
- Immunobiology Program, The Anlyan Center, New Haven, Connecticut, USA
- Yale Comprehensive Cancer Center, New Haven, Connecticut, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
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3
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Al-Moussawy M, Abdelsamed HA, Lakkis FG. Immunoglobulin-like receptors and the generation of innate immune memory. Immunogenetics 2022; 74:179-195. [PMID: 35034136 PMCID: PMC10074160 DOI: 10.1007/s00251-021-01240-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/25/2021] [Indexed: 12/22/2022]
Abstract
Host immunity is classically divided into "innate" and "adaptive." While the former has always been regarded as the first, rapid, and antigen-nonspecific reaction to invading pathogens, the latter represents the more sophisticated and antigen-specific response that has the potential to persist and generate memory. Recent work however has challenged this dogma, where murine studies have successfully demonstrated the ability of innate immune cells (monocytes and macrophages) to acquire antigen-specific memory to allogeneic major histocompatibility complex (MHC) molecules. The immunoreceptors so far identified that mediate innate immune memory are the paired immunoglobulin-like receptors (PIRs) in mice, which are orthologous to human leukocyte immunoglobulin-like receptors (LILRs). These receptor families are mainly expressed by the myelomonocytic cell lineage, suggesting an important role in the innate immune response. In this review, we will discuss the role of immunoglobulin-like receptors in the development of innate immune memory across species.
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Affiliation(s)
- Mouhamad Al-Moussawy
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, USA.
| | - Hossam A Abdelsamed
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, USA. .,Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, USA.
| | - Fadi G Lakkis
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, USA. .,Department of Immunology, University of Pittsburgh, Pittsburgh, USA. .,Department of Medicine, University of Pittsburgh, Pittsburgh, USA.
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4
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Yu Z, Seim I, Yin M, Tian R, Sun D, Ren W, Yang G, Xu S. Comparative analyses of aging-related genes in long-lived mammals provide insights into natural longevity. Innovation (N Y) 2021; 2:100108. [PMID: 34557758 PMCID: PMC8454735 DOI: 10.1016/j.xinn.2021.100108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Abstract
Extreme longevity has evolved multiple times during the evolution of mammals, yet its underlying molecular mechanisms remain largely underexplored. Here, we compared the evolution of 115 aging-related genes in 11 long-lived species and 25 mammals with non-increased lifespan (control group) in the hopes of better understanding the common molecular mechanisms behind longevity. We identified 16 unique positively selected genes and 23 rapidly evolving genes in long-lived species, which included nine genes involved in regulating lifespan through the insulin/IGF-1 signaling (IIS) pathway and 11 genes highly enriched in immune-response-related pathways, suggesting that the IIS pathway and immune response play a particularly important role in exceptional mammalian longevity. Interestingly, 11 genes related to cancer progression, including four positively selected genes and seven genes with convergent amino acid changes, were shared by two or more long-lived lineages, indicating that long-lived mammals might have evolved convergent or similar mechanisms of cancer resistance that extended their lifespan. This suggestion was further corroborated by our identification of 12 robust candidates for longevity-related genes closely related to cancer. Evolution analyses of 115 aging-related genes exploring natural longevity in mammals Positively selected genes & rapidly evolved genes enriched in IIS and immune pathways Convergent mutations in genes associated with cancer in long-lived species Evolution of longevity through cancer resistance in long-lived mammals
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Affiliation(s)
- Zhenpeng Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Inge Seim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.,Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.,School of Biology and Environmental Science, Faculty of Science and Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mengxin Yin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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5
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Emery Thompson M, Rosati AG, Snyder-Mackler N. Insights from evolutionarily relevant models for human ageing. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190605. [PMID: 32951550 PMCID: PMC7540954 DOI: 10.1098/rstb.2019.0605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
As the world confronts the health challenges of an ageing population, there has been dramatically increased interest in the science of ageing. This research has overwhelmingly focused on age-related disease, particularly in industrialized human populations and short-lived laboratory animal models. However, it has become clear that humans and long-lived primates age differently than many typical model organisms, and that many of the diseases causing death and disability in the developed world are greatly exacerbated by modern lifestyles. As such, research on how the human ageing process evolved is vital to understanding the origins of prolonged human lifespan and factors increasing vulnerability to degenerative disease. In this issue, we highlight emerging comparative research on primates, highlighting the physical, physiological, behavioural and cognitive processes of ageing. This work comprises data and theory on non-human primates, as well as under-represented data on humans living in small-scale societies, which help elucidate how environment shapes senescence. Component papers address (i) the critical processes that comprise senescence in long-lived primates; (ii) the social, ecological or individual characteristics that predict variation in the pace of ageing; and (iii) the complicated relationship between ageing trajectories and disease outcomes. Collectively, this work provides essential comparative, evolutionary data on ageing and demonstrates its unique potential to inform our understanding of the human ageing process. This article is part of the theme issue 'Evolution of the primate ageing process'.
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Affiliation(s)
- Melissa Emery Thompson
- Department of Anthropology, University of New Mexico, 500 University Boulevard NE, Albuquerque, NM 87131, USA
| | - Alexandra G. Rosati
- Department of Psychology and Anthropology, University of Michigan, 530 Church Street, Ann Arbor, MI 48109, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85281, USA
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6
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Taormina G, Ferrante F, Vieni S, Grassi N, Russo A, Mirisola MG. Longevity: Lesson from Model Organisms. Genes (Basel) 2019; 10:genes10070518. [PMID: 31324014 PMCID: PMC6678192 DOI: 10.3390/genes10070518] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022] Open
Abstract
Research on longevity and healthy aging promises to increase our lifespan and decrease the burden of degenerative diseases with important social and economic effects. Many aging theories have been proposed, and important aging pathways have been discovered. Model organisms have had a crucial role in this process because of their short lifespan, cheap maintenance, and manipulation possibilities. Yeasts, worms, fruit flies, or mammalian models such as mice, monkeys, and recently, dogs, have helped shed light on aging processes. Genes and molecular mechanisms that were found to be critical in simple eukaryotic cells and species have been confirmed in humans mainly by the functional analysis of mammalian orthologues. Here, we review conserved aging mechanisms discovered in different model systems that are implicated in human longevity as well and that could be the target of anti-aging interventions in human.
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Affiliation(s)
- Giusi Taormina
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Federica Ferrante
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Salvatore Vieni
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Nello Grassi
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Antonio Russo
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Mario G Mirisola
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy.
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7
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Dansereau G, Wey TW, Legault V, Brunet MA, Kemnitz JW, Ferrucci L, Cohen AA. Conservation of physiological dysregulation signatures of aging across primates. Aging Cell 2019; 18:e12925. [PMID: 30746836 PMCID: PMC6413749 DOI: 10.1111/acel.12925] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/14/2018] [Accepted: 01/24/2019] [Indexed: 12/14/2022] Open
Abstract
Two major goals in the current biology of aging are to identify general mechanisms underlying the aging process and to explain species differences in aging. Recent research in humans suggests that one important driver of aging is dysregulation, the progressive loss of homeostasis in complex biological networks. Yet, there is a lack of comparative data for this hypothesis, and we do not know whether dysregulation is widely associated with aging or how well signals of homeostasis are conserved. To address this knowledge gap, we use unusually detailed longitudinal biomarker data from 10 species of nonhuman primates housed in research centers and data from two human populations to test the hypotheses that (a) greater dysregulation is associated with aging across primates and (b) physiological states characterizing homeostasis are conserved across primates to degrees associated with phylogenetic proximity. To evaluate dysregulation, we employed a multivariate distance measure, calculated from sets of biomarkers, that is associated with aging and mortality in human populations. Dysregulation scores positively correlated with age and risk of mortality in most nonhuman primates studied, and signals of homeostatic state were significantly conserved across species, declining with phylogenetic distance. Our study provides the first broad demonstration of physiological dysregulation associated with aging and mortality risk in multiple nonhuman primates. Our results also imply that emergent signals of homeostasis are evolutionarily conserved, although with notable variation among species, and suggest promising directions for future comparative studies on dysregulation and the aging process.
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Affiliation(s)
- Gabriel Dansereau
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
| | - Tina W. Wey
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
| | - Véronique Legault
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
| | - Marie A. Brunet
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
- Department of Biochemistry; University of Sherbrooke; Sherbrooke Quebec Canada
- PROTEO; Quebec Network for Research on Protein Function, Structure, and Engineering; Quebec Canada
| | - Joseph W. Kemnitz
- Department of Cell and Regenerative Biology; University of Wisconsin; School of Medicine and Public Health; Madison Wisconsin
- Wisconsin National Primate Research Center; University of Wisconsin-Madison; Madison Wisconsin
| | - Luigi Ferrucci
- Translational Gerontology Branch, Longitudinal Studies Section; National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital; Baltimore Maryland
| | - Alan A. Cohen
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
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8
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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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9
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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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10
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Didier ES, MacLean AG, Mohan M, Didier PJ, Lackner AA, Kuroda MJ. Contributions of Nonhuman Primates to Research on Aging. Vet Pathol 2016; 53:277-90. [PMID: 26869153 PMCID: PMC5027759 DOI: 10.1177/0300985815622974] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aging is the biological process of declining physiologic function associated with increasing mortality rate during advancing age. Humans and higher nonhuman primates exhibit unusually longer average life spans as compared with mammals of similar body mass. Furthermore, the population of humans worldwide is growing older as a result of improvements in public health, social services, and health care systems. Comparative studies among a wide range of organisms that include nonhuman primates contribute greatly to our understanding about the basic mechanisms of aging. Based on their genetic and physiologic relatedness to humans, nonhuman primates are especially important for better understanding processes of aging unique to primates, as well as for testing intervention strategies to improve healthy aging and to treat diseases and disabilities in older people. Rhesus and cynomolgus macaques are the predominant monkeys used in studies on aging, but research with lower nonhuman primate species is increasing. One of the priority topics of research about aging in nonhuman primates involves neurologic changes associated with cognitive decline and neurodegenerative diseases. Additional areas of research include osteoporosis, reproductive decline, caloric restriction, and their mimetics, as well as immune senescence and chronic inflammation that affect vaccine efficacy and resistance to infections and cancer. The purpose of this review is to highlight the findings from nonhuman primate research that contribute to our understanding about aging and health span in humans.
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Affiliation(s)
- E S Didier
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA, USA
| | - A G MacLean
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | - M Mohan
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | - P J Didier
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | - A A Lackner
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | - M J Kuroda
- Division of Immunology, Tulane National Primate Research Center, Covington, LA, USA
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11
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A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels. BMC Evol Biol 2015; 15:259. [PMID: 26589719 PMCID: PMC4654840 DOI: 10.1186/s12862-015-0534-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022] Open
Abstract
Background A deeper understanding of differences and similarities in transcriptional regulation between species can uncover important information about gene functions and the role of genes in disease. Deciphering such patterns between mice and humans is especially important since mice play an essential role in biomedical research. Results Here, in order to characterize evolutionary changes between humans and mice, we compared gene co-expression maps to evaluate the conservation of co-expression. We show that the conservation of co-expression connectivity of homologous genes is negatively correlated with molecular evolution rates, as expected. Then we investigated evolutionary aspects of gene sets related to functions, tissues, pathways and diseases. Genes expressed in the testis, eye and skin, and those associated with regulation of transcription, olfaction, PI3K signalling, response to virus and bacteria were more divergent between mice and humans in terms of co-expression connectivity. Surprisingly, a deeper investigation of the PI3K signalling cascade revealed that its divergence is caused by the most crucial genes of this pathway, such as mTOR and AKT2. On the other hand, our analysis revealed that genes expressed in the brain and in the bone, and those associated with cell adhesion, cell cycle, DNA replication and DNA repair are most strongly conserved in terms of co-expression network connectivity as well as having a lower rate of duplication events. Genes involved in lipid metabolism and genes specific to blood showed a signature of increased co-expression connectivity in the mouse. In terms of diseases, co-expression connectivity of genes related to metabolic disorders is the most strongly conserved between mice and humans and tumor-related genes the most divergent. Conclusions This work contributes to discerning evolutionary patterns between mice and humans in terms of gene interactions. Conservation of co-expression is a powerful approach to identify gene targets and processes with potential similarity and divergence between mice and humans, which has implications for drug testing and other studies employing the mouse as a model organism. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0534-7) contains supplementary material, which is available to authorized users.
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12
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Hippocampal Pruning as a New Theory of Schizophrenia Etiopathogenesis. Mol Neurobiol 2015; 53:2065-2081. [PMID: 25902861 DOI: 10.1007/s12035-015-9174-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/13/2015] [Indexed: 12/20/2022]
Abstract
Pruning in neurons has been suggested to be strongly involved in Schizophrenia's (SKZ) etiopathogenesis in recent biological, imaging, and genetic studies. We investigated the impact of protein-coding genes known to be involved in pruning, collected by a systematic literature research, in shaping the risk for SKZ in a case-control sample of 9,490 subjects (Psychiatric Genomics Consortium). Moreover, their modifications through evolution (humans, chimpanzees, and rats) and subcellular localization (as indicative of their biological function) were also investigated. We also performed a biological pathways (Gene Ontology) analysis. Genetics analyses found four genes (DLG1, NOS1, THBS4, and FADS1) and 17 pathways strongly involved in pruning and SKZ in previous literature findings to be significantly associated with the sample under analysis. The analysis of the subcellular localization found that secreted genes, and so regulatory ones, are the least conserved through evolution and also the most associated with SKZ. Their cell line and regional brain expression analysis found that their areas of primary expression are neuropil and the hippocampus, respectively. At the best of our knowledge, for the first time, we were able to describe the SKZ neurodevelopmental hypothesis starting from a single biological process. We can also hypothesize how alterations in pruning fine regulation and orchestration, strongly related with the evolutionary newest (and so more sensitive) secreted proteins, may be of particular relevance in the hippocampus. This early alteration may lead to a mis-structuration of neural connectivity, resulting in the different brain alteration that characterizes SKZ patients.
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13
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Neill D. Evolution of lifespan. J Theor Biol 2014; 358:232-45. [PMID: 24992233 DOI: 10.1016/j.jtbi.2014.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 11/26/2022]
Abstract
Present-day evolutionary theory, modern synthesis and evo-devo, appear to explain evolution. There remain however several points of contention. These include: biological time, direction, macroevolution verses microevolution, ageing and the extent of internal as opposed to external mediation. A new theoretical model for the control of biological time in vertebrates/bilaterians is introduced. Rather than biological time being controlled solely by a molecular cascade domino effect, it is suggested there is also an intracellular oscillatory clock. This clock (life's timekeeper) is synchronised across all cells in an organism and runs at a constant frequency throughout life. Slower frequencies extend lifespan, increase body/brain size and advance behaviour. They also create a time void which could aid additional evolutionary change. Faster frequencies shorten lifespan, reduce body/brain size and diminish behaviour. They are therefore less likely to mediate evolution in vertebrates/mammals. It is concluded that in vertebrates, especially mammals, there is a direction in evolution towards longer lifespan/advanced behaviour. Lifespan extension could equate with macroevolution and subsequent modifications with microevolution. As life's timekeeper controls the rate of ageing it constitutes a new genetic theory of ageing. Finally, as lifespan extension is internally mediated, this suggests a major role for internal mediation in evolution.
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Affiliation(s)
- David Neill
- University of Newcastle, Wear Base Unit, Monkwearmouth Hospital, Newcastle Road, Sunderland SR5 1NB, UK.
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14
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Li Y, de Magalhães JP. Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity. AGE (DORDRECHT, NETHERLANDS) 2013; 35:301-314. [PMID: 22205409 PMCID: PMC3592953 DOI: 10.1007/s11357-011-9361-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 12/05/2011] [Indexed: 05/31/2023]
Abstract
The genetic basis of the large species differences in longevity and aging remains a mystery. Thanks to recent large-scale genome sequencing efforts, the genomes of multiple species have been sequenced and can be used for cross-species comparisons to study species divergence in longevity. By analyzing proteins under accelerated evolution in several mammalian lineages where maximum lifespan increased, we identified genes and processes that are candidate targets of selection when longevity evolves. We identified several proteins with longevity-specific selection patterns, including COL3A1 that has previously been related to aging and proteins related to DNA damage repair and response such as DDB1 and CAPNS1. Moreover, we found that processes such as lipid metabolism and cholesterol catabolism show such patterns of selection and suggest a link between the evolution of lipid metabolism, cholesterol catabolism, and the evolution of longevity. Lastly, we found evidence that the proteasome-ubiquitin system is under selection specific to lineages where longevity increased and suggest that its selection had a role in the evolution of longevity. These results provide evidence that natural selection acts on species when longevity evolves, give insights into adaptive genetic changes associated with the evolution of longevity in mammals, and provide evidence that at least some repair systems are selected for when longevity increases.
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Affiliation(s)
- Yang Li
- />Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Room 245, Crown Street, Liverpool, L69 7ZB UK
- />Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - João Pedro de Magalhães
- />Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Room 245, Crown Street, Liverpool, L69 7ZB UK
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15
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Neill D. Life's timekeeper. Ageing Res Rev 2013; 12:567-78. [PMID: 23354279 DOI: 10.1016/j.arr.2013.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/08/2013] [Accepted: 01/10/2013] [Indexed: 12/18/2022]
Abstract
Life's timekeeper is a 'free-running' intracellular oscillator synchronised across all cells. It runs throughout life splitting lifespan into equal length phases. During the maturational period it controls the overall rate of progression whereas in the post-maturational period it controls the overall rate of ageing. This includes the rate of senescence and hence time to death. As such life's timekeeper equates maturational and post-maturational time, hence explains the tight correlation between these time periods that has existed throughout mammalian evolution. Life's timekeeper is proposed to have played an important role in vertebrate evolution. A slower oscillatory frequency results in proportional life phase prolongation. This leads to increased body and brain size, together with extended lifespan. Higher brain centres, neocortex in mammals, are disproportionately enlarged. Hence behavioural capacity is increased. The extended post-maturational period ensures that there is enough time in order that the behavioural advantages can be fully manifest in the environment. A faster oscillatory frequency would result in proportional life phase reduction. This process however would lead to reduced behavioural capacity, and is hence unlikely to be positively selected. Therefore throughout evolution life's timekeeper has operated to extend lifespan. It has hence functioned to promote longevity as opposed to ageing.
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Affiliation(s)
- David Neill
- Department of Psychiatry, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
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16
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Samusik N, Krukovskaya L, Meln I, Shilov E, Kozlov AP. PBOV1 is a human de novo gene with tumor-specific expression that is associated with a positive clinical outcome of cancer. PLoS One 2013; 8:e56162. [PMID: 23418531 PMCID: PMC3572036 DOI: 10.1371/journal.pone.0056162] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 01/10/2013] [Indexed: 01/20/2023] Open
Abstract
PBOV1 is a known human protein-coding gene with an uncharacterized function. We have previously found that PBOV1 lacks orthologs in non-primate genomes and is expressed in a wide range of tumor types. Here we report that PBOV1 protein-coding sequence is human-specific and has originated de novo in the primate evolution through a series of frame-shift and stop codon mutations. We profiled PBOV1 expression in multiple cancer and normal tissue samples and found that it was expressed in 19 out of 34 tumors of various origins but completely lacked expression in any of the normal adult or fetal human tissues. We found that, unlike the cancer/testis antigens that are typically controlled by CpG island-containing promoters, PBOV1 was expressed from a GC-poor TATA-containing promoter which was not influenced by CpG demethylation and was inactive in testis. Our analysis of public microarray data suggests that PBOV1 activation in tumors could be dependent on the Hedgehog signaling pathway. Despite the recent de novo origin and the lack of identifiable functional signatures, a missense SNP in the PBOV1 coding sequence has been previously associated with an increased risk of breast cancer. Using publicly available microarray datasets, we found that high levels of PBOV1 expression in breast cancer and glioma samples were significantly associated with a positive outcome of the cancer disease. We also found that PBOV1 was highly expressed in primary but not in recurrent high-grade gliomas, suggesting the presence of a negative selection against PBOV1-expressing cancer cells. Our findings could contribute to the understanding of the mechanisms behind de novo gene origin and the possible role of tumors in this process.
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Affiliation(s)
- Nikolay Samusik
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany.
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17
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Miki T. [The deal with the super-aged society ~to anti-aging research and epidemiological studies from genomic medicine~]. Nihon Ronen Igakkai Zasshi 2013; 50:608-14. [PMID: 24622125 DOI: 10.3143/geriatrics.50.608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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18
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Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PLoS Genet 2012; 8:e1002834. [PMID: 22912585 PMCID: PMC3415404 DOI: 10.1371/journal.pgen.1002834] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 06/04/2012] [Indexed: 01/19/2023] Open
Abstract
Dietary restriction (DR), limiting nutrient intake from diet without causing malnutrition, delays the aging process and extends lifespan in multiple organisms. The conserved life-extending effect of DR suggests the involvement of fundamental mechanisms, although these remain a subject of debate. To help decipher the life-extending mechanisms of DR, we first compiled a list of genes that if genetically altered disrupt or prevent the life-extending effects of DR. We called these DR–essential genes and identified more than 100 in model organisms such as yeast, worms, flies, and mice. In order for other researchers to benefit from this first curated list of genes essential for DR, we established an online database called GenDR (http://genomics.senescence.info/diet/). To dissect the interactions of DR–essential genes and discover the underlying lifespan-extending mechanisms, we then used a variety of network and systems biology approaches to analyze the gene network of DR. We show that DR–essential genes are more conserved at the molecular level and have more molecular interactions than expected by chance. Furthermore, we employed a guilt-by-association method to predict novel DR–essential genes. In budding yeast, we predicted nine genes related to vacuolar functions; we show experimentally that mutations deleting eight of those genes prevent the life-extending effects of DR. Three of these mutants (OPT2, FRE6, and RCR2) had extended lifespan under ad libitum, indicating that the lack of further longevity under DR is not caused by a general compromise of fitness. These results demonstrate how network analyses of DR using GenDR can be used to make phenotypically relevant predictions. Moreover, gene-regulatory circuits reveal that the DR–induced transcriptional signature in yeast involves nutrient-sensing, stress responses and meiotic transcription factors. Finally, comparing the influence of gene expression changes during DR on the interactomes of multiple organisms led us to suggest that DR commonly suppresses translation, while stimulating an ancient reproduction-related process. Dietary restriction has been shown to extend lifespan in diverse, evolutionarily distant species, yet its underlying mechanisms remain unknown. We first constructed a database of genes essential for the life-extending effects of dietary restriction in various model organisms and then studied their interactions using a variety of network and systems biology approaches. This enabled us to predict novel genes related to dietary restriction, which we validated experimentally in yeast. By comparing large-scale data compilations (interactomes and transcriptomes) from multiple organisms, we were able to condense this -omics information to the most conserved essential elements, eliminating species-specific adaptive responses. These results lead us to the rather surprising conclusion that lifespan extension by a restricted diet commonly may exploit an ancient rejuvenation process derived from gametogenesis.
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19
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Ortutay C, Vihinen M. Conserved and quickly evolving immunome genes have different evolutionary paths. Hum Mutat 2012; 33:1456-63. [PMID: 22623381 DOI: 10.1002/humu.22125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 05/15/2012] [Indexed: 12/11/2022]
Abstract
Genetic, transcript, and protein level variations have important functional and evolutionary consequences. We performed systematic data collection and analysis of copy-number variations, single-nucleotide polymorphisms, disease-causing variations, messenger RNA splicing variants, and protein posttranslational modifications for the genes and proteins essential for human immune system. Information about polymorphic and evolutionarily fixed genetic variations was used to group immunome genes to the most conserved and the most quickly changing ones under directed selection during the recent immunome evolution. Gene Ontology terms related to adaptive immunity are associated with gene groups subject to recent directing selection. In addition, several other characteristics of the immunome genes and proteins in these two categories have statistically significant differences. The presented findings question the usability of directed mouse genes as models for human diseases and conditions and shed light on the fine tuning of human immunity and its diverse functions.
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Affiliation(s)
- Csaba Ortutay
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
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20
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Murabito JM, Yuan R, Lunetta KL. The search for longevity and healthy aging genes: insights from epidemiological studies and samples of long-lived individuals. J Gerontol A Biol Sci Med Sci 2012; 67:470-9. [PMID: 22499766 DOI: 10.1093/gerona/gls089] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genetic factors clearly contribute to exceptional longevity and healthy aging in humans, yet the identification of the underlying genes remains a challenge. Longevity is a complex phenotype with modest heritability. Age-related phenotypes with higher heritability may have greater success in gene discovery. Candidate gene and genome-wide association studies (GWAS) for longevity have had only limited success to date. The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium conducted a meta-analysis of GWAS data for longevity, defined as survival to age 90 years or older, that identified several interesting associations but none achieved genome-wide significance. A recent GWAS of longevity conducted in the Leiden Longevity Study identified the ApoE E4 isoform as deleterious to longevity that was confirmed in an independent GWAS of long-lived individuals of German descent. Notably, no other genetic loci for longevity have been identified in these GWAS. To examine the conserved genetic mechanisms between the mouse and humans for life span, we mapped the top Cohorts for Heart and Aging Research in Genomic Epidemiology GWAS associations for longevity to the mouse chromosomal map and noted that eight of the ten top human associations were located within a previously reported mouse life-span quantitative trait loci. This work suggests that the mouse and human may share mechanisms leading to aging and that the mouse model may help speed the understanding of how genes identified in humans affect the biology of aging. We expect these ongoing collaborations and the translational work with basic scientists to accelerate the identification of genes that delay aging and promote a healthy life span.
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Affiliation(s)
- Joanne M Murabito
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA 01702, USA.
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21
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de Magalhães JP, Matsuda A. Genome-wide patterns of genetic distances reveal candidate Loci contributing to human population-specific traits. Ann Hum Genet 2011; 76:142-58. [PMID: 22188222 DOI: 10.1111/j.1469-1809.2011.00695.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Modern humans originated in Africa before migrating across the world with founder effects and adaptations to new environments contributing to their present phenotypic diversity. Determining the genetic basis of differences between populations may provide clues about our evolutionary history and may have clinical implications. Herein, we develop a method to detect genes and biological processes in which populations most differ by calculating the genetic distance between modern populations and a hypothetical ancestral population. We apply our method to large-scale single nucleotide polymorphism (SNP) data from human populations of African, European and Asian origin. As expected, ancestral alleles were more conserved in the African populations and we found evidence of high divergence in genes previously suggested as targets of selection related to skin pigmentation, immune response, senses and dietary adaptations. Our genome-wide scan also reveals novel candidates for contributing to population-specific traits. These include genes related to neuronal development and behavior that may have been influenced by cultural processes. Moreover, in the African populations, we found a high divergence in genes related to UV protection and to the male reproductive system. Taken together, these results confirm and expand previous findings, providing new clues about the evolution and genetics of human phenotypic diversity.
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Affiliation(s)
- João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
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22
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Li YH, Dong MQ, Guo Z. Systematic analysis and prediction of longevity genes in Caenorhabditis elegans. Mech Ageing Dev 2010; 131:700-9. [DOI: 10.1016/j.mad.2010.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/14/2010] [Accepted: 10/01/2010] [Indexed: 10/19/2022]
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23
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de Magalhães JP, Finch CE, Janssens G. Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions. Ageing Res Rev 2010; 9:315-23. [PMID: 19900591 DOI: 10.1016/j.arr.2009.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 10/17/2009] [Accepted: 10/28/2009] [Indexed: 01/08/2023]
Abstract
Recent technological advances that allow faster and cheaper DNA sequencing are now driving biological and medical research. In this review, we provide an overview of state-of-the-art next-generation sequencing (NGS) platforms and their applications, including in genome sequencing and resequencing, transcriptional profiling (RNA-Seq) and high-throughput survey of DNA-protein interactions (ChIP-Seq) and of the epigenome. Particularly, we focus on how new methods made possible by NGS can help unravel the biological and genetic mechanisms of aging, longevity and age-related diseases. In the same way, however, NGS platforms open discovery not available before, they also give rise to new challenges, in particular in processing, analyzing and interpreting the data. Bioinformatics and software issues plus statistical difficulties in genome-wide studies are discussed, as well as the use of targeted sequencing to decrease costs and facilitate statistical analyses. Lastly, we discuss a number of methods to gather biological insights from massive amounts of data, such as functional enrichment, transcriptional regulation and network analyses. Although in the fast-moving field of NGS new platforms will soon take center stage, the approaches made possible by NGS will be at the basis of molecular biology, genetics and systems biology for years to come, making them instrumental for research on aging.
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24
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Hawkes K. Colloquium paper: how grandmother effects plus individual variation in frailty shape fertility and mortality: guidance from human-chimpanzee comparisons. Proc Natl Acad Sci U S A 2010; 107 Suppl 2:8977-84. [PMID: 20445089 PMCID: PMC3024018 DOI: 10.1073/pnas.0914627107] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In the first paper to present formal theory explaining that senescence is a consequence of natural selection, W. D. Hamilton concluded that human postmenopausal longevity results from the contributions of ancestral grandmothers to the reproduction of their relatives. A grandmother hypothesis, subsequently elaborated with additional lines of evidence, helps explain both exceptional longevity and additional features of life history that distinguish humans from the other great apes. However, some of the variation observed in aging rates seems inconsistent with the tradeoffs between current and future reproduction identified by theory. In humans and chimpanzees, our nearest living relatives, individuals who bear offspring at faster rates do not cease bearing sooner. They continue to be fertile longer instead. Furthermore, within both species, groups with lower overall mortality rates have faster rates of increase in death risk with advancing age. These apparent contradictions to the expected life history tradeoffs likely result from heterogeneity in frailty among individuals. Whereas robust and frail alike must allocate investments between current and future reproduction, the more robust can afford more of both. This heterogeneity, combined with evolutionary tradeoffs and the key role of ancestral grandmothers they identify, helps explain aspects of human aging that increasingly concern us all.
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Affiliation(s)
- Kristen Hawkes
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112
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25
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Finch CE. Evolution in health and medicine Sackler colloquium: Evolution of the human lifespan and diseases of aging: roles of infection, inflammation, and nutrition. Proc Natl Acad Sci U S A 2010; 107 Suppl 1:1718-24. [PMID: 19966301 PMCID: PMC2868286 DOI: 10.1073/pnas.0909606106] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Humans have evolved much longer lifespans than the great apes, which rarely exceed 50 years. Since 1800, lifespans have doubled again, largely due to improvements in environment, food, and medicine that minimized mortality at earlier ages. Infections cause most mortality in wild chimpanzees and in traditional forager-farmers with limited access to modern medicine. Although we know little of the diseases of aging under premodern conditions, in captivity, chimpanzees present a lower incidence of cancer, ischemic heart disease, and neurodegeneration than current human populations. These major differences in pathology of aging are discussed in terms of genes that mediate infection, inflammation, and nutrition. Apolipoprotein E alleles are proposed as a prototype of pleiotropic genes, which influence immune responses, arterial and Alzheimer's disease, and brain development.
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Affiliation(s)
- Caleb E. Finch
- Davis School of Gerontology and the University of Southern California, Los Angeles, CA 90089
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26
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de Magalhães JP, Budovsky A, Lehmann G, Costa J, Li Y, Fraifeld V, Church GM. The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell 2009; 8:65-72. [PMID: 18986374 DOI: 10.1111/j.1474-9726.2008.00442.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aging is a complex, challenging phenomenon that requires multiple, interdisciplinary approaches to unravel its puzzles. To assist basic research on aging, we developed the Human Ageing Genomic Resources (HAGR). This work provides an overview of the databases and tools in HAGR and describes how the gerontology research community can employ them. Several recent changes and improvements to HAGR are also presented. The two centrepieces in HAGR are GenAge and AnAge. GenAge is a gene database featuring genes associated with aging and longevity in model organisms, a curated database of genes potentially associated with human aging, and a list of genes tested for their association with human longevity. A myriad of biological data and information is included for hundreds of genes, making GenAge a reference for research that reflects our current understanding of the genetic basis of aging. GenAge can also serve as a platform for the systems biology of aging, and tools for the visualization of protein-protein interactions are also included. AnAge is a database of aging in animals, featuring over 4000 species, primarily assembled as a resource for comparative and evolutionary studies of aging. Longevity records, developmental and reproductive traits, taxonomic information, basic metabolic characteristics, and key observations related to aging are included in AnAge. Software is also available to aid researchers in the form of Perl modules to automate numerous tasks and as an SPSS script to analyse demographic mortality data. The HAGR are available online at http://genomics.senescence.info.
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27
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Budovsky A, Tacutu R, Yanai H, Abramovich A, Wolfson M, Fraifeld V. Common gene signature of cancer and longevity. Mech Ageing Dev 2009; 130:33-9. [DOI: 10.1016/j.mad.2008.04.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 03/23/2008] [Accepted: 04/06/2008] [Indexed: 11/28/2022]
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28
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Thompson FJ, Barker GLA, Nolan T, Gems D, Viney ME. Transcript profiles of long- and short-lived adults implicate protein synthesis in evolved differences in ageing in the nematode Strongyloides ratti. Mech Ageing Dev 2008; 130:167-72. [PMID: 19056418 DOI: 10.1016/j.mad.2008.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 10/21/2008] [Accepted: 11/04/2008] [Indexed: 02/04/2023]
Abstract
The nematode Strongyloides ratti shows remarkable phenotypic plasticity in ageing, with parasitic adults living at least 80-times longer than free-living adults. Given that long- and short-lived adults are genetically identical, this plasticity is likely to be due to differences in gene expression. To try and understand how this inter-morph difference in longevity evolved, we compared gene expression in long- and short-lived adults. DNA microarray analysis of long- and short-lived adults identified 32 genes that were up-regulated in long-lived adults, and 96 genes up-regulated in short-lived adults. Strikingly, 38.5% of the genes expressed more in the short-lived morph are predicted to encode ribosomal proteins, compared with only 9% in the long-lived morph. Among the 32 longevity-associated genes there was very little enrichment of genes linked to cellular maintenance. Overall, we have therefore observed a negative correlation between expression of ribosomal protein genes and longevity in S. ratti. Interestingly, engineered reduction of expression of ribosomal protein genes increases lifespan in the free-living nematode Caenorhabditis elegans. Our study therefore suggests that differences in levels of protein synthesis could contribute to evolved differences in animal longevity.
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Affiliation(s)
- Fiona J Thompson
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK
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