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Moses E, Atlan T, Sun X, Franěk R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. NATURE AGING 2024; 4:791-813. [PMID: 38750187 DOI: 10.1038/s43587-024-00632-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. In this study, we used the turquoise killifish (Nothobranchius furzeri) to genetically arrest germline development at discrete stages and examine how different modes of infertility impact life history. We first constructed a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. We show here that germline depletion-but not arresting germline differentiation-enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted Caenorhabditis elegans. Our results, therefore, demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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Affiliation(s)
- Eitan Moses
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Tehila Atlan
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Xue Sun
- Department of Biochemistry, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Roman Franěk
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Atif Siddiqui
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | | | - Sagiv Shifman
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - David M Zucker
- Department of Statistics and Data Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Oron-Gottesman
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | - Oren Ram
- Department of Biochemistry, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Itamar Harel
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel.
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2
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Moses E, Atlan T, Sun X, Franek R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572041. [PMID: 38187630 PMCID: PMC10769255 DOI: 10.1101/2023.12.18.572041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Classical evolutionary theories propose tradeoffs between reproduction, damage repair, and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. Here, we use the turquoise killifish ( N. furzeri ) to genetically arrest germline development at discrete stages, and examine how different modes of infertility impact life-history. We first construct a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. Next, we show that germline depletion - but not arresting germline differentiation - enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted C. elegans . Our results therefore demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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3
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Ogamino S, Yamamichi M, Sato K, Ishitani T. Dynamics of Wnt/β-catenin reporter activity throughout whole life in a naturally short-lived vertebrate. NPJ AGING 2024; 10:23. [PMID: 38684674 PMCID: PMC11059364 DOI: 10.1038/s41514-024-00149-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Wnt/β-catenin signaling plays a major role in regulation of embryogenesis, organogenesis, and adult tissue homeostasis and regeneration. However, the roles played by Wnt/β-catenin and the spatiotemporal regulation of its activity throughout life, including during aging, are not fully understood. To address these issues, we introduced a Wnt/β-catenin signaling sensitive reporter into African turquoise killifish (Nothobranchius furzeri), a naturally ultra-short-lived fish that allows for the analysis of its whole life within a short period of time. Using this reporter killifish, we unraveled the previously unidentified dynamics of Wnt/β-catenin signaling during development and aging. Using the reporter strain, we detected Wnt/β-catenin activity in actively developing tissues as reported in previous reports, but also observed activation and attenuation of Wnt/β-catenin activity during embryonic reaggregation and diapause, respectively. During the aging process, the reporter was activated in the choroidal layer and liver, but its expression decreased in the kidneys. In addition, the reporter also revealed that aging disrupts the spatial regulation and intensity control of Wnt/β-catenin activity seen during fin regeneration, which interferes with precise regeneration. Thus, the employed reporter killifish is a highly useful model for investigating the dynamics of Wnt/β-catenin signaling during both the developmental and aging process.
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Affiliation(s)
- Shohei Ogamino
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- Institute for Molecular & Cellular Regulation, Gunma University, Gunma, 371-8512, Japan
| | - Moeko Yamamichi
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Ken Sato
- Institute for Molecular & Cellular Regulation, Gunma University, Gunma, 371-8512, Japan
| | - Tohru Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
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Boos F, Chen J, Brunet A. The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes. Cold Spring Harb Protoc 2024; 2024:107737. [PMID: 37100468 PMCID: PMC10890783 DOI: 10.1101/pdb.over107737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The African turquoise killifish Nothobranchius furzeri is currently the shortest-lived vertebrate that can be bred in captivity. Because of its short life span of only 4-6 months, rapid generation time, high fecundity, and low cost of maintenance, the African turquoise killifish has emerged as an attractive model organism that combines the scalability of invertebrate models with the unique features of vertebrate organisms. A growing community of researchers is using the African turquoise killifish for studies in diverse fields, including aging, organ regeneration, development, "suspended animation," evolution, neuroscience, and disease. A wide range of techniques is now available for killifish research, from genetic manipulations and genomic tools to specialized assays for studying life span, organ biology, response to injury, etc. This protocol collection provides detailed descriptions of the methods that are generally applicable to all killifish laboratories and those that are limited to specific disciplines. Here, we give an overview of the features that render the African turquoise killifish a unique fast-track vertebrate model organism.
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Affiliation(s)
- Felix Boos
- Department of Genetics, Stanford, California 94305, USA
| | - Jingxun Chen
- Department of Genetics, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford, California 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, California 94305, USA
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Mariën V, Piskin I, Zandecki C, Van houcke J, Arckens L. Age-related alterations in the behavioral response to a novel environment in the African turquoise killifish ( Nothobranchius furzeri). Front Behav Neurosci 2024; 17:1326674. [PMID: 38259633 PMCID: PMC10800983 DOI: 10.3389/fnbeh.2023.1326674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
The African turquoise killifish (Nothobranchius furzeri) has emerged as a popular model organism for neuroscience research in the last decade. One of the reasons for its popularity is its short lifespan for a vertebrate organism. However, little research has been carried out using killifish in behavioral tests, especially looking at changes in their behavior upon aging. Therefore, we used the open field and the novel tank diving test to unravel killifish locomotion, exploration-related behavior, and behavioral changes over their adult lifespan. The characterization of this behavioral baseline is important for future experiments involving pharmacology to improve the aging phenotype. In this study, two cohorts of fish were used, one cohort was tested in the open field test and one cohort was tested in the novel tank diving test. Each cohort was tested from the age of 6 weeks to the age of 24 weeks and measurements were performed every three weeks. In the open field test, we found an increase in the time spent in the center zone from 18 weeks onward, which could indicate altered exploration behavior. However, upon aging, the fish also showed an increased immobility frequency and duration. In addition, after the age of 15 weeks, their locomotion decreased. In the novel tank diving test, we did not observe this aging effect on locomotion or exploration. Killifish spent around 80% of their time in the bottom half of the tank, and we could not observe habituation effects, indicating slow habituation to novel environments. Moreover, we observed that killifish showed homebase behavior in both tests. These homebases are mostly located near the edges of the open field test and at the bottom of the novel tank diving test. Altogether, in the open field test, the largest impact of aging on locomotion and exploration was observed beyond the age of 15 weeks. In the novel tank diving test, no effect of age was found. Therefore, to test the effects of pharmacology on innate behavior, the novel tank diving test is ideally suited because there is no confounding effect of aging.
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Affiliation(s)
- Valerie Mariën
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Ilayda Piskin
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Caroline Zandecki
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jolien Van houcke
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Lutgarde Arckens
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
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Ruparelia AA, Salavaty A, Barlow CK, Lu Y, Sonntag C, Hersey L, Eramo MJ, Krug J, Reuter H, Schittenhelm RB, Ramialison M, Cox A, Ryan MT, Creek DJ, Englert C, Currie PD. The African killifish: A short-lived vertebrate model to study the biology of sarcopenia and longevity. Aging Cell 2024; 23:e13862. [PMID: 37183563 PMCID: PMC10776123 DOI: 10.1111/acel.13862] [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: 03/13/2022] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023] Open
Abstract
Sarcopenia, the age-related decline in muscle function, places a considerable burden on health-care systems. While the stereotypic hallmarks of sarcopenia are well characterized, their contribution to muscle wasting remains elusive, which is partly due to the limited availability of animal models. Here, we have performed cellular and molecular characterization of skeletal muscle from the African killifish-an extremely short-lived vertebrate-revealing that while many characteristics deteriorate with increasing age, supporting the use of killifish as a model for sarcopenia research, some features surprisingly reverse to an "early-life" state in the extremely old stages. This suggests that in extremely old animals, there may be mechanisms that prevent further deterioration of skeletal muscle, contributing to an extension of life span. In line with this, we report a reduction in mortality rates in extremely old killifish. To identify mechanisms for this phenomenon, we used a systems metabolomics approach, which revealed that during aging there is a striking depletion of triglycerides, mimicking a state of calorie restriction. This results in the activation of mitohormesis, increasing Sirt1 levels, which improves lipid metabolism and maintains nutrient homeostasis in extremely old animals. Pharmacological induction of Sirt1 in aged animals was sufficient to induce a late life-like metabolic profile, supporting its role in life span extension in vertebrate populations that are naturally long-lived. Collectively, our results demonstrate that killifish are not only a novel model to study the biological processes that govern sarcopenia, but they also provide a unique vertebrate system to dissect the regulation of longevity.
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Affiliation(s)
- Avnika A. Ruparelia
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health SciencesUniversity of MelbourneMelbourneAustralia
- Centre for Muscle Research, Department of Anatomy and PhysiologyUniversity of MelbourneMelbourneAustralia
| | - Adrian Salavaty
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
- Systems Biology Institute Australia, Monash UniversityClaytonAustralia
| | - Christopher K. Barlow
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
- Monash Proteomics and Metabolomics FacilityMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Yansong Lu
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
| | - Carmen Sonntag
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
| | - Lucy Hersey
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
| | - Matthew J. Eramo
- Department of Biochemistry and Molecular BiologyMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Johannes Krug
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI)JenaGermany
| | - Hanna Reuter
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI)JenaGermany
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
- Monash Proteomics and Metabolomics FacilityMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
- Systems Biology Institute Australia, Monash UniversityClaytonAustralia
| | - Andrew Cox
- Peter MacCallum Cancer CentreMelbourneAustralia
- Department of Biochemistry and PharmacologyThe University of MelbourneMelbourneAustralia
| | - Michael T. Ryan
- Department of Biochemistry and Molecular BiologyMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Darren J. Creek
- Monash Proteomics and Metabolomics FacilityMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
- Drug Delivery, Disposition and DynamicsMonash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Christoph Englert
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI)JenaGermany
- Institute of Biochemistry and Biophysics, Friedrich‐Schiller‐University JenaJenaGermany
| | - Peter D. Currie
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
- EMBL Australia, Victorian NodeMonash UniversityClaytonAustralia
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Borgonovo J, Allende-Castro C, Medinas DB, Cárdenas D, Cuevas MP, Hetz C, Concha ML. Immunohistochemical characterisation of the adult Nothobranchius furzeri intestine. Cell Tissue Res 2024; 395:21-38. [PMID: 38015266 DOI: 10.1007/s00441-023-03845-8] [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: 04/24/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Nothobranchius furzeri is emerging as an exciting vertebrate organism in the field of biomedicine, developmental biology and ecotoxicology research. Its short generation time, compressed lifespan and accelerated ageing make it a versatile model for longitudinal studies with high traceability. Although in recent years the use of this model has increased enormously, there is still little information on the anatomy, morphology and histology of its main organs. In this paper, we present a description of the digestive system of N. furzeri, with emphasis on the intestine. We note that the general architecture of the intestinal tissue is shared with other vertebrates, and includes a folding mucosa, an outer muscle layer and a myenteric plexus. By immunohistochemical analysis, we reveal that the mucosa harbours the same type of epithelial cells observed in mammals, including enterocytes, goblet cells and enteroendocrine cells, and that the myenteric neurons express neurotransmitters common to other species, such as serotonin, substance P and tyrosine hydroxylase. In addition, we detect the presence of a proliferative compartment at the base of the intestinal folds. The description of the normal intestinal morphology provided here constitutes a baseline information to contrast with tissue alterations in future lines of research assessing pathologies, ageing-related diseases or damage caused by toxic agents.
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Affiliation(s)
- Janina Borgonovo
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Biomedical Neuroscience Institute, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Camilo Allende-Castro
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Biomedical Neuroscience Institute, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Danilo B Medinas
- Biomedical Neuroscience Institute, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
- Cellular and Molecular Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Deyanira Cárdenas
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
- Medical Technology School, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - María Paz Cuevas
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
- Medical Technology School, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
- Cellular and Molecular Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Miguel L Concha
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.
- Biomedical Neuroscience Institute, Santiago, Chile.
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile.
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de Bakker DEM, Valenzano DR. Turquoise killifish: A natural model of age-dependent brain degeneration. Ageing Res Rev 2023; 90:102019. [PMID: 37482345 DOI: 10.1016/j.arr.2023.102019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
Turquoise killifish (Nothobranchius furzeri) are naturally short-lived vertebrates that display a wide range of spontaneous age-related changes, including onset of cancer, reduced mobility, and cognitive decline. Here, we focus on describing the phenotypic spectrum of the aging killifish brain. As turquoise killifish age, their dopaminergic and noradrenergic neurons undergo a significant decline in number. Furthermore, brain aging in turquoise killifish is associated with several glial-specific changes, such as an increase in the astrocyte-covered surface area and an increase in the numbers of microglial cells, i.e. the brain-specific macrophage population. Killifish brains undergo age-dependent reduced proteasome activity and increased protein aggregation, including the aggregation of the Parkinson's disease marker α-synuclein. Parallel to brain degeneration, turquoise killifish develop spontaneous age-related gut dysbiosis, which has been proposed to affect human neurodegenerative disease. Finally, aged turquoise killifish display declined learning capacity. We argue that, taken together, the molecular, cellular and functional changes that spontaneously take place during aging in killifish brains are consistent with a robust degenerative process that shares remarkable similarities with human neurodegenerative diseases. Hence, we propose that turquoise killifish represent a powerful model of spontaneous brain degeneration which can be effectively used to explore the causal mechanisms underlying neurodegenerative diseases.
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Affiliation(s)
- Dennis E M de Bakker
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745, Jena, Germany
| | - Dario R Valenzano
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745, Jena, Germany.
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Součková K, Jasík M, Sovadinová I, Sember A, Sychrová E, Konieczna A, Bystrý V, Dyková I, Blažek R, Lukšíková K, Pavlica T, Jankásek M, Altmanová M, Žák J, Zbončáková A, Reichard M, Slabý O. From fish to cells: Establishment of continuous cell lines from embryos of annual killifish Nothobranchius furzeri and N. kadleci. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 259:106517. [PMID: 37087860 DOI: 10.1016/j.aquatox.2023.106517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
There is a growing need of alternative experimental models that avoid or minimize the use of animals due to ethical, economical, and scientific reasons. Surprisingly, the stable embryonic cell lines representing Nothobranchius spp., emerging vertebrate models in aging research, regenerative medicine, ecotoxicology, or genomics, have been not derived so far. This paper reports establishment and deep characterization of ten continuous cell lines from annual killifish embryos of N. furzeri and N. kadleci. The established cell lines exhibited mostly fibroblast- and epithelial-like morphology and steady growth rates with cell doubling time ranging from 27 to 40 h. All cell lines retained very similar characteristics even after continuous subcultivation (more than 100 passages) and extended storage in liquid nitrogen (∼3 years). The cytogenetic analysis of the cell lines revealed a diploid chromosome number mostly equal to 38 elements (i.e., the native chromosome count for both killifish species), with minor but diverse line/passage-specific karyotype changes compared to the patterns observed in non-cultured N. furzeri and N. kadleci somatic cells. Based on transcriptional analysis of marker genes, the cell lines displayed features of an undifferentiated state without signs of senescence even in advanced passages. We confirmed that the cell lines are transfectable and can form viable 3-D spheroids. The applicability of the cell lines for (eco)toxicological surveys was confirmed by assessing the effect of cytotoxic and growth inhibitory agents. Properties of established Nothobranchius embryonic cell lines open new possibilities for the application of this model in various fields of life sciences including molecular mechanisms of aging, karyotype (in)stability or differences in lifespan.
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Affiliation(s)
- Kamila Součková
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
| | - Matej Jasík
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Iva Sovadinová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 602 00, Czech Republic
| | - Alexandr Sember
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic
| | - Eliška Sychrová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno 602 00, Czech Republic
| | - Anna Konieczna
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Vojtěch Bystrý
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Iva Dyková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic
| | - Radim Blažek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Karolína Lukšíková
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Tomáš Pavlica
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Marek Jankásek
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov 277 21, Czech Republic; Department of Ecology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Jakub Žák
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Adriana Zbončáková
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Martin Reichard
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno 603 00, Czech Republic; Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź 90-237, Poland
| | - Ondřej Slabý
- Ondřej Slabý Group, Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic; Department of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
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10
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Chopra K, Folkmanaitė M, Stockdale L, Shathish V, Ishibashi S, Bergin R, Amich J, Amaya E. Duox is the primary NADPH oxidase responsible for ROS production during adult caudal fin regeneration in zebrafish. iScience 2023; 26:106147. [PMID: 36843843 PMCID: PMC9950526 DOI: 10.1016/j.isci.2023.106147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/28/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Sustained elevated levels of reactive oxygen species (ROS) have been shown to be essential for regeneration in many organisms. This has been shown primarily via the use of pharmacological inhibitors targeting the family of NADPH oxidases (NOXes). To identify the specific NOXes involved in ROS production during adult caudal fin regeneration in zebrafish, we generated nox mutants for duox, nox5 and cyba (a key subunit of NOXes 1-4) and crossed these lines with a transgenic line ubiquitously expressing HyPer, which permits the measurement of ROS levels. Homozygous duox mutants had the greatest effect on ROS levels and rate of fin regeneration among the single mutants. However, duox:cyba double mutants showed a greater effect on fin regeneration than the single duox mutants, suggesting that Nox1-4 also play a role during regeneration. This work also serendipitously found that ROS levels in amputated adult zebrafish fins oscillate with a circadian rhythm.
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Affiliation(s)
- Kunal Chopra
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Milda Folkmanaitė
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Liam Stockdale
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Vishali Shathish
- Manchester Fungal Infection Group (MFIG), Division of Evolution, Infection, and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Shoko Ishibashi
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Rachel Bergin
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jorge Amich
- Manchester Fungal Infection Group (MFIG), Division of Evolution, Infection, and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.,Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda 28220 Madrid, Spain
| | - Enrique Amaya
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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11
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Krug J, Perner B, Albertz C, Mörl H, Hopfenmüller VL, Englert C. Generation of a transparent killifish line through multiplex CRISPR/Cas9mediated gene inactivation. eLife 2023; 12:81549. [PMID: 36820520 PMCID: PMC10010688 DOI: 10.7554/elife.81549] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/23/2023] [Indexed: 02/24/2023] Open
Abstract
Body pigmentation is a limitation for in vivo imaging and thus for the performance of longitudinal studies in biomedicine. A possibility to circumvent this obstacle is the employment of pigmentation mutants, which are used in fish species like zebrafish and medaka. To address the basis of aging, the short-lived African killifish Nothobranchius furzeri has recently been established as a model organism. Despite its short lifespan, N. furzeri shows typical signs of mammalian aging including telomere shortening, accumulation of senescent cells, and loss of regenerative capacity. Here, we report the generation of a transparent N. furzeri line by the simultaneous inactivation of three key loci responsible for pigmentation. We demonstrate that this stable line, named klara, can serve as a tool for different applications including behavioral experiments and the establishment of a senescence reporter by integration of a fluorophore into the cdkn1a (p21) locus and in vivo microscopy of the resulting line.
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Affiliation(s)
- Johannes Krug
- Molecular Genetics Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)JenaGermany
| | - Birgit Perner
- Molecular Genetics Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)JenaGermany
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Carolin Albertz
- Molecular Genetics Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)JenaGermany
| | - Hanna Mörl
- Molecular Genetics Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)JenaGermany
| | - Vera L Hopfenmüller
- Molecular Genetics Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)JenaGermany
| | - Christoph Englert
- Molecular Genetics Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)JenaGermany
- Institute of Biochemistry and Biophysics, Friedrich-Schiller-University JenaJenaGermany
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12
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Richter A, Krug J, Englert C. Molecular Sexing of Nothobranchius furzeri Embryos and Larvae. Cold Spring Harb Protoc 2022; 2022:630-640. [PMID: 36167675 DOI: 10.1101/pdb.prot107782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Differences between the sexes are of increasing interest in basic and applied research with regard to development, behavior, aging, and diseases. Although the African turquoise killifish Nothobranchius furzeri, a model for aging research well known for its remarkably short life span, develops strong sexual dimorphism in adulthood, there is no visible indicator of its sex in embryonic and juvenile stages. To address this issue, we developed a molecular sexing assay exploiting two large sequence polymorphisms in the minimal sex-determining region (SDR) of N. furzeri These polymorphisms are sequence deletions on the Y chromosome that involve the lack or truncation of one or multiple microsatellites. The simple polymerase chain reaction (PCR) readout of the assays described here allows the sexing of N. furzeri embryos and larvae in a medium- to high-throughput and cost-efficient manner.
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Affiliation(s)
- Annekatrin Richter
- Molecular Genetics, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Johannes Krug
- Molecular Genetics, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Christoph Englert
- Molecular Genetics, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany.,Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena, 07745 Jena, Germany
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13
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Bulavkina EV, Kudryavtsev AA, Goncharova MA, Lantsova MS, Shuvalova AI, Kovalev MA, Kudryavtseva AV. Multifaceted Nothobranchius. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1563-1578. [PMID: 36717447 DOI: 10.1134/s0006297922120136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Annual killifish of the genus Nothobranchius are seeing a rapid increase in scientific interest over the years. A variety of aspects surrounding the egg-laying Cyprinodontiformes is being extensively studied, including their aging. Inhabiting drying water bodies of Africa rarely allows survival through more than one rainy season for the Nothobranchius populations. Therefore, there is no lifespan-related bias in natural selection, which has ultimately led to the decreased efficiency of DNA repair system. Aging of the Nothobranchius species is studied both under normal conditions and under the influence of potential geroprotectors, as well as genetic modifications. Most biogerontological studies are conducted using the species Nothobranchius furzeri (GRZ isolate), which has a lifespan of 3 to 7 months. However, the list of model species of Nothobranchius is considerably wider, and the range of advanced research areas with their participation extends far beyond gerontology. This review summarizes the most interesting and promising topics developing in the studies of the fish of Nothobranchius genus. Both classical studies related to lifespan control and rather new ones are discussed, including mechanisms of diapause, challenges of systematics and phylogeny, evolution of sex determination mechanisms, changes in chromosome count, occurrence of multiple repeated DNA sequences in the genome, cognitive and behavioral features and social stratification, as well as methodological difficulties in working with Nothobranchius.
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Affiliation(s)
- Elizaveta V Bulavkina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexander A Kudryavtsev
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Margarita A Goncharova
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Margarita S Lantsova
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasija I Shuvalova
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Maxim A Kovalev
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anna V Kudryavtseva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia. .,Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
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14
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McKay A, Costa EK, Chen J, Hu CK, Chen X, Bedbrook CN, Khondker RC, Thielvoldt M, Priya Singh P, Wyss-Coray T, Brunet A. An automated feeding system for the African killifish reveals the impact of diet on lifespan and allows scalable assessment of associative learning. eLife 2022; 11:e69008. [PMID: 36354233 PMCID: PMC9788828 DOI: 10.7554/elife.69008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/09/2022] [Indexed: 11/11/2022] Open
Abstract
The African turquoise killifish is an exciting new vertebrate model for aging studies. A significant challenge for any model organism is the control over its diet in space and time. To address this challenge, we created an automated and networked fish feeding system. Our automated feeder is designed to be open-source, easily transferable, and built from widely available components. Compared to manual feeding, our automated system is highly precise and flexible. As a proof of concept for the feeding flexibility of these automated feeders, we define a favorable regimen for growth and fertility for the African killifish and a dietary restriction regimen where both feeding time and quantity are reduced. We show that this dietary restriction regimen extends lifespan in males (but not in females) and impacts the transcriptomes of killifish livers in a sex-specific manner. Moreover, combining our automated feeding system with a video camera, we establish a quantitative associative learning assay to provide an integrative measure of cognitive performance for the killifish. The ability to precisely control food delivery in the killifish opens new areas to assess lifespan and cognitive behavior dynamics and to screen for dietary interventions and drugs in a scalable manner previously impossible with traditional vertebrate model organisms.
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Affiliation(s)
- Andrew McKay
- Department of Genetics, Stanford UniversityStanfordUnited States
- Biology Graduate Program, Stanford UniversityStanfordUnited States
| | - Emma K Costa
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
- Neurosciences Interdepartmental Program, Stanford University School of MedicineStanfordUnited States
| | - Jingxun Chen
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Chi-Kuo Hu
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Xiaoshan Chen
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Claire N Bedbrook
- Department of Genetics, Stanford UniversityStanfordUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | | | | | | | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
- Glenn Laboratories for the Biology of Aging, Stanford UniversityStanfordUnited States
- Wu Tsai Neurosciences Institute, Stanford UniversityStanfordUnited States
| | - Anne Brunet
- Department of Genetics, Stanford UniversityStanfordUnited States
- Glenn Laboratories for the Biology of Aging, Stanford UniversityStanfordUnited States
- Wu Tsai Neurosciences Institute, Stanford UniversityStanfordUnited States
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15
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Mason MW, Bertucci EM, Leri FM, Parrott BB. Transient Copper Exposure During Embryogenesis and Temperature Affect Developmental Rate, Survival, and Fin Regeneration in Japanese Medaka (Oryzias latipes). ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:748-757. [PMID: 34918380 DOI: 10.1002/etc.5276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Combined environmental stressors that an organism experiences can have both immediate and lasting consequences. In the present study, we exposed Japanese medaka (Oryzias latipes) embryos to sublethal copper sulfate (CuSO4 ; 0, 10, and 100 ppb) in combination with different rearing temperatures (27, 30, and 33 °C) to assess acute and latent effects on development, growth, and regenerative capacity. Embryos exposed to CuSO4 and/or higher temperatures hatched significantly earlier. At 4 months post-exposure, fish exposed to low levels of CuSO4 during development had higher survival, whereas fish exposed to both 100 ppb CuSO4 and 33 °C temperatures had significantly lower survival. In addition, a sex-specific effect of embryonic CuSO4 exposure was observed as female mass decreased with increasing Cu dose. We also assessed caudal fin regenerative capabilities in both embryo-exposed fish at 4 months of age and adult medaka that were exposed to 0, 10, and 100 ppb CuSO4 at room temperature during a 14-day trial. Whereas fin regeneration was unaffected by adult exposure to Cu, fish transiently exposed during embryogenesis displayed an initial increase in fin growth rate and an increased incidence of abnormal fin morphology following regrowth. Collectively, these data suggest that developmental Cu exposure has the potential to exert long-lasting impacts to organismal growth, survival, and function. Environ Toxicol Chem 2022;41:748-757. © 2021 SETAC.
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Affiliation(s)
- Marilyn W Mason
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
| | - Emily M Bertucci
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
- Odum School of Ecology, University of Georgia, Athens, Georgia, USA
| | - Faith M Leri
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
- Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Benjamin B Parrott
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
- Odum School of Ecology, University of Georgia, Athens, Georgia, USA
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16
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Chowdhury K, Lin S, Lai SL. Comparative Study in Zebrafish and Medaka Unravels the Mechanisms of Tissue Regeneration. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.783818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue regeneration has been in the spotlight of research for its fascinating nature and potential applications in human diseases. The trait of regenerative capacity occurs diversely across species and tissue contexts, while it seems to decline over evolution. Organisms with variable regenerative capacity are usually distinct in phylogeny, anatomy, and physiology. This phenomenon hinders the feasibility of studying tissue regeneration by directly comparing regenerative with non-regenerative animals, such as zebrafish (Danio rerio) and mice (Mus musculus). Medaka (Oryzias latipes) is a fish model with a complete reference genome and shares a common ancestor with zebrafish approximately 110–200 million years ago (compared to 650 million years with mice). Medaka shares similar features with zebrafish, including size, diet, organ system, gross anatomy, and living environment. However, while zebrafish regenerate almost every organ upon experimental injury, medaka shows uneven regenerative capacity. Their common and distinct biological features make them a unique platform for reciprocal analyses to understand the mechanisms of tissue regeneration. Here we summarize current knowledge about tissue regeneration in these fish models in terms of injured tissues, repairing mechanisms, available materials, and established technologies. We further highlight the concept of inter-species and inter-organ comparisons, which may reveal mechanistic insights and hint at therapeutic strategies for human diseases.
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17
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Reuter H, Perner B, Wahl F, Rohde L, Koch P, Groth M, Buder K, Englert C. Aging Activates the Immune System and Alters the Regenerative Capacity in the Zebrafish Heart. Cells 2022; 11:cells11030345. [PMID: 35159152 PMCID: PMC8834511 DOI: 10.3390/cells11030345] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 02/04/2023] Open
Abstract
Age-associated organ failure and degenerative diseases have a major impact on human health. Cardiovascular dysfunction has an increasing prevalence with age and is one of the leading causes of death. In contrast to humans, zebrafish have extraordinary regeneration capacities of complex organs including the heart. In addition, zebrafish has recently become a model organism in research on aging. Here, we have compared the ventricular transcriptome as well as the regenerative capacity after cryoinjury of old and young zebrafish hearts. We identified the immune system as activated in old ventricles and found muscle organization to deteriorate upon aging. Our data show an accumulation of immune cells, mostly macrophages, in the old zebrafish ventricle. Those immune cells not only increased in numbers but also showed morphological and behavioral changes with age. Our data further suggest that the regenerative response to cardiac injury is generally impaired and much more variable in old fish. Collagen in the wound area was already significantly enriched in old fish at 7 days post injury. Taken together, these data indicate an ‘inflammaging’-like process in the zebrafish heart and suggest a change in regenerative response in the old.
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Affiliation(s)
- Hanna Reuter
- Molecular Genetics Laboratory, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (H.R.); (B.P.); (F.W.); (L.R.)
| | - Birgit Perner
- Molecular Genetics Laboratory, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (H.R.); (B.P.); (F.W.); (L.R.)
- Core Facility Imaging, 07745 Jena, Germany
| | - Florian Wahl
- Molecular Genetics Laboratory, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (H.R.); (B.P.); (F.W.); (L.R.)
| | - Luise Rohde
- Molecular Genetics Laboratory, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (H.R.); (B.P.); (F.W.); (L.R.)
| | - Philipp Koch
- Core Facility Life Science Computing, 07735 Jena, Germany;
| | - Marco Groth
- Core Facility DNA Sequencing, 07745 Jena, Germany;
| | - Katrin Buder
- Core Service Histology/Pathology/EM, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany;
| | - Christoph Englert
- Molecular Genetics Laboratory, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (H.R.); (B.P.); (F.W.); (L.R.)
- Institute of Biochemistry and Biophysics, Friedrich-Schiller-University Jena, 07745 Jena, Germany
- Correspondence: ; Tel.: +49-3641-656042
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18
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Vanhunsel S, Bergmans S, Beckers A, Etienne I, Van Bergen T, De Groef L, Moons L. The age factor in optic nerve regeneration: Intrinsic and extrinsic barriers hinder successful recovery in the short-living killifish. Aging Cell 2022; 21:e13537. [PMID: 34927348 PMCID: PMC8761009 DOI: 10.1111/acel.13537] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 01/06/2023] Open
Abstract
As the mammalian central nervous system matures, its regenerative ability decreases, leading to incomplete or non-recovery from the neurodegenerative diseases and central nervous system insults that we are increasingly facing in our aging world population. Current neuroregenerative research is largely directed toward identifying the molecular and cellular players that underlie central nervous system repair, yet it repeatedly ignores the aging context in which many of these diseases appear. Using an optic nerve crush model in a novel biogerontology model, that is, the short-living African turquoise killifish, the impact of aging on injury-induced optic nerve repair was investigated. This work reveals an age-related decline in axonal regeneration in female killifish, with different phases of the repair process being affected depending on the age. Interestingly, as in mammals, both a reduced intrinsic growth potential and a non-supportive cellular environment seem to lie at the basis of this impairment. Overall, we introduce the killifish visual system and its age-dependent regenerative ability as a model to identify new targets for neurorepair in non-regenerating individuals, thereby also considering the effects of aging on neurorepair.
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Affiliation(s)
- Sophie Vanhunsel
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
| | - Steven Bergmans
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
| | - An Beckers
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
| | | | | | - Lies De Groef
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
- Leuven Brain InstituteLeuvenBelgium
| | - Lieve Moons
- Neural Circuit Development and Regeneration Research GroupAnimal Physiology and Neurobiology SectionDepartment of BiologyKU LeuvenLeuvenBelgium
- Leuven Brain InstituteLeuvenBelgium
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19
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Louka A, Bagnoli S, Rupert J, Esapa B, Tartaglia GG, Cellerino A, Pastore A, Terzibasi Tozzini E. New lessons on TDP-43 from old N. furzeri killifish. Aging Cell 2022; 21:e13517. [PMID: 34939315 PMCID: PMC8761016 DOI: 10.1111/acel.13517] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/26/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022] Open
Abstract
Frontotemporal dementia and amyotrophic lateral sclerosis are fatal and incurable neurodegenerative diseases linked to the pathological aggregation of the TDP-43 protein. This is an essential DNA/RNA-binding protein involved in transcription regulation, pre-RNA processing, and RNA transport. Having suitable animal models to study the mechanisms of TDP-43 aggregation is crucial to develop treatments against disease. We have previously demonstrated that the killifish Nothobranchius furzeri offers the advantage of being the shortest-lived vertebrate with a clear aging phenotype. Here, we show that the two N. furzeri paralogs of TDP-43 share high sequence homology with the human protein and recapitulate its cellular and biophysical behavior. During aging, N. furzeri TDP-43 spontaneously forms insoluble intracellular aggregates with amyloid characteristics and colocalizes with stress granules. Our results propose this organism as a valuable new model of TDP-43-related pathologies making it a powerful tool for the study of disease mechanism.
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Affiliation(s)
- Alexandra Louka
- Department of Clinical and Basic Neuroscience King's College London UK‐DRI Centre at the Maurice Wohl Institute London UK
| | | | - Jakob Rupert
- Department of Clinical and Basic Neuroscience King's College London UK‐DRI Centre at the Maurice Wohl Institute London UK
- Universita' di Roma “La Sapienza” Rome Italy
| | - Benjamin Esapa
- Department of Clinical and Basic Neuroscience King's College London UK‐DRI Centre at the Maurice Wohl Institute London UK
| | | | - Alessandro Cellerino
- Bio@SNS Scuola Normale Superiore Pisa Italy
- Leibniz Institute on Aging Fritz Lipmann Institute Jena Germany
| | - Annalisa Pastore
- Department of Clinical and Basic Neuroscience King's College London UK‐DRI Centre at the Maurice Wohl Institute London UK
- European Synchrotron Radiation Facility Grenoble France
| | - Eva Terzibasi Tozzini
- Bio@SNS Scuola Normale Superiore Pisa Italy
- Stazione Zoologica Anton Dohrn (SZN) Naples Italy
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20
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Dyková I, Žák J, Reichard M, Součková K, Slabý O, Bystrý V, Blažek R. Histopathology of laboratory-reared Nothobranchius fishes: Mycobacterial infections versus neoplastic lesions. JOURNAL OF FISH DISEASES 2021; 44:1179-1190. [PMID: 33844322 DOI: 10.1111/jfd.13378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Short-lived killifishes of the genus Nothobranchius Peters, 1868 (Cyprinodontiformes) are considered promising model organisms for biomedical research on ageing and tumorigenesis. We conducted histopathological analysis of 411 adult individuals from three Nothobranchius species to study details on spontaneous age-related neoplastic lesions. Light microscopy based on H&E and toluidine blue-stained sections revealed (a) non-proliferative liver changes with pronounced vacuolation of hepatocytes; (b) proliferation of kidney haemopoietic tissue contributing to excretory system damage; (c) proliferation of splenic mononuclear haemoblasts accompanied by reduced erythropoiesis; (d) proliferation of mononuclear cell aggregates in the liver parenchyma; and (e) rare occurrence of hepatocellular adenomas. Ziehl-Neelsen (ZN) staining revealed that the proliferative lesions are a host defence response to mycobacterial infections manifested by activation of the mononuclear phagocytic system and atypical granulomatous inflammatory reaction. 16S rRNA analysis identified three species of Mycobacterium in our samples. Our findings turn attention to lesions which mimic neoplasms by their gross appearance and question the light microscopic interpretation of lesions unless differential ZN staining is included. Beyond the limitations of our morphological approach, the intensity of mycobacterial infections is a challenging opportunity for research into the molecular-genetic background of the mononuclear phagocytic system reaction in Nothobranchius killifish.
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Affiliation(s)
- Iva Dyková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jakub Žák
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Brno, Czech Republic
| | - Martin Reichard
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Kamila Součková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ondřej Slabý
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Vojtěch Bystrý
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Radim Blažek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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21
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Brunauer R, Xia IG, Asrar SN, Dawson LA, Dolan CP, Muneoka K. Aging delays epimorphic regeneration in mice. J Gerontol A Biol Sci Med Sci 2021; 76:1726-1733. [PMID: 33970250 DOI: 10.1093/gerona/glab131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Indexed: 11/14/2022] Open
Abstract
Epimorphic regeneration is a multi-tissue regeneration process where amputation does not lead to scarring, but blastema formation and patterned morphogenesis for which cell plasticity and concerted cell-cell interactions are pivotal. Tissue regeneration declines with aging, yet if and how aging impairs epimorphic regeneration is unknown. Here we show for the first time that aging derails the spatiotemporal regulation of epimorphic regeneration in mammals, first, by exacerbating tissue histolysis and delaying wound closure, and second, by impairing blastema differentiation and skeletal regrowth. Surprisingly, aging did not limit stem cell availability in the blastema, but reduced osteoblast-dependent bone formation. Our data suggest that aging delays regeneration not by stem cell exhaustion, but functional defects of differentiated cells that may be driven by an aged wound environment and alterations in the spatiotemporal regulation of regeneration events. Our findings emphasize the importance of accurate timing of signaling events for regeneration, and highlight the need for carefully timed interventions in regenerative medicine.
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Affiliation(s)
- Regina Brunauer
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Ian G Xia
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Shabistan N Asrar
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Lindsay A Dawson
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Connor P Dolan
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Surgery, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD
| | - Ken Muneoka
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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22
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Van Houcke J, Mariën V, Zandecki C, Seuntjens E, Ayana R, Arckens L. Modeling Neuroregeneration and Neurorepair in an Aging Context: The Power of a Teleost Model. Front Cell Dev Biol 2021; 9:619197. [PMID: 33816468 PMCID: PMC8012675 DOI: 10.3389/fcell.2021.619197] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/19/2021] [Indexed: 01/10/2023] Open
Abstract
Aging increases the risk for neurodegenerative disease and brain trauma, both leading to irreversible and multifaceted deficits that impose a clear societal and economic burden onto the growing world population. Despite tremendous research efforts, there are still no treatments available that can fully restore brain function, which would imply neuroregeneration. In the adult mammalian brain, neuroregeneration is naturally limited, even more so in an aging context. In view of the significant influence of aging on (late-onset) neurological disease, it is a critical factor in future research. This review discusses the use of a non-standard gerontology model, the teleost brain, for studying the impact of aging on neurorepair. Teleost fish share a vertebrate physiology with mammals, including mammalian-like aging, but in contrast to mammals have a high capacity for regeneration. Moreover, access to large mutagenesis screens empowers these teleost species to fill the gap between established invertebrate and rodent models. As such, we here highlight opportunities to decode the factor age in relation to neurorepair, and we propose the use of teleost fish, and in particular killifish, to fuel new research in the neuro-gerontology field.
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Affiliation(s)
- Jolien Van Houcke
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Valerie Mariën
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Caroline Zandecki
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium.,Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.,Leuven Brain Institute, Leuven, Belgium
| | - Rajagopal Ayana
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium.,Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Lutgarde Arckens
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium.,Leuven Brain Institute, Leuven, Belgium
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23
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Terzibasi Tozzini E, Cellerino A. Nothobranchius annual killifishes. EvoDevo 2020; 11:25. [PMID: 33323125 PMCID: PMC7739477 DOI: 10.1186/s13227-020-00170-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Annual fishes of the genus Nothobranchius inhabit ephemeral habitats in Eastern and Southeastern Africa. Their life cycle is characterized by very rapid maturation, a posthatch lifespan of a few weeks to months and embryonic diapause to survive the dry season. The species N. furzeri holds the record of the fastest-maturing vertebrate and of the vertebrate with the shortest captive lifespan and is emerging as model organism in biomedical research, evolutionary biology, and developmental biology. Extensive characterization of age-related phenotypes in the laboratory and of ecology, distribution, and demography in the wild are available. Species/populations from habitats differing in precipitation intensity show parallel evolution of lifespan and age-related traits that conform to the classical theories on aging. Genome sequencing and the establishment of CRISPR/Cas9 techniques made this species particularly attractive to investigate the effects genetic and non-genetic intervention on lifespan and aging-related phenotypes. At the same time, annual fishes are a very interesting subject for comparative approaches, including genomics, transcriptomics, and proteomics. The N. furzeri community is highly diverse and rapidly expanding and organizes a biannual meeting.
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Affiliation(s)
| | - Alessandro Cellerino
- Scuola Normale Superiore, Pisa, Italy. .,Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.
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24
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Wang W, Hu CK, Zeng A, Alegre D, Hu D, Gotting K, Ortega Granillo A, Wang Y, Robb S, Schnittker R, Zhang S, Alegre D, Li H, Ross E, Zhang N, Brunet A, Sánchez Alvarado A. Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates. Science 2020; 369:369/6508/eaaz3090. [PMID: 32883834 DOI: 10.1126/science.aaz3090] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/05/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022]
Abstract
Vertebrates vary in their ability to regenerate, and the genetic mechanisms underlying such disparity remain elusive. Comparative epigenomic profiling and single-cell sequencing of two related teleost fish uncovered species-specific and evolutionarily conserved genomic responses to regeneration. The conserved response revealed several regeneration-responsive enhancers (RREs), including an element upstream to inhibin beta A (inhba), a known effector of vertebrate regeneration. This element activated expression in regenerating transgenic fish, and its genomic deletion perturbed caudal fin regeneration and abrogated cardiac regeneration altogether. The enhancer is present in mammals, shares functionally essential activator protein 1 (AP-1)-binding motifs, and responds to injury, but it cannot rescue regeneration in fish. This work suggests that changes in AP-1-enriched RREs are likely a crucial source of loss of regenerative capacities in vertebrates.
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Affiliation(s)
- Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Kansas City, MO 64110, USA
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - An Zeng
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Dana Alegre
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Deqing Hu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Kirsten Gotting
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sofia Robb
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Shasha Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Dillon Alegre
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Eric Ross
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Kansas City, MO 64110, USA
| | - Ning Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Glenn Laboratories for the Biology of Aging. Stanford University, Stanford, CA 94305, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA. .,Howard Hughes Medical Institute, Kansas City, MO 64110, USA
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25
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Willemsen D, Cui R, Reichard M, Valenzano DR. Intra-species differences in population size shape life history and genome evolution. eLife 2020; 9:e55794. [PMID: 32869739 PMCID: PMC7462614 DOI: 10.7554/elife.55794] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/14/2020] [Indexed: 12/16/2022] Open
Abstract
The evolutionary forces shaping life history divergence within species are largely unknown. Turquoise killifish display differences in lifespan among wild populations, representing an ideal natural experiment in evolution and diversification of life history. By combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among wild turquoise killifish populations. We generate an improved reference genome assembly and identify genes under positive and purifying selection, as well as those evolving neutrally. Short-lived populations from the outer margin of the species range have small population size and accumulate deleterious mutations in genes significantly enriched in the WNT signaling pathway, neurodegeneration, cancer and the mTOR pathway. We propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by increasing the genome-wide mutation load, exacerbates the effects of mutation accumulation and cumulatively contribute to the short adult lifespan.
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Affiliation(s)
| | - Rongfeng Cui
- Max Planck Institute for Biology of AgeingCologneGermany
| | - Martin Reichard
- Czech Academy of Sciences, Institute of Vertebrate BiologyBrnoCzech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk UniversityBrnoCzech Republic
| | - Dario Riccardo Valenzano
- Max Planck Institute for Biology of AgeingCologneGermany
- CECAD, University of CologneCologneGermany
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26
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Fumagalli MR, Font-Clos F, Milan S, Zapperi S, La Porta CAM. Comparative analysis of metabolic and transcriptomic features of Nothobranchius furzeri. J R Soc Interface 2020; 17:20200217. [PMID: 32603650 PMCID: PMC7423413 DOI: 10.1098/rsif.2020.0217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Some species have a longer lifespan than others, but usually lifespan is correlated with typical body weight. Here, we study the lifetime evolution of the metabolic behaviour of Nothobranchius furzeri, a killifish with an extremely short lifespan with respect to other fishes, even when taking into account rescaling by body weight. Comparison of the gene expression patterns of N. furzeri with those of zebrafish Danio rerio and mouse (Mus musculus) shows that a broad set of metabolic genes and pathways are affected in N. furzeri during ageing in a way that is consistent with a global deregulation of chromatin. Computational analysis of the glycolysis pathway for the three species highlights a rapid increase in the metabolic activity during the lifetime of N. furzeri with respect to the other species. Our results highlight that the unusually short lifespan of N. furzeri is associated with peculiar patterns in the metabolic activities and in chromatin dynamics.
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Affiliation(s)
- Maria Rita Fumagalli
- CNR - Consiglio Nazionale delle Ricerche, Biophysics Institute, Via De Marini 6, Genova, Italy
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Francesc Font-Clos
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
| | - Simone Milan
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Stefano Zapperi
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica della Materia Condensata e di Tecnologie per l’Energia, Via R. Cozzi 53, 20125 Milano, Italy
| | - Caterina A. M. La Porta
- CNR - Consiglio Nazionale delle Ricerche, Biophysics Institute, Via De Marini 6, Genova, Italy
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133 Milano, Italy
- Innovation for Well-Being and Environment (CR-I-WE), University of Milan, Milan, Italy
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27
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Poeschla M, Valenzano DR. The turquoise killifish: a genetically tractable model for the study of aging. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb209296. [PMID: 32034047 DOI: 10.1242/jeb.209296] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lifespan is a remarkably diverse trait in nature, ranging from just hours in adult mayflies to hundreds of years in the Greenland shark and quahog clam. Great disparities in lifespan are often observed even among somewhat closely related species; for example, in the laboratory, wild-derived strains of the common house mouse have a maximum observed lifespan of approximately 6 years, while a similarly sized rodent, the naked mole rat, can live for over 30 years. Comparative biology of aging across the tree of life provides a tremendous opportunity for understanding the molecular and genetic basis underlying lifespan and aging. However, a lack of molecular and laboratory tools has limited the ability of researchers to take full advantage of the incredible diversity of aging phenotypes in nature. Recent developments in genomic technology have made it increasingly possible to study non-canonical model organisms for aging. One promising new genetic model organism amenable to a range of experimental interventions is the turquoise killifish (Nothobranchius furzeri). This fish species has a naturally short lifespan and undergoes a wide range of aging-related transformations. These fish have a fully sequenced genome and transcriptome, and killifish embryos are accessible to transgenesis and genome editing. Furthermore, different killifish species and populations show striking differences in lifespan, providing the opportunity for comparative analysis of aging. This Review introduces the natural life history of the turquoise killifish, its emerging applicability as an aging model system, the genetic tools that have been developed to study aging for this species and a summary of recent studies facilitated by these new tools.
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Affiliation(s)
- Michael Poeschla
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.,CECAD, University of Cologne, 50931 Cologne, Germany
| | - Dario R Valenzano
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany .,CECAD, University of Cologne, 50931 Cologne, Germany
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28
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Dolfi L, Ripa R, Antebi A, Valenzano DR, Cellerino A. Cell cycle dynamics during diapause entry and exit in an annual killifish revealed by FUCCI technology. EvoDevo 2019; 10:29. [PMID: 31728179 PMCID: PMC6842169 DOI: 10.1186/s13227-019-0142-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/17/2019] [Indexed: 12/31/2022] Open
Abstract
Background Annual killifishes are adapted to surviving and reproducing over alternating dry and wet seasons. During the dry season, all adults die and desiccation-resistant embryos remain encased in dry mud for months or years in a state of diapause where their development is halted in anticipation of the months that have to elapse before their habitats are flooded again. Embryonic development of annual killifishes deviates from canonical teleost development. Epiblast cells disperse during epiboly, and a “dispersed phase” precedes gastrulation. In addition, annual fish have the ability to enter diapause and block embryonic development at the dispersed phase (diapause I), mid-somitogenesis (diapause II) and the final phase of development (diapause III). Developmental transitions associated with diapause entry and exit can be linked with cell cycle events. Here we set to image this transition in living embryos. Results To visibly explore cell cycle dynamics during killifish development in depth, we created a stable transgenic line in Nothobranchius furzeri that expresses two fluorescent reporters, one for the G1 phase and one for the S/G2 phases of the cell cycle, respectively (Fluorescent Ubiquitination-based Cell Cycle Indicator, FUCCI). Using this tool, we observed that, during epiboly, epiblast cells progressively become quiescent and exit the cell cycle. All embryos transit through a phase where dispersed cells migrate, without showing any mitotic activity, possibly blocked in the G1 phase (diapause I). Thereafter, exit from diapause I is synchronous and cells enter directly into the S phase without transiting through G1. The developmental trajectories of embryos entering diapause and of those that continue to develop are different. In particular, embryos entering diapause have reduced growth along the medio-lateral axis. Finally, exit from diapause II is synchronous for all cells and is characterized by a burst of mitotic activity and growth along the medio-lateral axis such that, by the end of this phase, the morphology of the embryos is identical to that of direct-developing embryos. Conclusions Our study reveals surprising levels of coordination of cellular dynamics during diapause and provides a reference framework for further developmental analyses of this remarkable developmental quiescent state.
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Affiliation(s)
- Luca Dolfi
- 1Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Roberto Ripa
- 2Bio@SNS, Scuola Normale Superiore, Pisa, Italy.,4Present Address: Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Adam Antebi
- 1Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | | | - Alessandro Cellerino
- 2Bio@SNS, Scuola Normale Superiore, Pisa, Italy.,3Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
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29
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No Correlation between Endo- and Exoskeletal Regenerative Capacities in Teleost Species. FISHES 2019. [DOI: 10.3390/fishes4040051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The regeneration of paired appendages in certain fish and amphibian lineages is a well established and extensively studied regenerative phenomenon. The teleost fin is comprised of a proximal endoskeletal part (considered homologous to the Tetrapod limb) and a distal exoskeletal one, and these two parts form their bony elements through different ossification processes. In the past decade, a significant body of literature has been generated about the biology of exoskeletal regeneration in zebrafish. However, it is still not clear if this knowledge can be applied to the regeneration of endoskeletal parts. To address this question, we decided to compare endo- and exoskeletal regenerative capacity in zebrafish (Danio rerio) and mudskippers (Periophthalmus barbarous). In contrast to the reduced endoskeleton of zebrafish, Periophthalmus has well developed pectoral fins with a large and easily accessible endoskeleton. We performed exo- and endoskeletal amputations in both species and followed the regenerative processes. Unlike the almost flawless exoskeletal regeneration observed in zebrafish, regeneration following endoskeletal amputation is often impaired in this species. This difference is even more pronounced in Periophthalmus where we could observe no regeneration in endoskeletal structures. Therefore, regeneration is regulated differentially in the exo- and endoskeleton of teleost species.
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30
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Cencioni C, Heid J, Krepelova A, Rasa SMM, Kuenne C, Guenther S, Baumgart M, Cellerino A, Neri F, Spallotta F, Gaetano C. Aging Triggers H3K27 Trimethylation Hoarding in the Chromatin of Nothobranchius furzeri Skeletal Muscle. Cells 2019; 8:cells8101169. [PMID: 31569376 PMCID: PMC6829443 DOI: 10.3390/cells8101169] [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: 07/30/2019] [Revised: 09/15/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
Aging associates with progressive loss of skeletal muscle function, sometimes leading to sarcopenia, a process characterized by impaired mobility and weakening of muscle strength. Since aging associates with profound epigenetic changes, epigenetic landscape alteration analysis in the skeletal muscle promises to highlight molecular mechanisms of age-associated alteration in skeletal muscle. This study was conducted exploiting the short-lived turquoise killifish Nothobranchius furzeri (Nfu), a relatively new model for aging studies. The epigenetic analysis suggested a less accessible and more condensed chromatin in old Nfu skeletal muscle. Specifically, an accumulation of heterochromatin regions was observed as a consequence of increased levels of H3K27me3, HP1α, polycomb complex subunits, and senescence-associated heterochromatic foci (SAHFs). Consistently, euchromatin histone marks, including H3K9ac, were significantly reduced. In this context, integrated bioinformatics analysis of RNASeq and ChIPSeq, related to skeletal muscle of Nfu at different ages, revealed a down-modulation of genes involved in cell cycle, differentiation, and DNA repair and an up-regulation of inflammation and senescence genes. Undoubtedly, more studies are needed to disclose the detailed mechanisms; however, our approach enlightened unprecedented features of Nfu skeletal muscle aging, potentially associated with swimming impairment and reduced mobility typical of old Nfu.
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Affiliation(s)
- Chiara Cencioni
- National Research Council, Institute for Systems Analysis and Computer Science, 00185 Rome, Italy.
| | - Johanna Heid
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Anna Krepelova
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | | | - Carsten Kuenne
- ECCPS Bioinformatics and deep sequencing platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.
| | - Stefan Guenther
- ECCPS Bioinformatics and deep sequencing platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.
| | - Mario Baumgart
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | - Alessandro Cellerino
- Laboratory of Biology (Bio@SNS), Scuola Normale Superiore, c/o Istituto di Biofisica del CNR, 56124 Pisa, Italy.
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | - Francesco Spallotta
- Department of Oncology, University of Turin, 10060 Candiolo (TO), Italy.
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (TO), Italy.
| | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy.
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31
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Rossi GS, Cochrane PV, Tunnah L, Wright PA. Ageing impacts phenotypic flexibility in an air-acclimated amphibious fish. J Comp Physiol B 2019; 189:567-579. [PMID: 31520114 DOI: 10.1007/s00360-019-01234-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/24/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022]
Abstract
The ability to tolerate environmental change may decline as fishes age. We tested the hypothesis that ageing influences the scope for phenotypic flexibility in the mangrove rivulus (Kryptolebias marmoratus), an amphibious fish that transitions between two vastly different environments, water and land. We found that older fish (4-6 years old) exhibited marked signs of ageing; older fish were reproductively senescent, had reduced fin regenerative capacity and body condition, and exhibited atrophy of both oxidative and glycolytic muscle fibers relative to younger adult fish (1-2 years old). However, age did not affect routine O2 consumption. We then acclimated adult fish (1-6 years) to water (control) or air for 10 days to assess the scope for phenotypic flexibility in response to terrestrial exposure. In support of our hypothesis, we found that older air-acclimated fish had a diminished scope for gill remodeling relative to younger fish. We also found that older fish exhibited poorer terrestrial locomotor performance relative to younger adult fish, particularly when acclimated to air. Our results indicate that ageing diminishes skeletal muscle integrity and locomotor performance of amphibious fishes, and may, therefore, impair terrestrial foraging ability, predator avoidance, or dispersal across the terrestrial environment. Remarkably, older fish voluntarily left water to a similar degree as younger fish despite the age-related deterioration of traits important for terrestrial life.
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Affiliation(s)
- Giulia S Rossi
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Paige V Cochrane
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Louise Tunnah
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Patricia A Wright
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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32
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Miller BM, Johnson K, Whited JL. Common themes in tetrapod appendage regeneration: a cellular perspective. EvoDevo 2019; 10:11. [PMID: 31236203 PMCID: PMC6572735 DOI: 10.1186/s13227-019-0124-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/08/2019] [Indexed: 01/13/2023] Open
Abstract
Complete and perfect regeneration of appendages is a process that has fascinated and perplexed biologists for centuries. Some tetrapods possess amazing regenerative abilities, but the regenerative abilities of others are exceedingly limited. The reasons underlying these differences have largely remained mysterious. A great deal has been learned about the morphological events that accompany successful appendage regeneration, and a handful of experimental manipulations can be reliably applied to block the process. However, only in the last decade has the goal of attaining a thorough molecular and cellular biological understanding of appendage regeneration in tetrapods become within reach. Advances in molecular and genetic tools for interrogating these remarkable events are now allowing for unprecedented access to the fundamental biology at work in appendage regeneration in a variety of species. This information will be critical for integrating the large body of detailed observations from previous centuries with a modern understanding of how cells sense and respond to severe injury and loss of body parts. Understanding commonalities between regenerative modes across diverse species is likely to illuminate the most important aspects of complex tissue regeneration.
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Affiliation(s)
- Bess M. Miller
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138 USA
| | - Kimberly Johnson
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138 USA
| | - Jessica L. Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138 USA
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33
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Reichard M, Polačik M. Nothobranchius furzeri, an 'instant' fish from an ephemeral habitat. eLife 2019; 8:41548. [PMID: 30616713 PMCID: PMC6324871 DOI: 10.7554/elife.41548] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022] Open
Abstract
The turquoise killifish, Nothobranchius furzeri, is a promising vertebrate model in ageing research and an emerging model organism in genomics, regenerative medicine, developmental biology and ecotoxicology. Its lifestyle is adapted to the ephemeral nature of shallow pools on the African savannah. Its rapid and short active life commences when rains fill the pool: fish hatch, grow rapidly and mature in as few as two weeks, and then reproduce daily until the pool dries out. Its embryos then become inactive, encased in the dry sediment and protected from the harsh environment until the rains return. This invertebrate-like life cycle (short active phase and long developmental arrest) combined with a vertebrate body plan provide the ideal attributes for a laboratory animal.
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Affiliation(s)
- Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Matej Polačik
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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34
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Mokalled MH, Poss KD. A Regeneration Toolkit. Dev Cell 2019; 47:267-280. [PMID: 30399333 DOI: 10.1016/j.devcel.2018.10.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/13/2022]
Abstract
The ability of animals to replace injured body parts has been a subject of fascination for centuries. The emerging importance of regenerative medicine has reinvigorated investigations of innate tissue regeneration, and the development of powerful genetic tools has fueled discoveries into how tissue regeneration occurs. Here, we present an overview of the armamentarium employed to probe regeneration in vertebrates, highlighting areas where further methodology advancement will deepen mechanistic findings.
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Affiliation(s)
- Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Kenneth D Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Regeneration Next, Duke University, Durham, NC 27710, USA.
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Motamedi M, Shamsaldini F, Teimori A, Hesni MA. Histomicroscopy and normal anatomy of the adult killifish
Aphanius hormuzensis
(Teleostei; Aphaniidae) from the Persian Gulf coastal environment. Microsc Res Tech 2018; 82:466-480. [DOI: 10.1002/jemt.23190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/30/2018] [Accepted: 11/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Mina Motamedi
- Department of Biology, Faculty of SciencesShahid Bahonar University of Kerman Kerman Iran
| | - Fatemeh Shamsaldini
- Department of Biology, Faculty of SciencesShahid Bahonar University of Kerman Kerman Iran
| | - Azad Teimori
- Department of Biology, Faculty of SciencesShahid Bahonar University of Kerman Kerman Iran
| | - Majid Askari Hesni
- Department of Biology, Faculty of SciencesShahid Bahonar University of Kerman Kerman Iran
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Telomere maintenance during anterior regeneration and aging in the freshwater annelid Aeolosoma viride. Sci Rep 2018; 8:18078. [PMID: 30584242 PMCID: PMC6305377 DOI: 10.1038/s41598-018-36396-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022] Open
Abstract
Aging is a complex process involving declines in various cellular and physical functionalities, including regenerative ability. Telomere maintenance is thought to be necessary for regeneration, and telomere attrition is one mechanism that contributes to aging. However, it is unclear if aging affects regeneration owing to deterioration of telomeric maintenance. We introduce Aeolosoma viride—a freshwater annelid with strong regenerative abilities—as a new model for studying the effects of aging on telomere functions and regeneration. We show that the anterior regenerative ability of A. viride declines with age. We characterized the A. viride telomere sequence as being composed of TTAGGG repeats and identifyied the telomerase gene Avi-tert. In adult A. viride, telomerase was constantly active and telomere lengths were similar among different body sections and stably maintained with age. Notably, we found that regeneration did not result in telomere shortening at regenerating sites. Moreover, transient up-regulation of Avi-tert expression and telomerase activity was observed at regenerating sites, which might promote telomere lengthening to counteract telomere erosion resulting from cell proliferation. Our study suggests that although aging affects A. viride regeneration independent of steady-state telomere length, timely regulation of telomerase functions is critical for the regeneration process in A. viride.
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Zupkovitz G, Lagger S, Martin D, Steiner M, Hagelkruys A, Seiser C, Schöfer C, Pusch O. Histone deacetylase 1 expression is inversely correlated with age in the short-lived fish Nothobranchius furzeri. Histochem Cell Biol 2018; 150:255-269. [PMID: 29951776 PMCID: PMC6096771 DOI: 10.1007/s00418-018-1687-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2018] [Indexed: 12/19/2022]
Abstract
Aging is associated with profound changes in the epigenome, resulting in alterations of gene expression, epigenetic landscape, and genome architecture. Class I Histone deacetylases (HDACs), consisting of HDAC1, HDAC2, HDAC3, and HDAC8, play a major role in epigenetic regulation of chromatin structure and transcriptional control, and have been implicated as key players in the pathogenesis of age-dependent diseases and disorders affecting health and longevity. Here, we report the identification of class I Hdac orthologs and their detailed spatio-temporal expression profile in the short-lived fish Nothobranchius furzeri from the onset of embryogenesis until old age covering the entire lifespan of the organism. Database search of the recently annotated N. furzeri genomes retrieved four distinct genes: two copies of hdac1 and one copy of each hdac3 and hdac8. However, no hdac2 ortholog could be identified. Phylogenetic analysis grouped the individual killifish class I Hdacs within the well-defined terminal clades. We find that upon aging, Hdac1 is significantly down-regulated in muscle, liver, and brain, and this age-dependent down-regulation in brain clearly correlates with increased mRNA levels of the cyclin-dependent kinase inhibitor cdkn1a (p21). Furthermore, this apparent reduction of class I HDACs in transcript and protein levels is mirrored in the mouse brain, highlighting an evolutionarily conserved role of class I HDACs during normal development and in the aging process.
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Affiliation(s)
- Gordin Zupkovitz
- Center of Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria
| | - Sabine Lagger
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1210 Vienna, Austria
| | - David Martin
- Center of Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria
| | - Marianne Steiner
- Center of Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria
| | - Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Christian Seiser
- Center of Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria
| | - Christian Schöfer
- Center of Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria
| | - Oliver Pusch
- Center of Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria
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Hu CK, Brunet A. The African turquoise killifish: A research organism to study vertebrate aging and diapause. Aging Cell 2018; 17:e12757. [PMID: 29573324 PMCID: PMC5946070 DOI: 10.1111/acel.12757] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2018] [Indexed: 02/06/2023] Open
Abstract
The African turquoise killifish has recently gained significant traction as a new research organism in the aging field. Our understanding of aging has strongly benefited from canonical research organisms—yeast, C. elegans, Drosophila, zebrafish, and mice. Many characteristics that are essential to understand aging—for example, the adaptive immune system or the hypothalamo‐pituitary axis—are only present in vertebrates (zebrafish and mice). However, zebrafish and mice live more than 3 years and their relatively long lifespans are not compatible with high‐throughput studies. Therefore, the turquoise killifish, a vertebrate with a naturally compressed lifespan of only 4–6 months, fills an essential gap to understand aging. With a recently developed genomic and genetic toolkit, the turquoise killifish not only provides practical advantages for lifespan and longitudinal experiments, but also allows more systematic characterizations of the interplay between genetics and environment during vertebrate aging. Interestingly, the turquoise killifish can also enter a long‐term dormant state during development called diapause. Killifish embryos in diapause already have some organs and tissues, and they can last in this state for years, exhibiting exceptional resistance to stress and to damages due to the passage of time. Understanding the diapause state could give new insights into strategies to prevent the damage caused by aging and to better preserve organs, tissues, and cells. Thus, the African turquoise killifish brings two interesting aspects to the aging field—a compressed lifespan and a long‐term resistant diapause state, both of which should spark new discoveries in the field.
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Affiliation(s)
- Chi-Kuo Hu
- Department of Genetics; Stanford University; Stanford CA USA
| | - Anne Brunet
- Department of Genetics; Stanford University; Stanford CA USA
- Glenn Laboratories for the Biology of Aging; Stanford CA USA
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Vrtílek M, Žák J, Polačik M, Blažek R, Reichard M. Longitudinal demographic study of wild populations of African annual killifish. Sci Rep 2018; 8:4774. [PMID: 29555942 PMCID: PMC5859278 DOI: 10.1038/s41598-018-22878-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022] Open
Abstract
The natural history of model organisms is often overlooked despite its importance to correctly interpret the outcome of laboratory studies. Ageing is particularly understudied in natural populations. To address this gap, we present lifetime demographic data from wild populations of an annual species, the turquoise killifish, Nothobranchius furzeri, a model species in ageing research, and two other species of coexisting annual killifishes. Annual killifish hatch synchronously, have non-overlapping generations, and reproduce daily after reaching sexual maturity. Data from 13 isolated savanna pools in southern Mozambique demonstrate that the pools supporting killifish populations desiccated 1–4 months after their filling, though some pools persisted longer. Declines in population size over the season were stronger than predicted, because they exceeded the effect of steady habitat shrinking on population density that, contrary to the prediction, decreased. Populations of N. furzeri also became more female-biased with progressing season suggesting that males had lower survival. Nothobranchius community composition did not significantly vary across the season. Our data clearly demonstrate that natural populations of N. furzeri and its congeners suffer strong mortality throughout their lives, with apparent selective disappearance (condition-dependent mortality) at the individual level. This represents selective force that can shape the evolution of lifespan, and its variation across populations, beyond the effects of the gradient in habitat persistence.
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Affiliation(s)
- Milan Vrtílek
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic
| | - Jakub Žák
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic.,Faculty of Sciences, Charles University, Viničná 7, Praha 2, 128 44, Czech Republic
| | - Matej Polačik
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic
| | - Radim Blažek
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic
| | - Martin Reichard
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic.
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40
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Reuter H, Krug J, Singer P, Englert C. The African turquoise killifish Nothobranchius furzeri as a model for aging research. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ddmod.2018.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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41
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Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A. Non-model model organisms. BMC Biol 2017; 15:55. [PMID: 28662661 PMCID: PMC5492503 DOI: 10.1186/s12915-017-0391-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.
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Affiliation(s)
- James J Russell
- Department of Biology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA
| | - Julie A Theriot
- Departments of Biochemistry and of Microbiology & Immunology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA.
| | - Pranidhi Sood
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA
| | - Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA.
| | - Laura F Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, 10032, USA
| | | | - Jessica K Polka
- Visiting Scholar, Whitehead Institute, 9 Cambridge Center, Cambridge, MA, 02142, USA
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Therese Gerbich
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Amy Gladfelter
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - James Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA
| | | | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH, Cambridge, UK
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, CA, 94305, USA
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Ripa R, Dolfi L, Terrigno M, Pandolfini L, Savino A, Arcucci V, Groth M, Terzibasi Tozzini E, Baumgart M, Cellerino A. MicroRNA miR-29 controls a compensatory response to limit neuronal iron accumulation during adult life and aging. BMC Biol 2017; 15:9. [PMID: 28193224 PMCID: PMC5304403 DOI: 10.1186/s12915-017-0354-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/25/2017] [Indexed: 02/07/2023] Open
Abstract
Background A widespread modulation of gene expression occurs in the aging brain, but little is known as to the upstream drivers of these changes. MicroRNAs emerged as fine regulators of gene expression in many biological contexts and they are modulated by age. MicroRNAs may therefore be part of the upstream drivers of the global gene expression modulation correlated with aging and aging-related phenotypes. Results Here, we show that microRNA-29 (miR-29) is induced during aging in short-lived turquoise killifish brain and genetic antagonism of its function induces a gene-expression signature typical of aging. Mechanicistically, we identified Ireb2 (a master gene for intracellular iron delivery that encodes for IRP2 protein), as a novel miR-29 target. MiR-29 is induced by iron loading and, in turn, it reduces IRP2 expression in vivo, therefore limiting intracellular iron delivery in neurons. Genetically modified fish with neuro-specific miR-29 deficiency exhibit increased levels of IRP2 and transferrin receptor, increased iron content, and oxidative stress. Conclusions Our results demonstrate that age-dependent miR-29 upregulation is an adaptive mechanism that counteracts the expression of some aging-related phenotypes and its anti-aging activity is primarily exerted by regulating intracellular iron homeostasis limiting excessive iron-exposure in neurons. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0354-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roberto Ripa
- Scuola Normale Superiore, Laboratory of Biology (Bio@SNS), c/o Istituto di Biofisica del CNR, via 17 Moruzzi 1, 56124, Pisa, Italy
| | - Luca Dolfi
- Scuola Normale Superiore, Laboratory of Biology (Bio@SNS), c/o Istituto di Biofisica del CNR, via 17 Moruzzi 1, 56124, Pisa, Italy
| | - Marco Terrigno
- Scuola Normale Superiore, Laboratory of Biology (Bio@SNS), c/o Istituto di Biofisica del CNR, via 17 Moruzzi 1, 56124, Pisa, Italy
| | - Luca Pandolfini
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
| | | | - Valeria Arcucci
- Scuola Normale Superiore, Laboratory of Biology (Bio@SNS), c/o Istituto di Biofisica del CNR, via 17 Moruzzi 1, 56124, Pisa, Italy
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745, Jena, Germany
| | - Eva Terzibasi Tozzini
- Scuola Normale Superiore, Laboratory of Biology (Bio@SNS), c/o Istituto di Biofisica del CNR, via 17 Moruzzi 1, 56124, Pisa, Italy
| | - Mario Baumgart
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745, Jena, Germany
| | - Alessandro Cellerino
- Scuola Normale Superiore, Laboratory of Biology (Bio@SNS), c/o Istituto di Biofisica del CNR, via 17 Moruzzi 1, 56124, Pisa, Italy. .,Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745, Jena, Germany.
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Kim Y, Nam HG, Valenzano DR. The short-lived African turquoise killifish: an emerging experimental model for ageing. Dis Model Mech 2016; 9:115-29. [PMID: 26839399 PMCID: PMC4770150 DOI: 10.1242/dmm.023226] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human ageing is a fundamental biological process that leads to functional decay, increased risk for various diseases and, ultimately, death. Some of the basic biological mechanisms underlying human ageing are shared with other organisms; thus, animal models have been invaluable in providing key mechanistic and molecular insights into the common bases of biological ageing. In this Review, we briefly summarise the major applications of the most commonly used model organisms adopted in ageing research and highlight their relevance in understanding human ageing. We compare the strengths and limitations of different model organisms and discuss in detail an emerging ageing model, the short-lived African turquoise killifish. We review the recent progress made in using the turquoise killifish to study the biology of ageing and discuss potential future applications of this promising animal model.
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Affiliation(s)
- Yumi Kim
- Max Planck Institute for Biology of Ageing, D50931, Cologne, Germany Department of New Biology, DGIST, 711-873, Daegu, Republic of Korea
| | - Hong Gil Nam
- Department of New Biology, DGIST, 711-873, Daegu, Republic of Korea Center for Plant Aging Research, Institute for Basic Science, 711-873, Daegu, Republic of Korea
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Nothobranchius furzeri : A Model for Aging Research and More. Trends Genet 2016; 32:543-552. [DOI: 10.1016/j.tig.2016.06.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/10/2016] [Accepted: 06/27/2016] [Indexed: 12/13/2022]
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45
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Polačik M, Blažek R, Reichard M. Laboratory breeding of the short-lived annual killifish Nothobranchius furzeri. Nat Protoc 2016; 11:1396-413. [DOI: 10.1038/nprot.2016.080] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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46
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Harel I, Brunet A. The African Turquoise Killifish: A Model for Exploring Vertebrate Aging and Diseases in the Fast Lane. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:275-279. [PMID: 26642856 DOI: 10.1101/sqb.2015.80.027524] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Why and how organisms age remains a mystery, and it defines one of the biggest challenges in biology. Aging is also the primary risk factor for many human pathologies, such as cancer, diabetes, cardiovascular diseases, and neurodegenerative diseases. Thus, manipulating the aging rate and potentially postponing the onset of these devastating diseases could have a tremendous impact on human health. Recent studies, relying primarily on nonvertebrate short-lived model systems, have shown the importance of both genetic and environmental factors in modulating the aging rate. However, relatively little is known about aging in vertebrates or what processes may be unique and specific to these complex organisms. Here we discuss how advances in genomics and genome editing have significantly expanded our ability to probe the aging process in a vertebrate system. We highlight recent findings from a naturally short-lived vertebrate, the African turquoise killifish, which provides an attractive platform for exploring mechanisms underlying vertebrate aging and age-related diseases.
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Affiliation(s)
- Itamar Harel
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, California 94305 Glenn Laboratories for the Biology of Aging at Stanford, Stanford, California 94305
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