1
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Mouton SN, Boersma AJ, Veenhoff LM. A physicochemical perspective on cellular ageing. Trends Biochem Sci 2023; 48:949-962. [PMID: 37716870 DOI: 10.1016/j.tibs.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Cellular ageing described at the molecular level is a multifactorial process that leads to a spectrum of ageing trajectories. There has been recent discussion about whether a decline in physicochemical homeostasis causes aberrant phase transitions, which are a driver of ageing. Indeed, the function of all biological macromolecules, regardless of their participation in biomolecular condensates, depends on parameters such as pH, crowding, and redox state. We expand on the physicochemical homeostasis hypothesis and summarise recent evidence that the intracellular milieu influences molecular processes involved in ageing.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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2
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Rolland A, Pasquier E, Malvezin P, Cassandra C, Dumas M, Dussutour A. Behavioural changes in slime moulds over time. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220063. [PMID: 36802777 PMCID: PMC9939273 DOI: 10.1098/rstb.2022.0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/21/2022] [Indexed: 02/21/2023] Open
Abstract
Changes in behaviour over the lifetime of single-cell organisms have primarily been investigated in response to environmental stressors. However, growing evidence suggests that unicellular organisms undergo behavioural changes throughout their lifetime independently of the external environment. Here we studied how behavioural performances across different tasks vary with age in the acellular slime mould Physarum polycephalum. We tested slime moulds aged from 1 week to 100 weeks. First, we showed that migration speed decreases with age in favourable and adverse environments. Second, we showed that decision making and learning abilities do not deteriorate with age. Third, we revealed that old slime moulds can recover temporarily their behavioural performances if they go throughout a dormant stage or if they fuse with a young congener. Last, we observed the response of slime mould facing a choice between cues released by clone mates of different age. We found that both old and young slime moulds are attracted preferentially toward cues left by young slime moulds. Although many studies have studied behaviour in unicellular organisms, few have taken the step of looking for changes in behaviour over the lifetime of individuals. This study extends our knowledge of the behavioural plasticity of single-celled organisms and establishes slime moulds as a promising model to investigate the effect of ageing on behaviour at the cellular level. This article is part of a discussion meeting issue 'Collective behaviour through time'.
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Affiliation(s)
- Angèle Rolland
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse 31062, France
| | - Emilie Pasquier
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse 31062, France
| | - Paul Malvezin
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse 31062, France
| | - Craig Cassandra
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse 31062, France
| | - Mathilde Dumas
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse 31062, France
| | - A. Dussutour
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse 31062, France
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3
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Paxman J, Zhou Z, O'Laughlin R, Liu Y, Li Y, Tian W, Su H, Jiang Y, Holness SE, Stasiowski E, Tsimring LS, Pillus L, Hasty J, Hao N. Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis. eLife 2022; 11:e75978. [PMID: 36194205 PMCID: PMC9578700 DOI: 10.7554/elife.75978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin instability and protein homeostasis (proteostasis) stress are two well-established hallmarks of aging, which have been considered largely independent of each other. Using microfluidics and single-cell imaging approaches, we observed that, during the replicative aging of Saccharomyces cerevisiae, a challenge to proteostasis occurs specifically in the fraction of cells with decreased stability within the ribosomal DNA (rDNA). A screen of 170 yeast RNA-binding proteins identified ribosomal RNA (rRNA)-binding proteins as the most enriched group that aggregate upon a decrease in rDNA stability induced by inhibition of a conserved lysine deacetylase Sir2. Further, loss of rDNA stability induces age-dependent aggregation of rRNA-binding proteins through aberrant overproduction of rRNAs. These aggregates contribute to age-induced proteostasis decline and limit cellular lifespan. Our findings reveal a mechanism underlying the interconnection between chromatin instability and proteostasis stress and highlight the importance of cell-to-cell variability in aging processes.
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Affiliation(s)
- Julie Paxman
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Zhen Zhou
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Richard O'Laughlin
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
| | - Yuting Liu
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yang Li
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Wanying Tian
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Hetian Su
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yanfei Jiang
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Shayna E Holness
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Elizabeth Stasiowski
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
| | - Lev S Tsimring
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
| | - Lorraine Pillus
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- UCSD Moores Cancer Center, University of California San, DiegoLa JollaUnited States
| | - Jeff Hasty
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
| | - Nan Hao
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
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4
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Passaro D, Garcia-Albornoz M, Diana G, Chakravarty P, Ariza-McNaughton L, Batsivari A, Borràs-Eroles C, Abarrategi A, Waclawiczek A, Ombrato L, Malanchi I, Gribben J, Bonnet D. Integrated OMICs unveil the bone-marrow microenvironment in human leukemia. Cell Rep 2021; 35:109119. [PMID: 33979628 PMCID: PMC8131581 DOI: 10.1016/j.celrep.2021.109119] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/20/2021] [Accepted: 04/21/2021] [Indexed: 12/21/2022] Open
Abstract
The bone-marrow (BM) niche is the spatial environment composed by a network of multiple stromal components regulating adult hematopoiesis. We use multi-omics and computational tools to analyze multiple BM environmental compartments and decipher their mutual interactions in the context of acute myeloid leukemia (AML) xenografts. Under homeostatic conditions, we find a considerable overlap between niche populations identified using current markers. Our analysis defines eight functional clusters of genes informing on the cellular identity and function of the different subpopulations and pointing at specific stromal interrelationships. We describe how these transcriptomic profiles change during human AML development and, by using a proximity-based molecular approach, we identify early disease onset deregulated genes in the mesenchymal compartment. Finally, we analyze the BM proteomic secretome in the presence of AML and integrate it with the transcriptome to predict signaling nodes involved in niche alteration in AML.
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Affiliation(s)
- Diana Passaro
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Manuel Garcia-Albornoz
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giovanni Diana
- Dynamic Neuronal Imaging Unit, Pasteur Institute, CNRS UMR, 3571 Paris, France
| | - Probir Chakravarty
- Bioinformatic Core Unit, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Linda Ariza-McNaughton
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Antoniana Batsivari
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Clara Borràs-Eroles
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ander Abarrategi
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alexander Waclawiczek
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Luigi Ombrato
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ilaria Malanchi
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - John Gribben
- Department of Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Dominique Bonnet
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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5
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Guo HB, Ghafari M, Dang W, Qin H. Protein interaction potential landscapes for yeast replicative aging. Sci Rep 2021; 11:7143. [PMID: 33785798 PMCID: PMC8010020 DOI: 10.1038/s41598-021-86415-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/15/2021] [Indexed: 11/17/2022] Open
Abstract
We proposed a novel interaction potential landscape approach to map the systems-level profile changes of gene networks during replicative aging in Saccharomyces cerevisiae. This approach enabled us to apply quasi-potentials, the negative logarithm of the probabilities, to calibrate the elevation of the interaction landscapes with young cells as a reference state. Our approach detected opposite landscape changes based on protein abundances from transcript levels, especially for intra-essential gene interactions. We showed that essential proteins play different roles from hub proteins on the age-dependent interaction potential landscapes. We verified that hub proteins tend to avoid other hub proteins, but essential proteins prefer to interact with other essential proteins. Overall, we showed that the interaction potential landscape is promising for inferring network profile change during aging and that the essential hub proteins may play an important role in the uncoupling between protein and transcript levels during replicative aging.
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Affiliation(s)
- Hao-Bo Guo
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- SimCenter, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH, 45433, USA.
| | - Mehran Ghafari
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hong Qin
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- SimCenter, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- Department of Biology, Geology and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
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6
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Li Y, Jiang Y, Paxman J, O'Laughlin R, Klepin S, Zhu Y, Pillus L, Tsimring LS, Hasty J, Hao N. A programmable fate decision landscape underlies single-cell aging in yeast. Science 2020; 369:325-329. [PMID: 32675375 DOI: 10.1126/science.aax9552] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 01/24/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
Chromatin instability and mitochondrial decline are conserved processes that contribute to cellular aging. Although both processes have been explored individually in the context of their distinct signaling pathways, the mechanism that determines which process dominates during aging of individual cells is unknown. We show that interactions between the chromatin silencing and mitochondrial pathways lead to an epigenetic landscape of yeast replicative aging with multiple equilibrium states that represent different types of terminal states of aging. The structure of the landscape drives single-cell differentiation toward one of these states during aging, whereby the fate is determined quite early and is insensitive to intracellular noise. Guided by a quantitative model of the aging landscape, we genetically engineered a long-lived equilibrium state characterized by an extended life span.
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Affiliation(s)
- Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julie Paxman
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen Klepin
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yuelian Zhu
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA. .,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
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7
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Chen KL, Ven TN, Crane MM, Brunner MLC, Pun AK, Helget KL, Brower K, Chen DE, Doan H, Dillard-Telm JD, Huynh E, Feng YC, Yan Z, Golubeva A, Hsu RA, Knight R, Levin J, Mobasher V, Muir M, Omokehinde V, Screws C, Tunali E, Tran RK, Valdez L, Yang E, Kennedy SR, Herr AJ, Kaeberlein M, Wasko BM. Loss of vacuolar acidity results in iron-sulfur cluster defects and divergent homeostatic responses during aging in Saccharomyces cerevisiae. GeroScience 2020; 42:749-764. [PMID: 31975050 PMCID: PMC7205917 DOI: 10.1007/s11357-020-00159-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 01/14/2020] [Indexed: 01/31/2023] Open
Abstract
The loss of vacuolar/lysosomal acidity is an early event during aging that has been linked to mitochondrial dysfunction. However, it is unclear how loss of vacuolar acidity results in age-related dysfunction. Through unbiased genetic screens, we determined that increased iron uptake can suppress the mitochondrial respiratory deficiency phenotype of yeast vma mutants, which have lost vacuolar acidity due to genetic disruption of the vacuolar ATPase proton pump. Yeast vma mutants exhibited nuclear localization of Aft1, which turns on the iron regulon in response to iron-sulfur cluster (ISC) deficiency. This led us to find that loss of vacuolar acidity with age in wild-type yeast causes ISC defects and a DNA damage response. Using microfluidics to investigate aging at the single-cell level, we observe grossly divergent trajectories of iron homeostasis within an isogenic and environmentally homogeneous population. One subpopulation of cells fails to mount the expected compensatory iron regulon gene expression program, and suffers progressively severe ISC deficiency with little to no activation of the iron regulon. In contrast, other cells show robust iron regulon activity with limited ISC deficiency, which allows extended passage and survival through a period of genomic instability during aging. These divergent trajectories suggest that iron regulation and ISC homeostasis represent a possible target for aging interventions.
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Affiliation(s)
- Kenneth L Chen
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Toby N Ven
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matthew M Crane
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | | | - Adrian K Pun
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Kathleen L Helget
- Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, TX, 77058, USA
| | - Katherine Brower
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Dexter E Chen
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Ha Doan
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | | | - Ellen Huynh
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Yen-Chi Feng
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Zili Yan
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alexandra Golubeva
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Roy A Hsu
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Raheem Knight
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jessie Levin
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Vesal Mobasher
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael Muir
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Victor Omokehinde
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Corey Screws
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Esin Tunali
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Rachael K Tran
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Luz Valdez
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Edward Yang
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alan J Herr
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Brian M Wasko
- Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, TX, 77058, USA.
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8
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Crane MM, Chen KL, Blue BW, Kaeberlein M. Trajectories of Aging: How Systems Biology in Yeast Can Illuminate Mechanisms of Personalized Aging. Proteomics 2020; 20:e1800420. [PMID: 31385433 PMCID: PMC7000301 DOI: 10.1002/pmic.201800420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/02/2019] [Indexed: 02/02/2023]
Abstract
All organisms age, but the extent to which all organisms age the same way remains a fundamental unanswered question in biology. Across species, it is now clear that at least some aspects of aging are highly conserved and are perhaps universal, but other mechanisms of aging are private to individual species or sets of closely related species. Within the same species, however, it has generally been assumed that the molecular mechanisms of aging are largely invariant from one individual to the next. With the development of new tools for studying aging at the individual cell level in budding yeast, recent data has called this assumption into question. There is emerging evidence that individual yeast mother cells may undergo fundamentally different trajectories of aging. Individual trajectories of aging are difficult to study by traditional population level assays, but through the application of systems biology approaches combined with novel microfluidic technologies, it is now possible to observe and study these phenomena in real time. Understanding the spectrum of mechanisms that determine how different individuals age is a necessary step toward the goal of personalized geroscience, where healthy longevity is optimized for each individual.
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Affiliation(s)
- Matthew M Crane
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Kenneth L Chen
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA,Department of Genome Sciences, University of Washington, Seattle, WA, USA,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Ben W. Blue
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA,Department of Genome Sciences, University of Washington, Seattle, WA, USA
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9
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Crane MM, Russell AE, Schafer BJ, Blue BW, Whalen R, Almazan J, Hong MG, Nguyen B, Goings JE, Chen KL, Kelly R, Kaeberlein M. DNA damage checkpoint activation impairs chromatin homeostasis and promotes mitotic catastrophe during aging. eLife 2019; 8:e50778. [PMID: 31714209 PMCID: PMC6850777 DOI: 10.7554/elife.50778] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/30/2019] [Indexed: 02/01/2023] Open
Abstract
Genome instability is a hallmark of aging and contributes to age-related disorders such as cancer and Alzheimer's disease. The accumulation of DNA damage during aging has been linked to altered cell cycle dynamics and the failure of cell cycle checkpoints. Here, we use single cell imaging to study the consequences of increased genomic instability during aging in budding yeast and identify striking age-associated genome missegregation events. This breakdown in mitotic fidelity results from the age-related activation of the DNA damage checkpoint and the resulting degradation of histone proteins. Disrupting the ability of cells to degrade histones in response to DNA damage increases replicative lifespan and reduces genomic missegregations. We present several lines of evidence supporting a model of antagonistic pleiotropy in the DNA damage response where histone degradation, and limited histone transcription are beneficial to respond rapidly to damage but reduce lifespan and genomic stability in the long term.
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Affiliation(s)
- Matthew M Crane
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Adam E Russell
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Brent J Schafer
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Ben W Blue
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Riley Whalen
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Jared Almazan
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Mung Gi Hong
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Bao Nguyen
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Joslyn E Goings
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Kenneth L Chen
- Department of PathologyUniversity of WashingtonSeattleUnited States
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Medical Scientist Training ProgramUniversity of WashingtonSeattleUnited States
| | - Ryan Kelly
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Matt Kaeberlein
- Department of PathologyUniversity of WashingtonSeattleUnited States
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10
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Mechanisms by which PE21, an extract from the white willow Salix alba, delays chronological aging in budding yeast. Oncotarget 2019; 10:5780-5816. [PMID: 31645900 PMCID: PMC6791382 DOI: 10.18632/oncotarget.27209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/27/2019] [Indexed: 01/05/2023] Open
Abstract
We have recently found that PE21, an extract from the white willow Salix alba, slows chronological aging and prolongs longevity of the yeast Saccharomyces cerevisiae more efficiently than any of the previously known pharmacological interventions. Here, we investigated mechanisms through which PE21 delays yeast chronological aging and extends yeast longevity. We show that PE21 causes a remodeling of lipid metabolism in chronologically aging yeast, thereby instigating changes in the concentrations of several lipid classes. We demonstrate that such changes in the cellular lipidome initiate three mechanisms of aging delay and longevity extension. The first mechanism through which PE21 slows aging and prolongs longevity consists in its ability to decrease the intracellular concentration of free fatty acids. This postpones an age-related onset of liponecrotic cell death promoted by excessive concentrations of free fatty acids. The second mechanism of aging delay and longevity extension by PE21 consists in its ability to decrease the concentrations of triacylglycerols and to increase the concentrations of glycerophospholipids within the endoplasmic reticulum membrane. This activates the unfolded protein response system in the endoplasmic reticulum, which then decelerates an age-related decline in protein and lipid homeostasis and slows down an aging-associated deterioration of cell resistance to stress. The third mechanisms underlying aging delay and longevity extension by PE21 consists in its ability to change lipid concentrations in the mitochondrial membranes. This alters certain catabolic and anabolic processes in mitochondria, thus amending the pattern of aging-associated changes in several key aspects of mitochondrial functionality.
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11
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O'Laughlin R, Jin M, Li Y, Pillus L, Tsimring LS, Hasty J, Hao N. Advances in quantitative biology methods for studying replicative aging in Saccharomyces cerevisiae. TRANSLATIONAL MEDICINE OF AGING 2019; 4:151-160. [PMID: 33880425 PMCID: PMC8054985 DOI: 10.1016/j.tma.2019.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Aging is a complex, yet pervasive phenomenon in biology. As human cells steadily succumb to the deteriorating effects of aging, so too comes a host of age-related ailments such as neurodegenerative disorders, cardiovascular disease and cancer. Therefore, elucidation of the molecular networks that drive aging is of paramount importance to human health. Progress toward this goal has been aided by studies from simple model organisms such as Saccharomyces cerevisiae. While work in budding yeast has already revealed much about the basic biology of aging as well as a number of evolutionarily conserved pathways involved in this process, recent technological advances are poised to greatly expand our knowledge of aging in this simple eukaryote. Here, we review the latest developments in microfluidics, single-cell analysis and high-throughput technologies for studying single-cell replicative aging in S. cerevisiae. We detail the challenges each of these methods addresses as well as the unique insights into aging that each has provided. We conclude with a discussion of potential future applications of these techniques as well as the importance of single-cell dynamics and quantitative biology approaches for understanding cell aging.
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Affiliation(s)
- Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Meng Jin
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nan Hao
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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Diaz-Rodriguez P, López-Álvarez M, Serra J, González P, Landín M. Current Stage of Marine Ceramic Grafts for 3D Bone Tissue Regeneration. Mar Drugs 2019; 17:md17080471. [PMID: 31443166 PMCID: PMC6723791 DOI: 10.3390/md17080471] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022] Open
Abstract
Bioceramic scaffolds are crucial in tissue engineering for bone regeneration. They usually provide hierarchical porosity, bioactivity, and mechanical support supplying osteoconductive properties and allowing for 3D cell culture. In the case of age-related diseases such as osteoarthritis and osteoporosis, or other bone alterations as alveolar bone resorption or spinal fractures, functional tissue recovery usually requires the use of grafts. These bone grafts or bone void fillers are usually based on porous calcium phosphate grains which, once disposed into the bone defect, act as scaffolds by incorporating, to their own porosity, the intergranular one. Despite their routine use in traumatology and dental applications, specific graft requirements such as osteoinductivity or balanced dissolution rate are still not completely fulfilled. Marine origin bioceramics research opens the possibility to find new sources of bone grafts given the wide diversity of marine materials still largely unexplored. The interest in this field has also been urged by the limitations of synthetic or mammalian-derived grafts already in use and broadly investigated. The present review covers the current stage of major marine origin bioceramic grafts for bone tissue regeneration and their promising properties. Both products already available on the market and those in preclinical phases are included. To understand their clear contribution to the field, the main clinical requirements and the current available biological-derived ceramic grafts with their advantages and limitations have been collected.
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Affiliation(s)
- Patricia Diaz-Rodriguez
- R + D Pharma Group (GI-1645), Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
- Department of Chemical Engineering and Pharmaceutical Technology, School of Sciences, Universidad de La Laguna (ULL), Campus de Anchieta, 38200 La Laguna (Tenerife), Spain.
| | - Miriam López-Álvarez
- New Materials Group, Department of Applied Physics, University of Vigo, IISGS, MTI-Campus Lagoas-Marcosende, Vigo 36310, Spain
| | - Julia Serra
- New Materials Group, Department of Applied Physics, University of Vigo, IISGS, MTI-Campus Lagoas-Marcosende, Vigo 36310, Spain
| | - Pío González
- New Materials Group, Department of Applied Physics, University of Vigo, IISGS, MTI-Campus Lagoas-Marcosende, Vigo 36310, Spain
| | - Mariana Landín
- R + D Pharma Group (GI-1645), Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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13
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Jin M, Li Y, O'Laughlin R, Bittihn P, Pillus L, Tsimring LS, Hasty J, Hao N. Divergent Aging of Isogenic Yeast Cells Revealed through Single-Cell Phenotypic Dynamics. Cell Syst 2019; 8:242-253.e3. [PMID: 30852250 DOI: 10.1016/j.cels.2019.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/28/2018] [Accepted: 02/07/2019] [Indexed: 12/27/2022]
Abstract
Although genetic mutations that alter organisms' average lifespans have been identified in aging research, our understanding of the dynamic changes during aging remains limited. Here, we integrate single-cell imaging, microfluidics, and computational modeling to investigate phenotypic divergence and cellular heterogeneity during replicative aging of single S. cerevisiae cells. Specifically, we find that isogenic cells diverge early in life toward one of two aging paths, which are characterized by distinct age-associated phenotypes. We captured the dynamics of single cells along the paths with a stochastic discrete-state model, which accurately predicts both the measured heterogeneity and the lifespan of cells on each path within a cell population. Our analysis suggests that genetic and environmental factors influence both a cell's choice of paths and the kinetics of paths themselves. Given that these factors are highly conserved throughout eukaryotes, divergent aging might represent a general scheme in cellular aging of other organisms.
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Affiliation(s)
- Meng Jin
- BioCircuits Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Richard O'Laughlin
- Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Philip Bittihn
- BioCircuits Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; UCSD Moores Cancer Center, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
| | - Nan Hao
- BioCircuits Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
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14
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Arlia-Ciommo A, Leonov A, Mohammad K, Beach A, Richard VR, Bourque SD, Burstein MT, Goldberg AA, Kyryakov P, Gomez-Perez A, Koupaki O, Titorenko VI. Mechanisms through which lithocholic acid delays yeast chronological aging under caloric restriction conditions. Oncotarget 2018; 9:34945-34971. [PMID: 30405886 PMCID: PMC6201858 DOI: 10.18632/oncotarget.26188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022] Open
Abstract
All presently known geroprotective chemical compounds of plant and microbial origin are caloric restriction mimetics because they can mimic the beneficial lifespan- and healthspan-extending effects of caloric restriction diets without the need to limit calorie supply. We have discovered a geroprotective chemical compound of mammalian origin, a bile acid called lithocholic acid, which can delay chronological aging of the budding yeast Saccharomyces cerevisiae under caloric restriction conditions. Here, we investigated mechanisms through which lithocholic acid can delay chronological aging of yeast limited in calorie supply. We provide evidence that lithocholic acid causes a stepwise development and maintenance of an aging-delaying cellular pattern throughout the entire chronological lifespan of yeast cultured under caloric restriction conditions. We show that lithocholic acid stimulates the aging-delaying cellular pattern and preserves such pattern because it specifically modulates the spatiotemporal dynamics of a complex cellular network. We demonstrate that this cellular network integrates certain pathways of lipid and carbohydrate metabolism, some intercompartmental communications, mitochondrial morphology and functionality, and liponecrotic and apoptotic modes of aging-associated cell death. Our findings indicate that lithocholic acid prolongs longevity of chronologically aging yeast because it decreases the risk of aging-associated cell death, thus increasing the chance of elderly cells to survive.
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Affiliation(s)
| | - Anna Leonov
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Karamat Mohammad
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Adam Beach
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Vincent R Richard
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Simon D Bourque
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | | | - Pavlo Kyryakov
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Olivia Koupaki
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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