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de Magalhães JP, Abidi Z, dos Santos GA, Avelar RA, Barardo D, Chatsirisupachai K, Clark P, De-Souza EA, Johnson EJ, Lopes I, Novoa G, Senez L, Talay A, Thornton D, To P. Human Ageing Genomic Resources: updates on key databases in ageing research. Nucleic Acids Res 2024; 52:D900-D908. [PMID: 37933854 PMCID: PMC10767973 DOI: 10.1093/nar/gkad927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023] Open
Abstract
Ageing is a complex and multifactorial process. For two decades, the Human Ageing Genomic Resources (HAGR) have aided researchers in the study of various aspects of ageing and its manipulation. Here, we present the key features and recent enhancements of these resources, focusing on its six main databases. One database, GenAge, focuses on genes related to ageing, featuring 307 genes linked to human ageing and 2205 genes associated with longevity and ageing in model organisms. AnAge focuses on ageing, longevity, and life-history across animal species, containing data on 4645 species. DrugAge includes information about 1097 longevity drugs and compounds in model organisms such as mice, rats, flies, worms and yeast. GenDR provides a list of 214 genes associated with the life-extending benefits of dietary restriction in model organisms. CellAge contains a catalogue of 866 genes associated with cellular senescence. The LongevityMap serves as a repository for genetic variants associated with human longevity, encompassing 3144 variants pertaining to 884 genes. Additionally, HAGR provides various tools as well as gene expression signatures of ageing, dietary restriction, and replicative senescence based on meta-analyses. Our databases are integrated, regularly updated, and manually curated by experts. HAGR is freely available online (https://genomics.senescence.info/).
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Affiliation(s)
- João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Zoya Abidi
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Gabriel Arantes dos Santos
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Roberto A Avelar
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Diogo Barardo
- NOVOS Labs, 100 Park Avenue, 16th Fl, New York, NY 10017, USA
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Peter Clark
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Evandro A De-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas 13083-970, SP, Brazil
| | - Emily J Johnson
- Computational Biology Facility, Liverpool Shared Research Facilities, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Inês Lopes
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Guy Novoa
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Ludovic Senez
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Angelo Talay
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Paul Ka Po To
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
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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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3
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Ribeiro C, Farmer CK, de Magalhães JP, Freitas AA. Predicting lifespan-extending chemical compounds for C. elegans with machine learning and biologically interpretable features. Aging (Albany NY) 2023; 15:6073-6099. [PMID: 37450404 PMCID: PMC10373959 DOI: 10.18632/aging.204866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Recently, there has been a growing interest in the development of pharmacological interventions targeting ageing, as well as in the use of machine learning for analysing ageing-related data. In this work, we use machine learning methods to analyse data from DrugAge, a database of chemical compounds (including drugs) modulating lifespan in model organisms. To this end, we created four types of datasets for predicting whether or not a compound extends the lifespan of C. elegans (the most frequent model organism in DrugAge), using four different types of predictive biological features, based on: compound-protein interactions, interactions between compounds and proteins encoded by ageing-related genes, and two types of terms annotated for proteins targeted by the compounds, namely Gene Ontology (GO) terms and physiology terms from the WormBase's Phenotype Ontology. To analyse these datasets, we used a combination of feature selection methods in a data pre-processing phase and the well-established random forest algorithm for learning predictive models from the selected features. In addition, we interpreted the most important features in the two best models in light of the biology of ageing. One noteworthy feature was the GO term "Glutathione metabolic process", which plays an important role in cellular redox homeostasis and detoxification. We also predicted the most promising novel compounds for extending lifespan from a list of previously unlabelled compounds. These include nitroprusside, which is used as an antihypertensive medication. Overall, our work opens avenues for future work in employing machine learning to predict novel life-extending compounds.
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Affiliation(s)
- Caio Ribeiro
- School of Computing, University of Kent, Canterbury, Kent, UK
| | | | - João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Alex A. Freitas
- School of Computing, University of Kent, Canterbury, Kent, UK
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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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5
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Sing TL, Brar GA, Ünal E. Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control. Annu Rev Genet 2022; 56:89-112. [PMID: 35878627 PMCID: PMC9712276 DOI: 10.1146/annurev-genet-080320-025104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription factor Ndt80 is sufficient to extend life span in mitotically dividing budding yeast, suggesting that meiotic rejuvenation pathways can be repurposed outside of their natural context. In this review, we highlight recent studies of gametogenesis that provide emerging insight into natural quality control, organelle remodeling, and rejuvenation strategies that exist within a cell. These include selective inheritance, programmed degradation, and de novo synthesis, all of which are governed by the meiotic gene expression program entailing many forms of noncanonical gene regulation. Finally, we highlight critical questions that remain in the field and provide perspective on the implications of gametogenesis research on human health span.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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Liu Q, Chang CE, Wooldredge AC, Fong B, Kennedy BK, Zhou C. Tom70-based transcriptional regulation of mitochondrial biogenesis and aging. eLife 2022; 11:e75658. [PMID: 35234609 PMCID: PMC8926401 DOI: 10.7554/elife.75658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial biogenesis has two major steps: the transcriptional activation of nuclear genome-encoded mitochondrial proteins and the import of nascent mitochondrial proteins that are synthesized in the cytosol. These nascent mitochondrial proteins are aggregation-prone and can cause cytosolic proteostasis stress. The transcription factor-dependent transcriptional regulations and the TOM-TIM complex-dependent import of nascent mitochondrial proteins have been extensively studied. Yet, little is known regarding how these two steps of mitochondrial biogenesis coordinate with each other to avoid the cytosolic accumulation of these aggregation-prone nascent mitochondrial proteins. Here, we show that in budding yeast, Tom70, a conserved receptor of the TOM complex, moonlights to regulate the transcriptional activity of mitochondrial proteins. Tom70's transcription regulatory role is conserved in Drosophila. The dual roles of Tom70 in both transcription/biogenesis and import of mitochondrial proteins allow the cells to accomplish mitochondrial biogenesis without compromising cytosolic proteostasis. The age-related reduction of Tom70, caused by reduced biogenesis and increased degradation of Tom70, is associated with the loss of mitochondrial membrane potential, mtDNA, and mitochondrial proteins. While loss of Tom70 accelerates aging and age-related mitochondrial defects, overexpressing TOM70 delays these mitochondrial dysfunctions and extends the replicative lifespan. Our results reveal unexpected roles of Tom70 in mitochondrial biogenesis and aging.
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Affiliation(s)
- Qingqing Liu
- Buck Institute for Research on AgingNovatoUnited States
| | | | | | - Benjamin Fong
- Buck Institute for Research on AgingNovatoUnited States
| | - Brian K Kennedy
- Buck Institute for Research on AgingNovatoUnited States
- Healthy Longevity Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
- Singapore Institute of Clinical Sciences, A(∗)STARSingaporeSingapore
| | - Chuankai Zhou
- Buck Institute for Research on AgingNovatoUnited States
- USC Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
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7
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Pandey M, Bansal S, Chawla G. Evaluation of lifespan promoting effects of biofortified wheat in Drosophila melanogaster. Exp Gerontol 2022; 160:111697. [PMID: 35016996 PMCID: PMC7613042 DOI: 10.1016/j.exger.2022.111697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/15/2021] [Accepted: 01/05/2022] [Indexed: 11/04/2022]
Abstract
Evaluation of nutritionally enhanced biofortified dietary interventions that increase lifespan may uncover cost-effective and sustainable approaches for treatment of age-related morbidities and increasing healthy life expectancy. In this study, we report that anthocyanin rich, high yielding crossbred blue wheat prolongs lifespan of Drosophila melanogaster in different dietary contexts. In addition to functioning as an antioxidant rich intervention, the biofortified blue wheat also works through modulating expression of DR pathway genes including AMPK alpha, SREBP, PEPCK and Cry. Supplementation with blue- or purple-colored wheat provided better protection against paraquat-induced oxidative stress than control diet and increased survivability of flies in which superoxide dismutase 2 was knocked down conditionally in adults. Lastly, our findings indicate that supplementing biofortified blue wheat formulated diet prevented the decrease in lifespan and cardiac structural pathologies associated with intake of high fat diet. Overall, our findings indicate that plant-based diets formulated with biofortified cereal crops promote healthy ageing and delay progression of diseases that are exacerbated by accumulation of oxidative damage.
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Affiliation(s)
- Manish Pandey
- RNA Biology Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Sakshi Bansal
- RNA Biology Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Geetanjali Chawla
- RNA Biology Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India.
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Vega Magdaleno GD, Bespalov V, Zheng Y, Freitas AA, de Magalhaes JP. Machine learning-based predictions of dietary restriction associations across ageing-related genes. BMC Bioinformatics 2022; 23:10. [PMID: 34983372 PMCID: PMC8729156 DOI: 10.1186/s12859-021-04523-8] [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: 07/28/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Dietary restriction (DR) is the most studied pro-longevity intervention; however, a complete understanding of its underlying mechanisms remains elusive, and new research directions may emerge from the identification of novel DR-related genes and DR-related genetic features. RESULTS This work used a Machine Learning (ML) approach to classify ageing-related genes as DR-related or NotDR-related using 9 different types of predictive features: PathDIP pathways, two types of features based on KEGG pathways, two types of Protein-Protein Interactions (PPI) features, Gene Ontology (GO) terms, Genotype Tissue Expression (GTEx) expression features, GeneFriends co-expression features and protein sequence descriptors. Our findings suggested that features biased towards curated knowledge (i.e. GO terms and biological pathways), had the greatest predictive power, while unbiased features (mainly gene expression and co-expression data) have the least predictive power. Moreover, a combination of all the feature types diminished the predictive power compared to predictions based on curated knowledge. Feature importance analysis on the two most predictive classifiers mostly corroborated existing knowledge and supported recent findings linking DR to the Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) signalling pathway and G protein-coupled receptors (GPCR). We then used the two strongest combinations of feature type and ML algorithm to predict DR-relatedness among ageing-related genes currently lacking DR-related annotations in the data, resulting in a set of promising candidate DR-related genes (GOT2, GOT1, TSC1, CTH, GCLM, IRS2 and SESN2) whose predicted DR-relatedness remain to be validated in future wet-lab experiments. CONCLUSIONS This work demonstrated the strong potential of ML-based techniques to identify DR-associated features as our findings are consistent with literature and recent discoveries. Although the inference of new DR-related mechanistic findings based solely on GO terms and biological pathways was limited due to their knowledge-driven nature, the predictive power of these two features types remained useful as it allowed inferring new promising candidate DR-related genes.
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Affiliation(s)
- Gustavo Daniel Vega Magdaleno
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, 6 West Derby St, Liverpool, L7 8TX, UK
| | - Vladislav Bespalov
- School of Computer Technologies and Controls, ITMO University, Kronverkskiy Prospekt 49, 197101, St Petersburg, Russia
| | - Yalin Zheng
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, 6 West Derby St, Liverpool, L7 8TX, UK
| | - Alex A Freitas
- School of Computing, University of Kent, Canterbury, CT2 7NF, UK
| | - Joao Pedro de Magalhaes
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, 6 West Derby St, Liverpool, L7 8TX, UK.
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Dato S, Crocco P, Rambaldi Migliore N, Lescai F. Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging. Front Genet 2021; 12:689824. [PMID: 34178042 PMCID: PMC8225294 DOI: 10.3389/fgene.2021.689824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Aging is a complex phenotype influenced by a combination of genetic and environmental factors. Although many studies addressed its cellular and physiological age-related changes, the molecular causes of aging remain undetermined. Considering the biological complexity and heterogeneity of the aging process, it is now clear that full understanding of mechanisms underlying aging can only be achieved through the integration of different data types and sources, and with new computational methods capable to achieve such integration. Recent Advances In this review, we show that an omics vision of the age-dependent changes occurring as the individual ages can provide researchers with new opportunities to understand the mechanisms of aging. Combining results from single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed during aging and disease. The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, able to investigate different biological markers and to monitor them simultaneously during the aging process with high accuracy and specificity, represents a unique opportunity offered to biogerontologists today. Critical Issues Although the capacity to produce big data drastically increased over the years, integration, interpretation and sharing of high-throughput data remain major challenges. In this paper we present a survey of the emerging omics approaches in aging research and provide a large collection of datasets and databases as a useful resource for the scientific community to identify causes of aging. We discuss their peculiarities, emphasizing the need for the development of methods focused on the integration of different data types. Future Directions We critically review the contribution of bioinformatics into the omics of aging research, and we propose a few recommendations to boost collaborations and produce new insights. We believe that significant advancements can be achieved by following major developments in bioinformatics, investing in diversity, data sharing and community-driven portable bioinformatics methods. We also argue in favor of more engagement and participation, and we highlight the benefits of new collaborations along these lines. This review aims at being a useful resource for many researchers in the field, and a call for new partnerships in aging research.
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Affiliation(s)
- Serena Dato
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | | | - Francesco Lescai
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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10
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Jin K, Wilson KA, Beck JN, Nelson CS, Brownridge GW, Harrison BR, Djukovic D, Raftery D, Brem RB, Yu S, Drton M, Shojaie A, Kapahi P, Promislow D. Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila. PLoS Genet 2020; 16:e1008835. [PMID: 32644988 PMCID: PMC7347105 DOI: 10.1371/journal.pgen.1008835] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/06/2020] [Indexed: 01/08/2023] Open
Abstract
In most organisms, dietary restriction (DR) increases lifespan. However, several studies have found that genotypes within the same species vary widely in how they respond to DR. To explore the mechanisms underlying this variation, we exposed 178 inbred Drosophila melanogaster lines to a DR or ad libitum (AL) diet, and measured a panel of 105 metabolites under both diets. Twenty four out of 105 metabolites were associated with the magnitude of the lifespan response. These included proteinogenic amino acids and metabolites involved in α-ketoglutarate (α-KG)/glutamine metabolism. We confirm the role of α-KG/glutamine synthesis pathways in the DR response through genetic manipulations. We used covariance network analysis to investigate diet-dependent interactions between metabolites, identifying the essential amino acids threonine and arginine as “hub” metabolites in the DR response. Finally, we employ a novel metabolic and genetic bipartite network analysis to reveal multiple genes that influence DR lifespan response, some of which have not previously been implicated in DR regulation. One of these is CCHa2R, a gene that encodes a neuropeptide receptor that influences satiety response and insulin signaling. Across the lines, variation in an intronic single nucleotide variant of CCHa2R correlated with variation in levels of five metabolites, all of which in turn were correlated with DR lifespan response. Inhibition of adult CCHa2R expression extended DR lifespan of flies, confirming the role of CCHa2R in lifespan response. These results provide support for the power of combined genomic and metabolomic analysis to identify key pathways underlying variation in this complex quantitative trait. Dietary restriction extends lifespan across most organisms in which it has been tested. However, several studies have now demonstrated that this effect can vary dramatically across different genotypes within a population. Within a population, dietary restriction might be beneficial for some, yet detrimental for others. Here, we measure the metabolome of 178 genetically characterized fly strains on fully fed and restricted diets. The fly strains vary widely in their lifespan response to dietary restriction. We then use information about each strain’s genome and metabolome (a measure of small molecules circulating in flies) to pinpoint cellular pathways that govern this variation in response. We identify a novel pathway involving the gene CCHa2R, which encodes a neuropeptide receptor that has not previously been implicated in dietary restriction or age-related signaling pathways. This study demonstrates the power of leveraging systems biology and network biology methods to understand how and why different individuals vary in their response to health and lifespan-extending interventions.
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Affiliation(s)
- Kelly Jin
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kenneth A. Wilson
- Buck Institute for Research on Aging, Novato, California, United States of America
- Davis School of Gerontology, University of Southern California, University Park, Los Angeles, California, United States of America
| | - Jennifer N. Beck
- Buck Institute for Research on Aging, Novato, California, United States of America
| | | | - George W. Brownridge
- Buck Institute for Research on Aging, Novato, California, United States of America
- Dominican University of California, San Rafael, California, United States of America
| | - Benjamin R. Harrison
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Danijel Djukovic
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington, United States of America
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington, United States of America
| | - Rachel B. Brem
- Buck Institute for Research on Aging, Novato, California, United States of America
- Davis School of Gerontology, University of Southern California, University Park, Los Angeles, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Shiqing Yu
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
| | - Mathias Drton
- Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Ali Shojaie
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, California, United States of America
- Davis School of Gerontology, University of Southern California, University Park, Los Angeles, California, United States of America
| | - Daniel Promislow
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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11
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Gleim LC, Karim MR, Zimmermann L, Kohlbacher O, Stenzhorn H, Decker S, Beyan O. Enabling ad-hoc reuse of private data repositories through schema extraction. J Biomed Semantics 2020; 11:6. [PMID: 32641124 PMCID: PMC7341611 DOI: 10.1186/s13326-020-00223-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 07/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sharing sensitive data across organizational boundaries is often significantly limited by legal and ethical restrictions. Regulations such as the EU General Data Protection Rules (GDPR) impose strict requirements concerning the protection of personal and privacy sensitive data. Therefore new approaches, such as the Personal Health Train initiative, are emerging to utilize data right in their original repositories, circumventing the need to transfer data. RESULTS Circumventing limitations of previous systems, this paper proposes a configurable and automated schema extraction and publishing approach, which enables ad-hoc SPARQL query formulation against RDF triple stores without requiring direct access to the private data. The approach is compatible with existing Semantic Web-based technologies and allows for the subsequent execution of such queries in a safe setting under the data provider's control. Evaluation with four distinct datasets shows that a configurable amount of concise and task-relevant schema, closely describing the structure of the underlying data, was derived, enabling the schema introspection-assisted authoring of SPARQL queries. CONCLUSIONS Automatically extracting and publishing data schema can enable the introspection-assisted creation of data selection and integration queries. In conjunction with the presented system architecture, this approach can enable reuse of data from private repositories and in settings where agreeing upon a shared schema and encoding a priori is infeasible. As such, it could provide an important step towards reuse of data from previously inaccessible sources and thus towards the proliferation of data-driven methods in the biomedical domain.
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Affiliation(s)
| | - Md Rezaul Karim
- Informatik 5, RWTH Aachen University, Ahornstr. 55, Aachen, 52062, Germany.,Fraunhofer FIT, Schloss Birlinghoven, Sankt Augustin, 53754, Germany
| | - Lukas Zimmermann
- Institute for Translational Bioinformatics, University Hospital Tübingen, Sand 14, Tübingen, 72076, Germany
| | - Oliver Kohlbacher
- Institute for Translational Bioinformatics, University Hospital Tübingen, Sand 14, Tübingen, 72076, Germany.,Applied Bioinformatics, Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany.,Quantitative Biology Center, University of Tübingen, Auf der Morgenstelle 10, Tübingen, 72076, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Holger Stenzhorn
- Institute for Translational Bioinformatics, University Hospital Tübingen, Sand 14, Tübingen, 72076, Germany.,Institute for Medical Biometry, Epidemiology und Medical Informatics, Saarland University Medical Center, Kirrberger Str., Building 86, Homburg, 66421, Germany
| | - Stefan Decker
- Informatik 5, RWTH Aachen University, Ahornstr. 55, Aachen, 52062, Germany.,Fraunhofer FIT, Schloss Birlinghoven, Sankt Augustin, 53754, Germany
| | - Oya Beyan
- Informatik 5, RWTH Aachen University, Ahornstr. 55, Aachen, 52062, Germany.,Fraunhofer FIT, Schloss Birlinghoven, Sankt Augustin, 53754, Germany
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12
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Kruempel JC, Howington MB, Leiser SF. Computational tools for geroscience. TRANSLATIONAL MEDICINE OF AGING 2019; 3:132-143. [PMID: 33241167 PMCID: PMC7685266 DOI: 10.1016/j.tma.2019.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The rapid progress of the past three decades has led the geroscience field near a point where human interventions in aging are plausible. Advances across scientific areas, such as high throughput "-omics" approaches, have led to an exponentially increasing quantity of data available for biogerontologists. To best translate the lifespan and healthspan extending interventions discovered by basic scientists into preventative medicine, it is imperative that the current data are comprehensively utilized to generate testable hypotheses about translational interventions. Building a translational pipeline for geroscience will require both systematic efforts to identify interventions that extend healthspan across taxa and diagnostics that can identify patients who may benefit from interventions prior to the onset of an age-related morbidity. Databases and computational tools that organize and analyze both the wealth of information available on basic biogerontology research and clinical data on aging populations will be critical in developing such a pipeline. Here, we review the current landscape of databases and computational resources available for translational aging research. We discuss key platforms and tools available for aging research, with a focus on how each tool can be used in concert with hypothesis driven experiments to move closer to human interventions in aging.
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Affiliation(s)
- Joseph C.P. Kruempel
- Molecular & Integrative Physiology Department, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marshall B. Howington
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Scott F. Leiser
- Molecular & Integrative Physiology Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
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13
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Abstract
Traditional animal models have been used to make seminal discoveries in biomedical research including a better understanding of the biology of the aging process. However, translation of these findings from laboratory to clinical populations has likely been hindered due to fundamental biological and physiological differences between common laboratory animals and humans. Non-human primates (NHP) may serve as an effective bridge towards translation, and short-lived NHP like the common marmoset offer many advantages as models for aging research. Here, we address these advantages and discuss what is currently understood about the changes in physiology and pathology that occur with age in the marmoset. In addition, we discuss how aging research might best utilize this model resource, and outline an ongoing study to address whether pharmaceutical intervention can slow aging in the marmoset. With this manuscript, we clarify how common marmosets might assist researchers in geroscience as a potential model for pre-clinical translation.
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Affiliation(s)
- Corinna N Ross
- Department of Science and Mathematics, Texas A&M University San Antonio, San Antonio, TX, USA.,The Sam and Ann Barshop Institute for Longevity and Aging Studies and The University of Texas Health Science Center at San Antonio, San Antonio TX, USA
| | - Adam B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and The University of Texas Health Science Center at San Antonio, San Antonio TX, USA.,Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Geriatric Research, Education and Clinical Center, South Texas Veterans Health Care System, San Antonio, TX, USA
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14
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Luo D, Li J, Chen K, Yin Y, Fang Z, Pang H, Rong X, Guo J. Study on Metabolic Trajectory of Liver Aging and the Effect of Fufang Zhenzhu Tiaozhi on Aging Mice. Front Pharmacol 2019; 10:926. [PMID: 31555127 PMCID: PMC6722462 DOI: 10.3389/fphar.2019.00926] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/22/2019] [Indexed: 01/22/2023] Open
Abstract
The aim of this study was to investigate the metabolic trajectory of liver aging, the effect of FTZ against liver aging in aging mice, and its mechanism using ultraperformance liquid chromatography/quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF/MS). Methods: A total of 80 C57BL/6J Narl mice were randomly divided into five groups: 3-month-old group, 9-month-old group, 14-month-old group, 20-month-old group, and FTZ treatment group (20 months old). The mice in the treatment group received a therapeutic dose of oral FTZ extract (1.0 g/kg, on raw material weight basis) once daily during the experiment. The other groups received the corresponding volume of oral normal saline solution. Liver samples of all five groups were collected after 12 weeks, and UPLC-Q-TOF/MS was used to analyze metabolic changes. Orthogonal partial least squares-discriminant analysis (OPLS-DA) was used to analyze the resulting data. Additionally, cholesterol (TC), triglyceride (TG), aspartate aminotransferase (AST), alanine aminotransferase (ALT), secretion levels of TNF-α, IL-6, 5-LOX, and COX-2, as well as their relative mRNA expression in the liver were determined. Results: The levels of TC, TG, AST, and ALT were increased, and liver tissue structure was damaged. The secretion levels of TNF-α, IL-6, 5-LOX, and COX-2, as well as their relative mRNA expression in the liver also increased with aging. FTZ administration reduced the symptoms of liver aging. The OPLS-DA score plot illustrated the effect of FTZ against liver aging, with N-acetyl-leukotriene E4, 20-hydroxy-leukotriene E4, leukotriene E4, and arachidonic acid among the key biomarkers. The pivotal pathways revealed by pathway analysis included arachidonic acid metabolism and biosynthesis of unsaturated fatty acids. The mechanism by which FTZ reduces the symptoms of liver aging in mice might be related to disorders of the abovementioned pathways. Conclusion: A metabolomic approach based on UPLC-Q-TOF/MS and multivariate statistical analysis was successfully applied to investigate the metabolic trajectory of liver aging. FTZ has a protective effect against liver aging, which may be mediated via interference with the metabolism of arachidonic acid, biosynthesis of unsaturated fatty acids, and downregulation of pro-inflammatory factors in the liver in mice in vivo.
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Affiliation(s)
- Duosheng Luo
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM (State Administration of Traditional Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangzhou, China
| | - Jingbiao Li
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM (State Administration of Traditional Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangzhou, China
| | - Kechun Chen
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM (State Administration of Traditional Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangzhou, China
| | - Yifan Yin
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM (State Administration of Traditional Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangzhou, China
| | - Zhaoyan Fang
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM (State Administration of Traditional Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangzhou, China
| | - Huiting Pang
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM (State Administration of Traditional Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangzhou, China
| | - Xianglu Rong
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM (State Administration of Traditional Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangzhou, China
| | - Jiao Guo
- Key Unit of Modulating Liver to Treat Hyperlipemia SATCM (State Administration of Traditional Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangzhou, China
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15
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Tacutu R, Thornton D, Johnson E, Budovsky A, Barardo D, Craig T, Diana E, Lehmann G, Toren D, Wang J, Fraifeld VE, de Magalhães JP. Human Ageing Genomic Resources: new and updated databases. Nucleic Acids Res 2019; 46:D1083-D1090. [PMID: 29121237 PMCID: PMC5753192 DOI: 10.1093/nar/gkx1042] [Citation(s) in RCA: 402] [Impact Index Per Article: 80.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/18/2017] [Indexed: 12/17/2022] Open
Abstract
In spite of a growing body of research and data, human ageing remains a poorly understood process. Over 10 years ago we developed the Human Ageing Genomic Resources (HAGR), a collection of databases and tools for studying the biology and genetics of ageing. Here, we present HAGR’s main functionalities, highlighting new additions and improvements. HAGR consists of six core databases: (i) the GenAge database of ageing-related genes, in turn composed of a dataset of >300 human ageing-related genes and a dataset with >2000 genes associated with ageing or longevity in model organisms; (ii) the AnAge database of animal ageing and longevity, featuring >4000 species; (iii) the GenDR database with >200 genes associated with the life-extending effects of dietary restriction; (iv) the LongevityMap database of human genetic association studies of longevity with >500 entries; (v) the DrugAge database with >400 ageing or longevity-associated drugs or compounds; (vi) the CellAge database with >200 genes associated with cell senescence. All our databases are manually curated by experts and regularly updated to ensure a high quality data. Cross-links across our databases and to external resources help researchers locate and integrate relevant information. HAGR is freely available online (http://genomics.senescence.info/).
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Affiliation(s)
- Robi Tacutu
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.,Computational Biology of Aging Group, Institute of Biochemistry, Romanian Academy, Bucharest 060031, Romania
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Emily Johnson
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - 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 84105, Israel.,Judea Regional Research & Development Center, Carmel 90404, Israel
| | - Diogo Barardo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City 117597, Singapore.,Science Division, Yale-NUS College, Singapore City 138527, Singapore
| | - Thomas Craig
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Eugene Diana
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Gilad Lehmann
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - 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 84105, Israel
| | - Jingwei Wang
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, 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 84105, Israel
| | - João P de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
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16
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Cai H, Dhondt I, Vandemeulebroucke L, Vlaeminck C, Rasulova M, Braeckman BP. CBP-1 Acts in GABAergic Neurons to Double Life Span in Axenically Cultured Caenorhabditis elegans. J Gerontol A Biol Sci Med Sci 2019; 74:1198-1205. [PMID: 29099917 PMCID: PMC6625597 DOI: 10.1093/gerona/glx206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/23/2017] [Indexed: 12/17/2022] Open
Abstract
When cultured in axenic medium, Caenorhabditis elegans shows the largest life-span extension compared with other dietary restriction regimens. However, the underlying molecular mechanism still remains elusive. The gene cbp-1, encoding the worm ortholog of p300/CBP (CREB-binding protein), is one of the very few key genes known to be essential for life span doubling under axenic dietary restriction (ADR). By using tissue-specific RNAi, we found that cbp-1 expression in the germline is essential for fertility, whereas this gene functions specifically in the GABAergic neurons to support the full life span-doubling effect of ADR. Surprisingly, GABA itself is not required for ADR-induced longevity, suggesting a role of neuropeptide signaling. In addition, chemotaxis assays illustrate that neuronal inactivation of CBP-1 affects the animals' food sensing behavior. Together, our results show that the strong life-span extension in axenic medium is under strict control of GABAergic neurons and may be linked to food sensing.
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Affiliation(s)
- Huaihan Cai
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
| | - Ineke Dhondt
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
| | | | - Caroline Vlaeminck
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
| | - Madina Rasulova
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
| | - Bart P Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
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17
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Functional genomics of dietary restriction and longevity in yeast. Mech Ageing Dev 2019; 179:36-43. [PMID: 30790575 DOI: 10.1016/j.mad.2019.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 02/11/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022]
Abstract
Dietary restriction-limitation of calories or other specific nutrients in the diet-is the sole non-genetic intervention known to extend the lifespan of a wide range of model organisms from yeast to mammals. Cell biology studies on the responses to dietary restriction have provided important clues about the mechanisms of longevity; however, a comprehensive genome-wide description of lifespan by dietary restriction has been mostly absent. Large-scale genetic analysis in the budding yeast Saccharomyces cerevisiae offers a great opportunity to uncover the conserved systems-level mechanisms that give way to longevity in response to diet. Here, we review recent advances in high-throughput phenotyping of the replicative and chronological life spans of yeast cells, which have contributed to our understanding of longevity by dietary restriction and the cellular crosstalks of nutrient-sensing regulation.
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18
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Campos SE, Avelar-Rivas JA, Garay E, Juárez-Reyes A, DeLuna A. Genomewide mechanisms of chronological longevity by dietary restriction in budding yeast. Aging Cell 2018; 17:e12749. [PMID: 29575540 PMCID: PMC5946063 DOI: 10.1111/acel.12749] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2018] [Indexed: 12/16/2022] Open
Abstract
Dietary restriction is arguably the most promising nonpharmacological intervention to extend human life and health span. Yet, only few genetic regulators mediating the cellular response to dietary restriction are known, and the question remains which other regulatory factors are involved. Here, we measured at the genomewide level the chronological lifespan of Saccharomyces cerevisiae gene deletion strains under two nitrogen source regimens, glutamine (nonrestricted) and γ‐aminobutyric acid (restricted). We identified 473 mutants with diminished or enhanced extension of lifespan. Functional analysis of such dietary restriction genes revealed novel processes underlying longevity by the nitrogen source quality, which also allowed us to generate a prioritized catalogue of transcription factors orchestrating the dietary restriction response. Importantly, deletions of transcription factors Msn2, Msn4, Snf6, Tec1, and Ste12 resulted in diminished lifespan extension and defects in cell cycle arrest upon nutrient starvation, suggesting that regulation of the cell cycle is a major mechanism of chronological longevity. We further show that STE12 overexpression is enough to extend lifespan, linking the pheromone/invasive growth pathway with cell survivorship. Our global picture of the genetic players of longevity by dietary restriction highlights intricate regulatory cross‐talks in aging cells.
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Affiliation(s)
- Sergio E. Campos
- Unidad de Genómica Avanzada (Langebio); Centro de Investigación y de Estudios Avanzados del IPN; Irapuato Guanajuato Mexico
| | - J. Abraham Avelar-Rivas
- Unidad de Genómica Avanzada (Langebio); Centro de Investigación y de Estudios Avanzados del IPN; Irapuato Guanajuato Mexico
| | - Erika Garay
- Unidad de Genómica Avanzada (Langebio); Centro de Investigación y de Estudios Avanzados del IPN; Irapuato Guanajuato Mexico
| | - Alejandro Juárez-Reyes
- Unidad de Genómica Avanzada (Langebio); Centro de Investigación y de Estudios Avanzados del IPN; Irapuato Guanajuato Mexico
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio); Centro de Investigación y de Estudios Avanzados del IPN; Irapuato Guanajuato Mexico
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19
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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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20
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Ross CN, Austad S, Brasky K, Brown CJ, Forney LJ, Gelfond JA, Lanford R, Richardson A, Tardif SD. The development of a specific pathogen free (SPF) barrier colony of marmosets ( Callithrix jacchus) for aging research. Aging (Albany NY) 2017; 9:2544-2558. [PMID: 29227963 PMCID: PMC5764392 DOI: 10.18632/aging.101340] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/01/2017] [Indexed: 11/25/2022]
Abstract
A specific pathogen free (SPF) barrier colony of breeding marmosets (Callithrix jacchus) was established at the Barshop Institute for Longevity and Aging Studies. Rodent and other animal models maintained as SPF barrier colonies have demonstrated improved health and lengthened lifespans enhancing the quality and repeatability of aging research. The marmosets were screened for two viruses and several bacterial pathogens prior to establishing the new SPF colony. Twelve founding animals successfully established a breeding colony with increased reproductive success, improved health parameters, and increased median lifespan when compared to a conventionally housed, open colony. The improved health and longevity of marmosets from the SPF barrier colony suggests that such management can be used to produce a unique resource for future studies of aging processes in a nonhuman primate model.
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Affiliation(s)
- Corinna N. Ross
- Department of Science and Mathematics, Texas A&M University San Antonio, San Antonio, TX 78224, USA
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, TX 78245, USA
| | - Steven Austad
- Nathan Shock Center of Excellence in the Basic Biology of Aging, Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kathy Brasky
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Celeste J. Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Larry J. Forney
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Jonathan A. Gelfond
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, TX 78245, USA
| | - Robert Lanford
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Arlan Richardson
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Suzette D. Tardif
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, TX 78245, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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21
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Li YH, Zhang GG. Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in Caenorhabditis elegans. Oncotarget 2017; 7:19185-92. [PMID: 27027346 PMCID: PMC4991374 DOI: 10.18632/oncotarget.8313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 11/25/2022] Open
Abstract
DAF-16, the C. elegans FOXO transcription factor, is an important determinant in aging and longevity. In this work, we manually curated FOXODB http://lyh.pkmu.cn/foxodb/, a database of FOXO direct targets. It now covers 208 genes. Bioinformatics analysis on 109 DAF-16 direct targets in C. elegans found interesting results. (i) DAF-16 and transcription factor PQM-1 co-regulate some targets. (ii) Seventeen targets directly regulate lifespan. (iii) Four targets are involved in lifespan extension induced by dietary restriction. And (iv) DAF-16 direct targets might play global roles in lifespan regulation.
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Affiliation(s)
- Yan-Hui Li
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Peking University Health Science Center, Beijing, P. R. China
| | - Gai-Gai Zhang
- Special Medical Ward (Geratology Department), First Hospital of Tsinghua University, Beijing, P. R. China
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The effects of graded levels of calorie restriction: VII. Topological rearrangement of hypothalamic aging networks. Aging (Albany NY) 2017; 8:917-32. [PMID: 27115072 PMCID: PMC4931844 DOI: 10.18632/aging.100944] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/31/2016] [Indexed: 12/31/2022]
Abstract
Connectivity in a gene-gene network declines with age, typically within gene clusters. We explored the effect of short-term (3 months) graded calorie restriction (CR) (up to 40 %) on network structure of aging-associated genes in the murine hypothalamus by using conditional mutual information. The networks showed a topological rearrangement when exposed to graded CR with a higher relative within cluster connectivity at 40CR. We observed changes in gene centrality concordant with changes in CR level, with Ppargc1a, and Ppt1 having increased centrality and Etfdh, Traf3 and Abcc1 decreased centrality as CR increased. This change in gene centrality in a graded manner with CR, occurred in the absence of parallel changes in gene expression levels. This study emphasizes the importance of augmenting traditional differential gene expression analyses to better understand structural changes in the transcriptome. Overall our results suggested that CR induced changes in centrality of biological relevant genes that play an important role in preventing the age-associated loss of network integrity irrespective of their gene expression levels.
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de Magalhães JP, Stevens M, Thornton D. The Business of Anti-Aging Science. Trends Biotechnol 2017; 35:1062-1073. [PMID: 28778607 DOI: 10.1016/j.tibtech.2017.07.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/18/2017] [Accepted: 07/06/2017] [Indexed: 12/16/2022]
Abstract
Age-related conditions are the leading causes of death and health-care costs. Reducing the rate of aging would have enormous medical and financial benefits. Myriad genes and pathways are known to regulate aging in model organisms, fostering a new crop of anti-aging companies. Approaches range from drug discovery efforts to big-data methods and direct-to-consumer (DTC) strategies. Challenges and pitfalls of commercialization include reliance on findings from short-lived model organisms, poor biological understanding of aging, and hurdles in performing clinical trials for aging. A large number of potential aging-associated interventions and targets exist, but given the long validation times only a small fraction can be explored for clinical applications. If even one company succeeds, however, the impact will be huge.
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Affiliation(s)
- João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK; Joint first authors.
| | - Michael Stevens
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK; Joint first authors
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
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Ashapkin VV, Kutueva LI, Vanyushin BF. Aging Epigenetics: Accumulation of Errors or Realization of a Specific Program? BIOCHEMISTRY (MOSCOW) 2016; 80:1406-17. [PMID: 26615432 DOI: 10.1134/s0006297915110024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aging in mammals is known to be accompanied by a progressive loss of methylated cytosines from DNA. This loss is tissue-specific to a certain extent and affects mainly repeated sequences, transposable elements, and intergenic genome parts. Age-dependent DNA hypomethylation is correlated with and perhaps partly caused by a diminished activity of DNA methyltransferases. Along with the global DNA demethylation during aging, hypermethylation of certain genes occurs. On the whole-genome scale, an age-dependent hypermethylation is typical for genes associated with promoter CG islands, whereas hypomethylation mostly affects CG-poor genes, besides the repeated sequences, transposable elements, and intergenic genome parts mentioned above. The methylation levels of certain CG sites display strict correlation to age and thus could be used as a molecular marker to predict biological age of cells, tissues, and organisms. Epigenetic cell reprogramming, such as induced pluripotent stem cell production, leads to complete resetting of their epigenetic age.
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Affiliation(s)
- V V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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25
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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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Wood SH, van Dam S, Craig T, Tacutu R, O'Toole A, Merry BJ, de Magalhães JP. Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. Genome Biol 2015; 16:285. [PMID: 26694192 PMCID: PMC4699360 DOI: 10.1186/s13059-015-0847-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 11/27/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Caloric restriction (CR) can increase longevity in rodents and improve memory function in humans. α-Lipoic acid (LA) has been shown to improve memory function in rats, but not longevity. While studies have looked at survival in rodents after switching from one diet to another, the underlying mechanisms of the beneficial effects of CR and LA supplementation are unknown. Here, we use RNA-seq in cerebral cortex from rats subjected to CR and LA-supplemented rats to understand how changes in diet can affect aging, neurodegeneration and longevity. RESULTS Gene expression changes during aging in ad libitum-fed rats are largely prevented by CR, and neuroprotective genes are overexpressed in response to both CR and LA diets with a strong overlap of differentially expressed genes between the two diets. Moreover, a number of genes are differentially expressed specifically in rat cohorts exhibiting diet-induced life extension. Finally, we observe that LA supplementation inhibits histone deacetylase (HDAC) protein activity in vitro in rat astrocytes. We find a single microRNA, miR-98-3p, that is overexpressed during CR feeding and LA dietary supplementation; this microRNA alters HDAC and histone acetyltransferase (HAT) activity, which suggests a role for HAT/HDAC homeostasis in neuroprotection. CONCLUSIONS This study presents extensive data on the effects of diet and aging on the cerebral cortex transcriptome, and also emphasises the importance of epigenetics and post-translational modifications in longevity and neuroprotection.
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Affiliation(s)
- Shona H Wood
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sipko van Dam
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Thomas Craig
- 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
| | - Amy O'Toole
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Brian J Merry
- 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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Lacroix S, Lauria M, Scott-Boyer MP, Marchetti L, Priami C, Caberlotto L. Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes. GENES & NUTRITION 2015; 10:58. [PMID: 26608884 PMCID: PMC4659783 DOI: 10.1007/s12263-015-0508-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 11/13/2015] [Indexed: 12/17/2022]
Abstract
Worldwide population is aging, and a large part of the growing burden associated with age-related conditions can be prevented or delayed by promoting healthy lifestyle and normalizing metabolic risk factors. However, a better understanding of the pleiotropic effects of available nutritional interventions and their influence on the multiple processes affected by aging is needed to select and implement the most promising actions. New methods of analysis are required to tackle the complexity of the interplay between nutritional interventions and aging, and to make sense of a growing amount of -omics data being produced for this purpose. In this paper, we review how various systems biology-inspired methods of analysis can be applied to the study of the molecular basis of nutritional interventions promoting healthy aging, notably caloric restriction and polyphenol supplementation. We specifically focus on the role that different versions of network analysis, molecular signature identification and multi-omics data integration are playing in elucidating the complex mechanisms underlying nutrition, and provide some examples on how to extend the application of these methods using available microarray data.
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Affiliation(s)
- Sébastien Lacroix
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068, Rovereto, Italy
| | - Mario Lauria
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068, Rovereto, Italy
| | - Marie-Pier Scott-Boyer
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068, Rovereto, Italy
| | - Luca Marchetti
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068, Rovereto, Italy
| | - Corrado Priami
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068, Rovereto, Italy
- Department of Mathematics, University of Trento, Via Sommarive 14, 38123, Povo, Italy
| | - Laura Caberlotto
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068, Rovereto, Italy.
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Nishimura Y, Sasagawa S, Ariyoshi M, Ichikawa S, Shimada Y, Kawaguchi K, Kawase R, Yamamoto R, Uehara T, Yanai T, Takata R, Tanaka T. Systems pharmacology of adiposity reveals inhibition of EP300 as a common therapeutic mechanism of caloric restriction and resveratrol for obesity. Front Pharmacol 2015; 6:199. [PMID: 26441656 PMCID: PMC4569862 DOI: 10.3389/fphar.2015.00199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 08/31/2015] [Indexed: 12/26/2022] Open
Abstract
Both caloric restriction (CR) and resveratrol (RSV) have beneficial effects on obesity. However, the biochemical pathways that mediate these beneficial effects might be complex and interconnected and have not been fully elucidated. To reveal the common therapeutic mechanism of CR and RSV, we performed a comparative transcriptome analysis of adipose tissues from diet-induced obese (DIO) zebrafish and obese humans. We identified nine genes in DIO zebrafish and seven genes in obese humans whose expressions were regulated by CR and RSV. Although the gene lists did not overlap except for one gene, the gene ontologies enriched in the gene lists were highly overlapped, and included genes involved in adipocyte differentiation, lipid storage and lipid metabolism. Bioinformatic analysis of cis-regulatory sequences of these genes revealed that their transcriptional regulators also overlapped, including EP300, HDAC2, CEBPB, CEBPD, FOXA1, and FOXA2. We also identified 15 and 46 genes that were dysregulated in the adipose tissue of DIO zebrafish and obese humans, respectively. Bioinformatics analysis identified EP300, HDAC2, and CEBPB as common transcriptional regulators for these genes. EP300 is a histone and lysyl acetyltransferase that modulates the function of histone and various proteins including CEBPB, CEBPD, FOXA1, and FOXA2. We demonstrated that adiposity in larval zebrafish was significantly reduced by C646, an inhibitor of EP300 that antagonizes acetyl-CoA. The reduction of adiposity by C646 was not significantly different from that induced by RSV or co-treatment of C646 and RSV. These results indicate that the inhibition of EP300 might be a common therapeutic mechanism between CR and RSV in adipose tissues of obese individuals.
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Affiliation(s)
- Yuhei Nishimura
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan ; Mie University Medical Zebrafish Research Center Tsu, Japan ; Department of Systems Pharmacology, Mie University Graduate School of Medicine Tsu, Japan ; Department of Omics Medicine, Mie University Industrial Technology Innovation Institute Tsu, Japan ; Department of Bioinformatics, Mie University Life Science Research Center Tsu, Japan
| | - Shota Sasagawa
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Michiko Ariyoshi
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Sayuri Ichikawa
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Yasuhito Shimada
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Koki Kawaguchi
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Reiko Kawase
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan
| | - Reiko Yamamoto
- Product Development Research Institute, Mercian Corporation Fujisawa, Japan
| | - Takuma Uehara
- Product Development Research Institute, Mercian Corporation Fujisawa, Japan
| | - Takaaki Yanai
- Product Development Research Institute, Mercian Corporation Fujisawa, Japan
| | - Ryoji Takata
- Product Development Research Institute, Mercian Corporation Fujisawa, Japan
| | - Toshio Tanaka
- Department of Molecular and Cellular Pharmacology, Pharmacogenomics and Pharmacoinformatics, Mie University Graduate School of Medicine Tsu, Japan ; Mie University Medical Zebrafish Research Center Tsu, Japan ; Department of Systems Pharmacology, Mie University Graduate School of Medicine Tsu, Japan ; Department of Omics Medicine, Mie University Industrial Technology Innovation Institute Tsu, Japan ; Department of Bioinformatics, Mie University Life Science Research Center Tsu, Japan
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29
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Callahan A, Cifuentes JJ, Dumontier M. An evidence-based approach to identify aging-related genes in Caenorhabditis elegans. BMC Bioinformatics 2015; 16:40. [PMID: 25888240 PMCID: PMC4339751 DOI: 10.1186/s12859-015-0469-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 01/15/2015] [Indexed: 12/21/2022] Open
Abstract
Background Extensive studies have been carried out on Caenorhabditis elegans as a model organism to elucidate mechanisms of aging and the effects of perturbing known aging-related genes on lifespan and behavior. This research has generated large amounts of experimental data that is increasingly difficult to integrate and analyze with existing databases and domain knowledge. To address this challenge, we demonstrate a scalable and effective approach for automatic evidence gathering and evaluation that leverages existing experimental data and literature-curated facts to identify genes involved in aging and lifespan regulation in C. elegans. Results We developed a semantic knowledge base for aging by integrating data about C. elegans genes from WormBase with data about 2005 human and model organism genes from GenAge and 149 genes from GenDR, and with the Bio2RDF network of linked data for the life sciences. Using HyQue (a Semantic Web tool for hypothesis-based querying and evaluation) to interrogate this knowledge base, we examined 48,231 C. elegans genes for their role in modulating lifespan and aging. HyQue identified 24 novel but well-supported candidate aging-related genes for further experimental validation. Conclusions We use semantic technologies to discover candidate aging genes whose effects on lifespan are not yet well understood. Our customized HyQue system, the aging research knowledge base it operates over, and HyQue evaluations of all C. elegans genes are freely available at http://hyque.semanticscience.org. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0469-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alison Callahan
- Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University, Stanford California, AC, USA.
| | - Juan José Cifuentes
- Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, 49 Santiago, CP, 8330025, Portugal. .,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
| | - Michel Dumontier
- Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University, Stanford California, AC, USA.
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Abstract
Dietary restriction (DR) reduces age-specific mortality and increases lifespan in many organisms. DR elicits a large number of physiological changes, however many are undoubtedly not related to longevity. Whole-genome gene expression studies have typically revealed hundreds to thousands of differentially expressed genes in response to DR, and a key open question is which subset of genes mediates longevity. Here we performed transcriptional profiling of fruit flies in a closely spaced time series immediately following a switch to the DR regime and identified four patterns of transcriptional dynamics. Most informatively we find 144 genes rapidly switched to the same level observed in the DR cohort and are hence strong candidates as proximal mediators of reduced mortality upon DR. This class was enriched for genes involved in carbohydrate and fatty acid metabolism. Folate biosynthesis was the only pathway enriched for gene up-regulated upon DR. Four among the down-regulated genes are involved in key regulatory steps within the pentose phosphate pathway, which has been previously associated with lifespan extension in Drosophila. Combined analysis of dietary switch with whole-genome time-course profiling can identify transcriptional responses that are closely associated with and perhaps causal to longevity assurance conferred by dietary restriction.
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31
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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: 28] [Impact Index Per Article: 2.8] [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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32
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Tiwari S, Singh S, Pandey P, Saikia SK, Negi AS, Gupta SK, Pandey R, Banerjee S. Isolation, structure determination, and antiaging effects of 2,3-pentanediol from endophytic fungus of Curcuma amada and docking studies. PROTOPLASMA 2014; 251:1089-98. [PMID: 24515569 DOI: 10.1007/s00709-014-0617-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/16/2014] [Indexed: 05/20/2023]
Abstract
An endophytic fungus was isolated from the rhizomes of Curcuma amada (Zingiberaceae), which was identified as Fusarium oxysporum on the basis of its morphological and molecular characters. Chromatographic separation and spectroscopic analysis of the fungal metabolite (chloroform extract) led to the identification of one pure compound having molecular formula C5H12O2, i.e., 2,3-pentanediol (1). Activity analysis of compound 1 demonstrated improved antiaging (antioxidant, thermotolerance) properties against Caenorhabditis elegans, in comparison to a similar, commercially available molecule i.e., 1,5-pentanediol (2). The effective (lower) concentration of 1 significantly showed (28.6%) higher survival percentage of the worms under thermal stress (37 ºC) compared to its higher concentration (25.3%), while similar trends were followed in oxidative stress where (22.2%) higher survival percentage was recorded in comparison to untreated control. The compound 1, however, lacked potential antimicrobial activity, indicating the plausible ramification of the position of OH group in such bioactive molecules. In silico evaluation of these molecules against common as well as unique targets corroborated better antiaging potential of 1 in comparison to that of 2. The results for the first time indicated that the utilization of the endophytic fungi of C. amada could, thus, be a possible source for obtaining non-plant-based bioactive compounds having broader therapeutic applications pertaining to age-related progressions.
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Affiliation(s)
- Sudeep Tiwari
- Microbial Technology and Nematology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, Uttar Pradesh, 226015, India
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Molin M, Demir AB. Linking Peroxiredoxin and Vacuolar-ATPase Functions in Calorie Restriction-Mediated Life Span Extension. Int J Cell Biol 2014; 2014:913071. [PMID: 24639875 PMCID: PMC3930189 DOI: 10.1155/2014/913071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 11/11/2013] [Accepted: 12/15/2013] [Indexed: 01/09/2023] Open
Abstract
Calorie restriction (CR) is an intervention extending the life spans of many organisms. The mechanisms underlying CR-dependent retardation of aging are still poorly understood. Despite mechanisms involving conserved nutrient signaling pathways proposed, few target processes that can account for CR-mediated longevity have so far been identified. Recently, both peroxiredoxins and vacuolar-ATPases were reported to control CR-mediated retardation of aging downstream of conserved nutrient signaling pathways. In this review, we focus on peroxiredoxin-mediated stress-defence and vacuolar-ATPase regulated acidification and pinpoint common denominators between the two mechanisms proposed for how CR extends life span. Both the activities of peroxiredoxins and vacuolar-ATPases are stimulated upon CR through reduced activities in conserved nutrient signaling pathways and both seem to stimulate cellular resistance to peroxide-stress. However, whereas vacuolar-ATPases have recently been suggested to control both Ras-cAMP-PKA- and TORC1-mediated nutrient signaling, neither the physiological benefits of a proposed role for peroxiredoxins in H2O2-signaling nor downstream targets regulated are known. Both peroxiredoxins and vacuolar-ATPases do, however, impinge on mitochondrial iron-metabolism and further characterization of their impact on iron homeostasis and peroxide-resistance might therefore increase our understanding of the beneficial effects of CR on aging and age-related diseases.
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Affiliation(s)
- Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90 Gothenburg, Sweden
| | - Ayse Banu Demir
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90 Gothenburg, Sweden
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, 35430 Urla, Izmir, Turkey
- Department of Oncology, Institute of Oncology, Dokuz Eylul University, 35340 Inciralti, Izmir, Turkey
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Hühne R, Thalheim T, Sühnel J. AgeFactDB--the JenAge Ageing Factor Database--towards data integration in ageing research. Nucleic Acids Res 2013; 42:D892-6. [PMID: 24217911 PMCID: PMC3964983 DOI: 10.1093/nar/gkt1073] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AgeFactDB (http://agefactdb.jenage.de) is a database aimed at the collection and integration of ageing phenotype data including lifespan information. Ageing factors are considered to be genes, chemical compounds or other factors such as dietary restriction, whose action results in a changed lifespan or another ageing phenotype. Any information related to the effects of ageing factors is called an observation and is presented on observation pages. To provide concise access to the complete information for a particular ageing factor, corresponding observations are also summarized on ageing factor pages. In a first step, ageing-related data were primarily taken from existing databases such as the Ageing Gene Database--GenAge, the Lifespan Observations Database and the Dietary Restriction Gene Database--GenDR. In addition, we have started to include new ageing-related information. Based on homology data taken from the HomoloGene Database, AgeFactDB also provides observation and ageing factor pages of genes that are homologous to known ageing-related genes. These homologues are considered as candidate or putative ageing-related genes. AgeFactDB offers a variety of search and browse options, and also allows the download of ageing factor or observation lists in TSV, CSV and XML formats.
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Affiliation(s)
- Rolf Hühne
- Biocomputing Group, Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena Centre for Systems Biology of Ageing - JenAge, Beutenbergstrasse 11, Jena, Germany
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Characterization of global gene expression during assurance of lifespan extension by caloric restriction in budding yeast. Exp Gerontol 2013; 48:1455-68. [PMID: 24126084 DOI: 10.1016/j.exger.2013.10.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 09/28/2013] [Accepted: 10/03/2013] [Indexed: 12/22/2022]
Abstract
Caloric restriction (CR) is the best-studied intervention known to delay aging and extend lifespan in evolutionarily distant organisms ranging from yeast to mammals in the laboratory. Although the effect of CR on lifespan extension has been investigated for nearly 80years, the molecular mechanisms of CR are still elusive. Consequently, it is important to understand the fundamental mechanisms of when and how lifespan is affected by CR. In this study, we first identified the time-windows during which CR assured cellular longevity by switching cells from culture media containing 2% or 0.5% glucose to water, which allows us to observe CR and non-calorically-restricted cells under the same conditions. We also constructed time-dependent gene expression profiles and selected 646 genes that showed significant changes and correlations with the lifespan-extending effect of CR. The positively correlated genes participated in transcriptional regulation, ribosomal RNA processing and nuclear genome stability, while the negatively correlated genes were involved in the regulation of several metabolic pathways, endoplasmic reticulum function, stress response and cell cycle progression. Furthermore, we discovered major upstream regulators of those significantly changed genes, including AZF1 (YOR113W), HSF1 (YGL073W) and XBP1 (YIL101C). Deletions of two genes, AZF1 and XBP1 (HSF1 is essential and was thus not tested), were confirmed to lessen the lifespan extension mediated by CR. The absence of these genes in the tor1Δ and ras2Δ backgrounds did show non-overlapping effects with regard to CLS, suggesting differences between the CR mechanism for Tor and Ras signaling.
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36
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Boyd-Kirkup JD, Green CD, Wu G, Wang D, Han JDJ. Epigenomics and the regulation of aging. Epigenomics 2013; 5:205-27. [PMID: 23566097 DOI: 10.2217/epi.13.5] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
It is tempting to assume that a gradual accumulation of damage 'causes' an organism to age, but other biological processes present during the lifespan, whether 'programmed' or 'hijacked', could control the type and speed of aging. Theories of aging have classically focused on changes at the genomic level; however, individuals with similar genetic backgrounds can age very differently. Epigenetic modifications include DNA methylation, histone modifications and ncRNA. Environmental cues may be 'remembered' during lifespan through changes to the epigenome that affect the rate of aging. Changes to the epigenomic landscape are now known to associate with aging, but so far causal links to longevity are only beginning to be revealed. Nevertheless, it is becoming apparent that there is significant reciprocal regulation occurring between the epigenomic levels. Future work utilizing new technologies and techniques should build a clearer picture of the link between epigenomic changes and aging.
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Affiliation(s)
- Jerome D Boyd-Kirkup
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
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37
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Huang X, Withers BR, Dickson RC. Sphingolipids and lifespan regulation. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:657-64. [PMID: 23954556 DOI: 10.1016/j.bbalip.2013.08.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/01/2013] [Accepted: 08/06/2013] [Indexed: 02/08/2023]
Abstract
Diseases including cancer, type 2 diabetes, cardiovascular and immune dysfunction and neurodegeneration become more prevalent as we age, and combined with the increase in average human lifespan, place an ever increasing burden on the health care system. In this chapter we focus on finding ways of modulating sphingolipids to prevent the development of age-associated diseases or delay their onset, both of which could improve health in elderly, fragile people. Reducing the incidence of or delaying the onset of diseases of aging has blossomed in the past decade because of advances in understanding signal transduction pathways and cellular processes, especially in model organisms, that are largely conserved in most eukaryotes and that can be modulated to reduce signs of aging and increase health span. In model organisms such interventions must also increase lifespan to be considered significant, but this is not a requirement for use in humans. The most encouraging interventions in model organisms involve lowering the concentration of one or more sphingolipids so as to reduce the activity of key signaling pathways, one of the most promising being the Target of Rapamycin Complex 1 (TORC1) protein kinase pathway. Other potential ways in which modulating sphingolipids may contribute to improving the health profile of the elderly is by reducing oxidative stresses, inflammatory responses and growth factor signaling. Lastly, perhaps the most interesting way to modulate sphingolipids and promote longevity is by lowering the activity of serine palmitoyltransferase, the first enzyme in the de novo sphingolipid biosynthesis pathway. Available data in yeasts and rodents are encouraging and as we gain insights into molecular mechanisms the strategies for improving human health by modulating sphingolipids will become more apparent. This article is part of a Special Issue entitled New Frontiers in Sphingolipid Biology.
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Affiliation(s)
- Xinhe Huang
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, 741 S. Limestone, Lexington, KY 40536, USA
| | - Bradley R Withers
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, 741 S. Limestone, Lexington, KY 40536, USA
| | - Robert C Dickson
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, 741 S. Limestone, Lexington, KY 40536, USA.
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38
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Alcedo J, Flatt T, Pasyukova EG. Neuronal inputs and outputs of aging and longevity. Front Genet 2013; 4:71. [PMID: 23653632 PMCID: PMC3644678 DOI: 10.3389/fgene.2013.00071] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/13/2013] [Indexed: 12/14/2022] Open
Abstract
An animal’s survival strongly depends on its ability to maintain homeostasis in response to the changing quality of its external and internal environment. This is achieved through intracellular and intercellular communication within and among different tissues. One of the organ systems that plays a major role in this communication and the maintenance of homeostasis is the nervous system. Here we highlight different aspects of the neuronal inputs and outputs of pathways that affect aging and longevity. Accordingly, we discuss how sensory inputs influence homeostasis and lifespan through the modulation of different types of neuronal signals, which reflects the complexity of the environmental cues that affect physiology. We also describe feedback, compensatory, and feed-forward mechanisms in these longevity-modulating pathways that are necessary for homeostasis. Finally, we consider the temporal requirements for these neuronal processes and the potential role of natural genetic variation in shaping the neurobiology of aging.
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Affiliation(s)
- Joy Alcedo
- Friedrich Miescher Institute for Biomedical Research Basel, Switzerland ; Department of Biological Sciences, Wayne State University Detroit, MI, USA
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39
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Kriete A. Robustness and aging--a systems-level perspective. Biosystems 2013; 112:37-48. [PMID: 23562399 DOI: 10.1016/j.biosystems.2013.03.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/11/2013] [Accepted: 03/15/2013] [Indexed: 12/24/2022]
Abstract
The theory of robustness describes a system level property of evolutionary systems, which predicts tradeoffs of great interest for the systems biology of aging, such as accumulation of non-heritable damage, occurrence of fragilities and limitations in performance, optimized allocation of restricted resources and confined redundancies. According to the robustness paradigm cells and organisms evolved into a state of highly optimized tolerance (HOT), which provides robustness to common perturbations, but causes tradeoffs generally characterized as "robust yet fragile". This raises the question whether the ultimate cause of aging is more than a lack of adaptation, but an inherent fragility of complex evolutionary systems. Since robustness connects to evolutionary designs, consideration of this theory provides a deeper connection between evolutionary aspects of aging, mathematical models and experimental data. In this review several mechanisms influential for aging are re-evaluated in support of robustness tradeoffs. This includes asymmetric cell division improving performance and specialization with limited capacities to prevent and repair age-related damage, as well as feedback control mechanisms optimized to respond to acute stressors, but unable to halt nor revert aging. Improvement in robustness by increasing efficiencies through cellular redundancies in larger organisms alleviates some of the damaging effects of cellular specialization, which can be expressed in allometric relationships. The introduction of the robustness paradigm offers unique insights for aging research and provides novel opportunities for systems biology endeavors.
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Affiliation(s)
- Andres Kriete
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Bossone Research Center, 3141 Chestnut St., Philadelphia, PA 19104, USA.
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Tacutu R, Craig T, Budovsky A, Wuttke D, Lehmann G, Taranukha D, Costa J, Fraifeld VE, de Magalhães JP. Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing. Nucleic Acids Res 2012. [PMID: 23193293 PMCID: PMC3531213 DOI: 10.1093/nar/gks1155] [Citation(s) in RCA: 365] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology.
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Affiliation(s)
- Robi Tacutu
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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