1
|
Harel I, Chen YR, Ziv I, Singh PP, Heinzer D, Navarro Negredo P, Goshtchevsky U, Wang W, Astre G, Moses E, McKay A, Machado BE, Hebestreit K, Yin S, Sánchez Alvarado A, Jarosz DF, Brunet A. Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties. Cell Rep 2024; 43:112787. [PMID: 38810650 PMCID: PMC11285089 DOI: 10.1016/j.celrep.2023.112787] [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: 03/21/2022] [Revised: 04/23/2023] [Accepted: 06/26/2023] [Indexed: 05/31/2024] Open
Abstract
Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here, we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA-binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms aggregate-like puncta in the brains of old killifish and mice. Interestingly, DDX5's prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the protein's ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.
Collapse
Affiliation(s)
- Itamar Harel
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel.
| | - Yiwen R Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Heinzer
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Uri Goshtchevsky
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gwendoline Astre
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Eitan Moses
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Andrew McKay
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ben E Machado
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Katja Hebestreit
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sifei Yin
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, 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.
| |
Collapse
|
2
|
Singh PP, Reeves GA, Contrepois K, Papsdorf K, Miklas JW, Ellenberger M, Hu CK, Snyder MP, Brunet A. Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape. Cell 2024; 187:3338-3356.e30. [PMID: 38810644 DOI: 10.1016/j.cell.2024.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.
Collapse
Affiliation(s)
| | - G Adam Reeves
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | | | - Jason W Miklas
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA; Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Morabito G, Ryabova A, Valenzano DR. Immune aging in annual killifish. Immun Ageing 2024; 21:18. [PMID: 38459521 PMCID: PMC10921792 DOI: 10.1186/s12979-024-00418-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Turquoise killifish (Nothobranchius furzeri) evolved a naturally short lifespan of about six months and exhibit aging hallmarks that affect multiple organs. These hallmarks include protein aggregation, telomere shortening, cellular senescence, and systemic inflammation. Turquoise killifish possess the full spectrum of vertebrate-specific innate and adaptive immune system. However, during their recent evolutionary history, they lost subsets of mucosal-specific antibody isoforms that are present in other teleosts. As they age, the immune system of turquoise killifish undergoes dramatic cellular and systemic changes. These changes involve increased inflammation, reduced antibody diversity, an increased prevalence of pathogenic microbes in the intestine, and extensive DNA damage in immune progenitor cell clusters. Collectively, the wide array of age-related changes occurring in turquoise killifish suggest that, despite an evolutionary separation spanning hundreds of millions of years, teleosts and mammals share common features of immune system aging. Hence, the spontaneous aging observed in the killifish immune system offers an excellent opportunity for discovering fundamental and conserved aspects associated with immune system aging across vertebrates. Additionally, the species' naturally short lifespan of only a few months, along with its experimental accessibility, offers a robust platform for testing interventions to improve age-related dysfunctions in the whole organism and potentially inform the development of immune-based therapies for human aging-related diseases.
Collapse
Affiliation(s)
| | - Alina Ryabova
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Dario Riccardo Valenzano
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.
- Friedrich Schiller University, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Ripa R, Ballhysa E, Steiner JD, Laboy R, Annibal A, Hochhard N, Latza C, Dolfi L, Calabrese C, Meyer AM, Polidori MC, Müller RU, Antebi A. Refeeding-associated AMPK γ1 complex activity is a hallmark of health and longevity. NATURE AGING 2023; 3:1544-1560. [PMID: 37957359 PMCID: PMC10724066 DOI: 10.1038/s43587-023-00521-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/05/2023] [Indexed: 11/15/2023]
Abstract
Late-life-initiated dietary interventions show limited efficacy in extending longevity or mitigating frailty, yet the underlying causes remain unclear. Here we studied the age-related fasting response of the short-lived killifish Nothobranchius furzeri. Transcriptomic analysis uncovered the existence of a fasting-like transcriptional program in the adipose tissue of old fish that overrides the feeding response, setting the tissue in persistent metabolic quiescence. The fasting-refeeding cycle triggers an inverse oscillatory expression of genes encoding the AMP-activated protein kinase (AMPK) regulatory subunits Prkag1 (γ1) and Prkag2 (γ2) in young individuals. Aging blunts such regulation, resulting in reduced Prkag1 expression. Transgenic fish with sustained AMPKγ1 countered the fasting-like transcriptional program, exhibiting a more youthful feeding and fasting response in older age, improved metabolic health and longevity. Accordingly, Prkag1 expression declines with age in human tissues and is associated with multimorbidity and multidimensional frailty risk. Thus, selective activation of AMPKγ1 prevents metabolic quiescence and preserves healthy aging in vertebrates, offering potential avenues for intervention.
Collapse
Affiliation(s)
- Roberto Ripa
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Eugen Ballhysa
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Graduate School for Ageing Research (CGA), Cologne, Germany
| | - Joachim D Steiner
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Raymond Laboy
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Andrea Annibal
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nadine Hochhard
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christian Latza
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Luca Dolfi
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Chiara Calabrese
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Graduate School for Ageing Research (CGA), Cologne, Germany
| | - Anna M Meyer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Maria Cristina Polidori
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Graduate School for Ageing Research (CGA), Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
| |
Collapse
|
8
|
Moses E, Franek R, Harel I. A scalable and tunable platform for functional interrogation of peptide hormones in fish. eLife 2023; 12:e85960. [PMID: 37872843 PMCID: PMC10597582 DOI: 10.7554/elife.85960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/16/2023] [Indexed: 10/25/2023] Open
Abstract
Pituitary hormones play a central role in shaping vertebrate life history events, including growth, reproduction, metabolism, and aging. The regulation of these traits often requires precise control of hormone levels across diverse timescales. However, fine tuning circulating hormones in-vivo has traditionally been experimentally challenging. Here, using the naturally short-lived turquoise killifish (N. furzeri), we describe a high-throughput platform that combines loss- and gain-of-function of peptide hormones. Mutation of three primary pituitary hormones, growth hormone (gh1), follicle stimulating hormone (fshb), and thyroid stimulating hormone (tshb), alters somatic growth and reproduction. Thus, suggesting that while the killifish undergoes extremely rapid growth and maturity, it still relies on vertebrate-conserved genetic networks. As the next stage, we developed a gain-of-function vector system in which a hormone is tagged using a self-cleavable fluorescent reporter, and ectopically expressed in-vivo through intramuscular electroporation. Following a single electroporation, phenotypes, such as reproduction, are stably rescued for several months. Notably, we demonstrate the versatility of this approach by using multiplexing, dose-dependent, and doxycycline-inducible systems to achieve tunable and reversible expression. In summary, this method is relatively high-throughput, and facilitates large-scale interrogation of life-history strategies in fish. Ultimately, this approach could be adapted for modifying aquaculture species and exploring pro-longevity interventions.
Collapse
Affiliation(s)
- Eitan Moses
- Department of Genetics, the Silberman Institute, The Hebrew University of JerusalemJerusalemIsrael
| | - Roman Franek
- Department of Genetics, the Silberman Institute, The Hebrew University of JerusalemJerusalemIsrael
- University of South Bohemia in Ceske Budejovice, South Bohemian Research Center of Aquaculture and Biodiversity of HydrocenosesVodnanyCzech Republic
| | - Itamar Harel
- Department of Genetics, the Silberman Institute, The Hebrew University of JerusalemJerusalemIsrael
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Astre G, Atlan T, Goshtchevsky U, Oron-Gottesman A, Smirnov M, Shapira K, Velan A, Deelen J, Levy T, Levanon EY, Harel I. Genetic perturbation of AMP biosynthesis extends lifespan and restores metabolic health in a naturally short-lived vertebrate. Dev Cell 2023; 58:1350-1364.e10. [PMID: 37321215 DOI: 10.1016/j.devcel.2023.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
During aging, the loss of metabolic homeostasis drives a myriad of pathologies. A central regulator of cellular energy, the AMP-activated protein kinase (AMPK), orchestrates organismal metabolism. However, direct genetic manipulations of the AMPK complex in mice have, so far, produced detrimental phenotypes. Here, as an alternative approach, we alter energy homeostasis by manipulating the upstream nucleotide pool. Using the turquoise killifish, we mutate APRT, a key enzyme in AMP biosynthesis, and extend the lifespan of heterozygous males. Next, we apply an integrated omics approach to show that metabolic functions are rejuvenated in old mutants, which also display a fasting-like metabolic profile and resistance to high-fat diet. At the cellular level, heterozygous cells exhibit enhanced nutrient sensitivity, reduced ATP levels, and AMPK activation. Finally, lifelong intermittent fasting abolishes the longevity benefits. Our findings suggest that perturbing AMP biosynthesis may modulate vertebrate lifespan and propose APRT as a promising target for promoting metabolic health.
Collapse
Affiliation(s)
- Gwendoline Astre
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Tehila Atlan
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Uri Goshtchevsky
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Adi Oron-Gottesman
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Margarita Smirnov
- Central Fish Health Laboratory, Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir David 10803, Israel
| | - Kobi Shapira
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ariel Velan
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Joris Deelen
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Tomer Levy
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Itamar Harel
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel.
| |
Collapse
|
11
|
Van Houcke J, Mariën V, Zandecki C, Ayana R, Pepermans E, Boonen K, Seuntjens E, Baggerman G, Arckens L. A short dasatinib and quercetin treatment is sufficient to reinstate potent adult neuroregenesis in the aged killifish. NPJ Regen Med 2023; 8:31. [PMID: 37328477 DOI: 10.1038/s41536-023-00304-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/23/2023] [Indexed: 06/18/2023] Open
Abstract
The young African turquoise killifish has a high regenerative capacity, but loses it with advancing age, adopting several aspects of the limited form of mammalian regeneration. We deployed a proteomic strategy to identify pathways that underpin the loss of regenerative power caused by aging. Cellular senescence stood out as a potential brake on successful neurorepair. We applied the senolytic cocktail Dasatinib and Quercetin (D + Q) to test clearance of chronic senescent cells from the aged killifish central nervous system (CNS) as well as rebooting the neurogenic output. Our results show that the entire aged killifish telencephalon holds a very high senescent cell burden, including the parenchyma and the neurogenic niches, which could be diminished by a short-term, late-onset D + Q treatment. Reactive proliferation of non-glial progenitors increased substantially and lead to restorative neurogenesis after traumatic brain injury. Our results provide a cellular mechanism for age-related regeneration resilience and a proof-of-concept of a potential therapy to revive the neurogenic potential in an already aged or diseased CNS.
Collapse
Affiliation(s)
- Jolien Van Houcke
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, 3000, Leuven, Belgium
| | - Valerie Mariën
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, 3000, Leuven, Belgium
| | - Caroline Zandecki
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, 3000, Leuven, Belgium
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, 3000, Leuven, Belgium
| | - Rajagopal Ayana
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, 3000, Leuven, Belgium
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, 3000, Leuven, Belgium
| | - Elise Pepermans
- Centre for Proteomics, University of Antwerp, 2020, Antwerpen, Belgium
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, 2020, Antwerpen, Belgium
- Health Unit, VITO, 2400, Mol, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, 3000, Leuven, Belgium
- KU Leuven Brain Institute, KU Leuven, 3000, Leuven, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp, 2020, Antwerpen, Belgium
- Health Unit, VITO, 2400, Mol, Belgium
| | - Lutgarde Arckens
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, 3000, Leuven, Belgium.
- KU Leuven Brain Institute, KU Leuven, 3000, Leuven, Belgium.
| |
Collapse
|
12
|
Thoré ESJ, Merckx W. Substrate colour guides turquoise killifish's (Nothobranchius furzeri) choice of preferred spawning habitat. JOURNAL OF FISH BIOLOGY 2023; 102:1434-1441. [PMID: 37009851 DOI: 10.1111/jfb.15392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/31/2023] [Indexed: 06/09/2023]
Abstract
Turquoise killifish (Nothobranchius furzeri) is a promising new model species used in biomedical and ecological laboratory experiments, and should be kept under optimal conditions to ensure fish welfare and the quality of science. While the popularity of this model species is rapidly increasing, we need to improve our understanding of how the species interacts with its environment to optimize its husbandry. Specifically, turquoise killifish are substrate spawners that bury their eggs in the sediment, which can be accommodated under captive conditions, but it is not yet known whether or not turquoise killifish have a preference for a specific sediment colour. Here, we performed a laboratory experiment in which fish could choose between white, orange and black sand for spawning, colours which are relevant in both laboratory and field conditions. We assessed their preference in the context of single breeding pairs, as well as in a social group setting. Additionally, we also assessed the preference of individuals for a white versus black background in a nonmating context. Single breeding pairs deposited over 3.5 times more eggs in black compared to orange or white sand. Similarly, fish in social groups deposited over 3.5 times more eggs in black compared to orange sand, which in turn was over two times higher than that in white sand. Fish showed a slight preference for the black compared to the white zone in a nonmating context, but this did not correlate with substrate choice during the spawning tests. The results suggest that turquoise killifish select their preferred spawning location based on the colour of the substrate. These findings contribute to our understanding of the species' biology and can help to guide good welfare and scientific practice.
Collapse
Affiliation(s)
- Eli S J Thoré
- TRANSfarm - Science, Engineering & Technology Group, Leuven, Belgium
- Laboratory of Animal Ecology, Global Change and Sustainable Development, Leuven, Belgium
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Wouter Merckx
- TRANSfarm - Science, Engineering & Technology Group, Leuven, Belgium
| |
Collapse
|
13
|
Bedbrook CN, Nath RD, Nagvekar R, Deisseroth K, Brunet A. Rapid and precise genome engineering in a naturally short-lived vertebrate. eLife 2023; 12:80639. [PMID: 37191291 DOI: 10.7554/elife.80639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The African turquoise killifish is a powerful vertebrate system to study complex phenotypes at scale, including aging and age-related disease. Here, we develop a rapid and precise CRISPR/Cas9-mediated knock-in approach in the killifish. We show its efficient application to precisely insert fluorescent reporters of different sizes at various genomic loci in order to drive cell-type- and tissue-specific expression. This knock-in method should allow the establishment of humanized disease models and the development of cell-type-specific molecular probes for studying complex vertebrate biology.
Collapse
Affiliation(s)
- Claire N Bedbrook
- Department of Genetics, Stanford University, Stanford, United States
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Ravi D Nath
- Department of Genetics, Stanford University, Stanford, United States
| | - Rahul Nagvekar
- Department of Genetics, Stanford University, Stanford, United States
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, United States
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, United States
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, United States
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Hu CK. Handling Diapause Embryos of the African Turquoise Killifish Nothobranchius furzeri. Cold Spring Harb Protoc 2023; 2023:130-137. [PMID: 36283839 DOI: 10.1101/pdb.prot107752] [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: 02/03/2023]
Abstract
The African turquoise killifish Nothobranchius furzeri is an emerging research organism known for its short life span and long-term diapause. Diapause is a unique dormant state that suspends embryonic development without tradeoffs in the adulthood life span. Recently, diapause has been gaining increasing interest from the research community. Here, we report our methods for handling the embryos of N. furzeri that go through diapause. We focus on a few key steps: (1) collecting N. furzeri embryos, (2) sorting embryos entering diapause, (3) storing diapause embryos, (4) screening embryos exiting diapause, and (5) hatching post-diapause and fully developed embryos. This method should help the need to obtain a large number of embryos in synchronization with their diapause-entering and -exiting status and satisfy the need for cell biology, genetic, genomic, and biochemistry experiments.
Collapse
Affiliation(s)
- Chi-Kuo Hu
- Department of Biochemistry and Cell Biology, Stony Brook University, New York 11794, USA
| |
Collapse
|
16
|
Rozenberg I, Moses E, Harel I. CRISPR-Cas9 Genome Editing in Nothobranchius furzeri for Gene Knockout and Knock-In. Cold Spring Harb Protoc 2023; 2023:90-99. [PMID: 36223984 DOI: 10.1101/pdb.prot107742] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The African turquoise killifish Nothobranchius furzeri has recently gained interest as an emerging vertebrate model system for the study of aging, owing to its naturally short life span and generation time. Here, we provide a step-by-step guide for effective genome engineering using the CRISPR-Cas9 system to generate loss-of-function (i.e., knockout) alleles and for precise editing (i.e., knock-in) of short sequences into the genome. Using this approach, a new stable line can be created within several months. The killifish's tough chorion, rapid growth, and short life span are considered in this protocol and account for the key deviations from similar protocols in other fish models.
Collapse
Affiliation(s)
- Itai Rozenberg
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem, 91904 Israel
| | - Eitan Moses
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem, 91904 Israel
| | - Itamar Harel
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem, 91904 Israel
| |
Collapse
|
17
|
Teefy BB, Adler A, Xu A, Hsu K, Singh PP, Benayoun BA. Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish. Genome Res 2023; 33:141-153. [PMID: 36577520 PMCID: PMC9977155 DOI: 10.1101/gr.277301.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022]
Abstract
Although germline cells are considered to be functionally "immortal," both the germline and supporting somatic cells in the gonad within an organism experience aging. With increased age at parenthood, the age-related decline in reproductive success has become an important biological issue for an aging population. However, molecular mechanisms underlying reproductive aging across sexes in vertebrates remain poorly understood. To decipher molecular drivers of vertebrate gonadal aging across sexes, we perform longitudinal characterization of the gonadal transcriptome throughout the lifespan in the naturally short-lived African turquoise killifish (Nothobranchius furzeri). By combining mRNA-seq and small RNA-seq from 26 individuals, we characterize the aging gonads of young-adult, middle-aged, and old female and male fish. We analyze changes in transcriptional patterns of genes, transposable elements (TEs), and piRNAs. We find that testes seem to undergo only marginal changes during aging. In contrast, in middle-aged ovaries, the time point associated with peak female fertility in this strain, PIWI pathway components are transiently down-regulated, TE transcription is elevated, and piRNA levels generally decrease, suggesting that egg quality may already be declining at middle-age. Furthermore, we show that piRNA ping-pong biogenesis declines steadily with age in ovaries, whereas it is maintained in aging testes. To our knowledge, this data set represents the most comprehensive transcriptomic data set for vertebrate gonadal aging. This resource also highlights important pathways that are regulated during reproductive aging in either ovaries or testes, which could ultimately be leveraged to help restore aspects of youthful reproductive function.
Collapse
Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA.,Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California 90089, USA.,USC Stem Cell Initiative, Los Angeles, California 90089, USA
| |
Collapse
|
18
|
Dohi E, Matsui H. The Utility of Small Fishes for the Genetic Study of Human Age-Related Disorders. Front Genet 2022; 13:928597. [PMID: 35910227 PMCID: PMC9335361 DOI: 10.3389/fgene.2022.928597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Animal models have been used to model human diseases, and among them, small fishes have been highlighted for their usefulness in various ways, such as the low cost of maintenance, ease of genetic modification, small size for easy handling, and strength in imaging studies due to their relative transparency. Recently, the use of turquoise killifish, Nothobranchius furzeri, which is known to exhibit various aging phenotypes in a short period, has attracted attention in research on aging and age-related diseases. However, when using animal models, it is important to keep their genetic background and interspecies differences in mind for translating them into human diseases. In this article, we obtained the gene symbols of protein-coding genes of turquoise killifish, medaka, zebrafish, and humans from NCBI datasets and extracted common shared genes among four species to explore the potential of interspecies translational research and to apply small fish models for human age-related disorders. Common shared protein-coding genes were analyzed with the Reactome Pathway Database to determine the coverage of these genes in each pathway in humans. We applied common shared genes to the Orphanet database to establish a list of human diseases that contain common shared genes among the four species. As examples, the senescence-related pathways and some pathways of human age-related diseases, such as Alzheimer’s disease, Parkinson’s disease, frontotemporal dementia, nonalcoholic fatty liver disease, progeria, hepatocellular carcinoma, and renal cell carcinoma, were extracted from the curated pathway and disease list to discuss the further utility of fish models for human age-related disorders.
Collapse
|
19
|
Oginuma M, Nishida M, Ohmura-Adachi T, Abe K, Ogamino S, Mogi C, Matsui H, Ishitani T. Rapid reverse genetics systems for Nothobranchius furzeri, a suitable model organism to study vertebrate aging. Sci Rep 2022; 12:11628. [PMID: 35804091 PMCID: PMC9270483 DOI: 10.1038/s41598-022-15972-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/01/2022] [Indexed: 11/09/2022] Open
Abstract
The African turquoise killifish Nothobranchius furzeri (N. furzeri) is a useful model organism for studying aging, age-related diseases, and embryonic diapause. CRISPR/Cas9-mediated gene knockout and Tol2 transposon-mediated transgenesis in N. furzeri have been reported previously. However, these methods take time to generate knockout and transgenic fish. In addition, knock-in technology that inserts large DNA fragments as fluorescent reporter constructs into the target gene in N. furzeri has not yet been established. Here, we show that triple-target CRISPR-mediated single gene disruption efficiently produces whole-body biallelic knockout and enables the examination of gene function in the F0 generation. In addition, we developed a method for creating the knock-in reporter N. furzeri without crossing by optimizing the CRISPR/Cas9 system. These methods drastically reduce the duration of experiments, and we think that these advances will accelerate aging and developmental studies using N. furzeri.
Collapse
Affiliation(s)
- Masayuki Oginuma
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Moana Nishida
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tomomi Ohmura-Adachi
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kota Abe
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - 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 and Cellular Regulation, Gunma University, Gunma, 371-8512, Japan
| | - Chihiro Mogi
- Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, 951-8585, 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.
| |
Collapse
|
20
|
Zebrafish, Medaka and Turquoise Killifish for Understanding Human Neurodegenerative/Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23031399. [PMID: 35163337 PMCID: PMC8836067 DOI: 10.3390/ijms23031399] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 12/21/2022] Open
Abstract
In recent years, small fishes such as zebrafish and medaka have been widely recognized as model animals. They have high homology in genetics and tissue structure with humans and unique features that mammalian model animals do not have, such as transparency of embryos and larvae, a small body size and ease of experiments, including genetic manipulation. Zebrafish and medaka have been used extensively in the field of neurology, especially to unveil the mechanisms of neurodegenerative diseases such as Parkinson's and Alzheimer's disease, and recently, these fishes have also been utilized to understand neurodevelopmental disorders such as autism spectrum disorder. The turquoise killifish has emerged as a new and unique model animal, especially for ageing research due to its unique life cycle, and this fish also seems to be useful for age-related neurological diseases. These small fishes are excellent animal models for the analysis of human neurological disorders and are expected to play increasing roles in this field. Here, we introduce various applications of these model fishes to improve our understanding of human neurological disorders.
Collapse
|
21
|
Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
Collapse
Affiliation(s)
- Tarun S. Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada,Corresponding authors: ,
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032,Lead Contact,Corresponding authors: ,
| |
Collapse
|
22
|
Sperm cryopreservation and in vitro fertilization techniques for the African turquoise killifish Nothobranchius furzeri. Sci Rep 2021; 11:17145. [PMID: 34433853 PMCID: PMC8387425 DOI: 10.1038/s41598-021-96383-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/05/2021] [Indexed: 11/23/2022] Open
Abstract
Over the last decade, the African turquoise killifish, Nothobranchius furzeri, has emerged as an important model system for the study of vertebrate biology and ageing. Propagation of laboratory inbred strains of Nothobranchius furzeri, such as GRZ, however, can pose challenges due to the short window of fertility, the efforts and space requirements involved in continuous strain maintenance, and the risks of further inbreeding. The current method for long term strain preservation relies on arrest of embryos in diapause. To create an alternative for long term maintenance, we developed a robust protocol to cryopreserve and revive sperm for in vitro fertilization (IVF). We tested a variety of extender and activator buffers for sperm IVF, as well as cryoprotectants to achieve practical long-term storage and fertilization conditions tailored to this species. Our protocol enabled sperm to be preserved in a cryogenic condition for months and to be revived with an average of 40% viability upon thawing. Thawed sperm were able to fertilize nearly the same number of eggs as natural fertilization, with an average of ~ 25% and peaks of ~ 55% fertilization. This technical advance will greatly facilitate the use of N. furzeri as a model organism.
Collapse
|
23
|
Holtze S, Gorshkova E, Braude S, Cellerino A, Dammann P, Hildebrandt TB, Hoeflich A, Hoffmann S, Koch P, Terzibasi Tozzini E, Skulachev M, Skulachev VP, Sahm A. Alternative Animal Models of Aging Research. Front Mol Biosci 2021; 8:660959. [PMID: 34079817 PMCID: PMC8166319 DOI: 10.3389/fmolb.2021.660959] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Most research on mechanisms of aging is being conducted in a very limited number of classical model species, i.e., laboratory mouse (Mus musculus), rat (Rattus norvegicus domestica), the common fruit fly (Drosophila melanogaster) and roundworm (Caenorhabditis elegans). The obvious advantages of using these models are access to resources such as strains with known genetic properties, high-quality genomic and transcriptomic sequencing data, versatile experimental manipulation capabilities including well-established genome editing tools, as well as extensive experience in husbandry. However, this approach may introduce interpretation biases due to the specific characteristics of the investigated species, which may lead to inappropriate, or even false, generalization. For example, it is still unclear to what extent knowledge of aging mechanisms gained in short-lived model organisms is transferable to long-lived species such as humans. In addition, other specific adaptations favoring a long and healthy life from the immense evolutionary toolbox may be entirely missed. In this review, we summarize the specific characteristics of emerging animal models that have attracted the attention of gerontologists, we provide an overview of the available data and resources related to these models, and we summarize important insights gained from them in recent years. The models presented include short-lived ones such as killifish (Nothobranchius furzeri), long-lived ones such as primates (Callithrix jacchus, Cebus imitator, Macaca mulatta), bathyergid mole-rats (Heterocephalus glaber, Fukomys spp.), bats (Myotis spp.), birds, olms (Proteus anguinus), turtles, greenland sharks, bivalves (Arctica islandica), and potentially non-aging ones such as Hydra and Planaria.
Collapse
Affiliation(s)
- Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ekaterina Gorshkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Stan Braude
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Alessandro Cellerino
- Biology Laboratory, Scuola Normale Superiore, Pisa, Italy
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Central Animal Laboratory, University Hospital Essen, Essen, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Faculty of Veterinary Medicine, Free University of Berlin, Berlin, Germany
| | - Andreas Hoeflich
- Division Signal Transduction, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Eva Terzibasi Tozzini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maxim Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir P. Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| |
Collapse
|
24
|
Riddle MR, Hu CK. Fish models for investigating nutritional regulation of embryonic development. Dev Biol 2021; 476:101-111. [PMID: 33831748 DOI: 10.1016/j.ydbio.2021.03.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/13/2023]
Abstract
In recent decades, biologist have focused on the spatiotemporal regulation and function of genes to understand embryogenesis. It is clear that maternal diet impacts fetal development but how nutrients, like lipids and vitamins, modify developmental programs is not completely understood. Fish are useful research organisms for such investigations. Most species of fish produce eggs that develop outside the mother, dependent on a finite amount of yolk to form and grow. The developing embryo is a closed system that can be readily biochemically analyzed, easily visualized, and manipulated to understand the role of nutrients in tissue specification, organogenesis, and growth. Natural variation in yolk composition observed across fish species may be related to unique developmental strategies. In this review, we discuss the reasons that teleost fishes are powerful models to understand nutritional control of development and highlight three species that are particularly valuable for future investigations: the zebrafish, Danio rerio, the African Killifish, Nothobranchius furzeri, and the Mexican tetra, Astyanax mexicanus. This review is a part of a special issue on nutritional, hormonal, and metabolic drivers of development.
Collapse
Affiliation(s)
- Misty R Riddle
- Department of Biology, University of Nevada, Reno, Reno, NV, USA.
| | - Chi-Kuo Hu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| |
Collapse
|
25
|
Baghdadi M, Hinterding HM, Partridge L, Deelen J. From mutation to mechanism: deciphering the molecular function of genetic variants linked to human ageing. Brief Funct Genomics 2021; 21:13-23. [PMID: 33690799 PMCID: PMC8789301 DOI: 10.1093/bfgp/elab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 01/20/2023] Open
Abstract
Many of the leading causes of death in humans, such as cardiovascular disease, type 2 diabetes and Alzheimer’s disease are influenced by biological mechanisms that become dysregulated with increasing age. Hence, by targeting these ageing-related mechanisms, we may be able to improve health in old age. Ageing is partly heritable and genetic studies have been moderately successful in identifying genetic variants associated with ageing-related phenotypes (lifespan, healthspan and longevity). To decipher the mechanisms by which the identified variants influence ageing, studies that focus on their functional validation are vital. In this perspective, we describe the steps that could be taken in the process of functional validation: (1) in silico characterisation using bioinformatic tools; (2) in vitro characterisation using cell lines or organoids; and (3) in vivo characterisation studies using model organisms. For the in vivo characterisation, it is important to focus on translational phenotypes that are indicative of both healthspan and lifespan, such as the frailty index, to inform subsequent intervention studies. The depth of functional validation of a genetic variant depends on its location in the genome and conservation in model organisms. Moreover, some variants may prove to be hard to characterise due to context-dependent effects related to the experimental environment or genetic background. Future efforts to functionally characterise the (newly) identified genetic variants should shed light on the mechanisms underlying ageing and will help in the design of targeted interventions to improve health in old age.
Collapse
|
26
|
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.
Collapse
Affiliation(s)
| | - Alessandro Cellerino
- Scuola Normale Superiore, Pisa, Italy. .,Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
McGaugh SE, Kowalko JE, Duboué E, Lewis P, Franz-Odendaal TA, Rohner N, Gross JB, Keene AC. Dark world rises: The emergence of cavefish as a model for the study of evolution, development, behavior, and disease. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:397-404. [PMID: 32638529 DOI: 10.1002/jez.b.22978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022]
Abstract
A central question in biology is how naturally occurring genetic variation accounts for morphological and behavioral diversity within a species. The Mexican tetra, Astyanax mexicanus, has been studied for nearly a century as a model for investigating trait evolution. In March of 2019, researchers representing laboratories from around the world met at the Sixth Astyanax International Meeting in Santiago de Querétaro, Mexico. The meeting highlighted the expanding applications of cavefish to investigations of diverse aspects of basic biology, including development, evolution, and disease-based applications. A broad range of integrative approaches are being applied in this system, including the application of state-of-the-art functional genetic assays, brain imaging, and genome sequencing. These advances position cavefish as a model organism for addressing fundamental questions about the genetics and evolution underlying the impressive trait diversity among individual populations within this species.
Collapse
Affiliation(s)
- Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota
| | - Johanna E Kowalko
- The Jupiter Life Science Initiative and Program in Neurogenetics, Florida Atlantic University, Jupiter, Florida.,Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida
| | - Erik Duboué
- The Jupiter Life Science Initiative and Program in Neurogenetics, Florida Atlantic University, Jupiter, Florida.,Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida
| | - Peter Lewis
- The Jupiter Life Science Initiative and Program in Neurogenetics, Florida Atlantic University, Jupiter, Florida
| | | | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Alex C Keene
- The Jupiter Life Science Initiative and Program in Neurogenetics, Florida Atlantic University, Jupiter, Florida
| |
Collapse
|
29
|
Hu CK, Wang W, Brind'Amour J, Singh PP, Reeves GA, Lorincz MC, Alvarado AS, Brunet A. Vertebrate diapause preserves organisms long term through Polycomb complex members. Science 2020; 367:870-874. [PMID: 32079766 DOI: 10.1126/science.aaw2601] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 11/26/2019] [Accepted: 12/23/2019] [Indexed: 12/27/2022]
Abstract
Diapause is a state of suspended development that helps organisms survive extreme environments. How diapause protects living organisms is largely unknown. Using the African turquoise killifish (Nothobranchius furzeri), we show that diapause preserves complex organisms for extremely long periods of time without trade-offs for subsequent adult growth, fertility, and life span. Transcriptome analyses indicate that diapause is an active state, with dynamic regulation of metabolism and organ development genes. The most up-regulated genes in diapause include Polycomb complex members. The chromatin mark regulated by Polycomb, H3K27me3, is maintained at key developmental genes in diapause, and the Polycomb member CBX7 mediates repression of metabolism and muscle genes in diapause. CBX7 is functionally required for muscle preservation and diapause maintenance. Thus, vertebrate diapause is a state of suspended life that is actively maintained by specific chromatin regulators, and this has implications for long-term organism preservation.
Collapse
Affiliation(s)
- Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Julie Brind'Amour
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - G Adam Reeves
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Graduate Program of Genetics, Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, 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
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
|
35
|
Abstract
Sleep is nearly ubiquitous throughout the animal kingdom, yet little is known about how ecological factors or perturbations to the environment shape the duration and timing of sleep. In diverse animal taxa, poor sleep negatively impacts development, cognitive abilities and longevity. In addition to mammals, sleep has been characterized in genetic model organisms, ranging from the nematode worm to zebrafish, and, more recently, in emergent models with simplified nervous systems such as Aplysia and jellyfish. In addition, evolutionary models ranging from fruit flies to cavefish have leveraged natural genetic variation to investigate the relationship between ecology and sleep. Here, we describe the contributions of classical and emergent genetic model systems to investigate mechanisms underlying sleep regulation. These studies highlight fundamental interactions between sleep and sensory processing, as well as a remarkable plasticity of sleep in response to environmental changes. Understanding how sleep varies throughout the animal kingdom will provide critical insight into fundamental functions and conserved genetic mechanisms underlying sleep regulation. Furthermore, identification of naturally occurring genetic variation regulating sleep may provide novel drug targets and approaches to treat sleep-related diseases.
Collapse
Affiliation(s)
- Alex C Keene
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Erik R Duboue
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Dodzian J, Kean S, Seidel J, Valenzano DR. A Protocol for Laboratory Housing of Turquoise Killifish (Nothobranchius furzeri). J Vis Exp 2018. [PMID: 29708537 PMCID: PMC5933446 DOI: 10.3791/57073] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The development of husbandry practices in non-model laboratory fish used for experimental purposes has greatly benefited from the establishment of reference fish model systems, such as zebrafish and medaka. In recent years, an emerging fish – the turquoise killifish (Nothobranchius furzeri) – has been adopted by a growing number of research groups in the fields of biology of aging and ecology. With a captive life span of 4 - 8 months, this species is the shortest-lived vertebrate raised in captivity and allows the scientific community to test – in a short time – experimental interventions that can lead to alterations of the aging rate and life expectancy. Given the unique biology of this species, characterized by embryonic diapause, explosive sexual maturation, marked morphological and behavioral sexual dimorphism - and their relatively short adult life span - ad hoc husbandry practices are in urgent demand. This protocol reports a set of key husbandry measures that allow optimal turquoise killifish laboratory care, enabling the scientific community to adopt this species as a powerful laboratory animal model.
Collapse
Affiliation(s)
- Joanna Dodzian
- Max Planck Institute for the Biology of Ageing; International Institute of Molecular and Cell Biology in Warsaw
| | - Sam Kean
- Max Planck Institute for the Biology of Ageing
| | - Jens Seidel
- Max Planck Institute for the Biology of Ageing
| | | |
Collapse
|
38
|
Zhu B, Ge W. Genome editing in fishes and their applications. Gen Comp Endocrinol 2018; 257:3-12. [PMID: 28919449 DOI: 10.1016/j.ygcen.2017.09.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 08/15/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022]
Abstract
There have been revolutionary progresses in genome engineering in the past few years. The newly-emerged genome editing technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats associated with Cas9 (CRISPR/Cas9) have enabled biological scientists to perform efficient and precise targeted genome editing in different species. Fish represent the largest group of vertebrates with many species having values for both scientific research and aquaculture industry. Genome editing technologies have found extensive applications in different fish species for basic functional studies as well asapplied research in such fields as disease modeling and aquaculture. This mini-review focuses on recent advancements and applications of the new generation of genome editing technologies in fish species, with particular emphasis on their applications in understanding reproductive functions because the reproductive axis has been most systematically and best studied among others and its function has been difficult to address with reverse genetics approach.
Collapse
Affiliation(s)
- Bo Zhu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China.
| |
Collapse
|
39
|
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]
|
40
|
Lee MB, Kaeberlein M. Translational Geroscience: From invertebrate models to companion animal and human interventions. TRANSLATIONAL MEDICINE OF AGING 2018; 2:15-29. [PMID: 32368707 PMCID: PMC7198054 DOI: 10.1016/j.tma.2018.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Translational geroscience is an interdisciplinary field descended from basic gerontology that seeks to identify, validate, and clinically apply interventions to maximize healthy, disease-free lifespan. In this review, we describe a research pipeline for the identification and validation of lifespan extending interventions. Beginning in invertebrate model systems, interventions are discovered and then characterized using other invertebrate model systems (evolutionary translation), models of genetic diversity, and disease models. Vertebrate model systems, particularly mice, can then be utilized to validate interventions in mammalian systems. Collaborative, multi-site efforts, like the Interventions Testing Program (ITP), provide a key resource to assess intervention robustness in genetically diverse mice. Mouse disease models provide a tool to understand the broader utility of longevity interventions. Beyond mouse models, we advocate for studies in companion pets. The Dog Aging Project is an exciting example of translating research in dogs, both to develop a model system and to extend their healthy lifespan as a goal in itself. Finally, we discuss proposed and ongoing intervention studies in humans, unmet needs for validating interventions in humans, and speculate on how differences in survival among human populations may influence intervention efficacy.
Collapse
Affiliation(s)
- Mitchell B. Lee
- Department of Pathology, University of Washington, Seattle, WA USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA USA
| |
Collapse
|
41
|
Age-dependent increase of oxidative stress regulates microRNA-29 family preserving cardiac health. Sci Rep 2017; 7:16839. [PMID: 29203887 PMCID: PMC5715159 DOI: 10.1038/s41598-017-16829-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/17/2017] [Indexed: 12/19/2022] Open
Abstract
The short-lived turquoise killifish Nothobranchius furzeri (Nfu) is a valid model for aging studies. Here, we investigated its age-associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs (miRNAs) in the aging heart. MiRNA-sequencing of 5 week (young), 12–21 week (adult) and 28–40 week (old) Nfu hearts revealed 23 up-regulated and 18 down-regulated miRNAs with age. MiR-29 family turned out as one of the most up-regulated miRNAs during aging. MiR-29 family increase induces a decrease of known targets like collagens and DNA methyl transferases (DNMTs) paralleled by 5´methyl-cytosine (5mC) level decrease. To further investigate miR-29 family role in the fish heart we generated a transgenic zebrafish model where miR-29 was knocked-down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up-regulation. To get insights the possible hypoxic regulation of miR-29 family, we exposed human cardiac fibroblasts to 1% O2 levels. In hypoxic condition we found miR-29 down-modulation responsible for the accumulation of collagens and 5mC. Overall, our data suggest that miR-29 family up-regulation might represent an endogenous mechanism aimed at ameliorating the age-dependent cardiac damage leading to hypertrophy and fibrosis.
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
He ZY, Men K, Qin Z, Yang Y, Xu T, Wei YQ. Non-viral and viral delivery systems for CRISPR-Cas9 technology in the biomedical field. SCIENCE CHINA. LIFE SCIENCES 2017; 60:458-467. [PMID: 28527117 DOI: 10.1007/s11427-017-9033-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/16/2017] [Indexed: 02/08/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system provides a novel genome editing technology that can precisely target a genomic site to disrupt or repair a specific gene. Some CRISPR-Cas9 systems from different bacteria or artificial variants have been discovered or constructed by biologists, and Cas9 nucleases and single guide RNAs (sgRNA) are the major components of the CRISPR-Cas9 system. These Cas9 systems have been extensively applied for identifying therapeutic targets, identifying gene functions, generating animal models, and developing gene therapies. Moreover, CRISPR-Cas9 systems have been used to partially or completely alleviate disease symptoms by mutating or correcting related genes. However, the efficient transfer of CRISPR-Cas9 system into cells and target organs remains a challenge that affects the robust and precise genome editing activity. The current review focuses on delivery systems for Cas9 mRNA, Cas9 protein, or vectors encoding the Cas9 gene and corresponding sgRNA. Non-viral delivery of Cas9 appears to help Cas9 maintain its on-target effect and reduce off-target effects, and viral vectors for sgRNA and donor template can improve the efficacy of genome editing and homology-directed repair. Safe, efficient, and producible delivery systems will promote the application of CRISPR-Cas9 technology in human gene therapy.
Collapse
Affiliation(s)
- Zhi-Yao He
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Ke Men
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Zhou Qin
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Ting Xu
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
| | - Yu-Quan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| |
Collapse
|