1
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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.
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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.
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2
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Frost PC, Caudle SL, Han S, O'Brien JMJ, Tobin SW. Rearing and Experimental Uses of Daphnia: Controlling Animal Nutrition and Assessing Lifespan and Life-History Traits. Curr Protoc 2024; 4:e1064. [PMID: 38837737 DOI: 10.1002/cpz1.1064] [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] [Indexed: 06/07/2024]
Abstract
Caloric restriction has been found to extend the lifespan of many organisms including mammals and other vertebrates. With lifespans exceeding months to years, age-related experiments involving fish and mammals can be overtly costly, both in terms of time and funding. The freshwater crustacean, Daphnia, has a relatively short lifespan (∼50 to 100 days), which makes it a cost-effective alternative animal model for longevity and aging studies. Besides age-specific mortality, there are a suite of physiological responses connected to "healthspan" that can be tracked as these animals age including growth, reproduction, and metabolic rates. These responses can be complemented by assessment of molecular and cellular processes connected to aging and health. Lifespan and metabolism of this model organism is responsive to long studied modulators of aging, such as rearing temperature and nutritional manipulation, but also pharmacological agents that target aging, e.g., rapamycin, which adds to its usefulness as a model organism. Here we describe how to culture Daphnia for aging experiments including maintaining laboratory populations of Daphnia mothers, growing algal food, and manipulating nutrition of these animals. In addition, we provide methods for tracking common physiological and longevity responses of Daphnia. This protocol provides researchers planning to use this model organism with methods to establish and maintain Daphnia populations and to standardize their experimental approaches. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Culturing algae for Daphnia food Basic Protocol 2: General methods for culturing Daphnia Basic Protocol 3: Standardizing and controlling nutrition for experimental Daphnia Basic Protocol 4: Monitoring Daphnia lifespan Basic Protocol 5: Evaluating Daphnia health: Heart rate and respiration, body mass and growth rates, and reproduction.
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Affiliation(s)
- Paul C Frost
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - Samatha L Caudle
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - Sen Han
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | | | - Stephanie W Tobin
- Department of Biology, Trent University, Peterborough, Ontario, Canada
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3
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Boos F, Chen J, Brunet A. The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes. Cold Spring Harb Protoc 2024; 2024:107737. [PMID: 37100468 PMCID: PMC10890783 DOI: 10.1101/pdb.over107737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The African turquoise killifish Nothobranchius furzeri is currently the shortest-lived vertebrate that can be bred in captivity. Because of its short life span of only 4-6 months, rapid generation time, high fecundity, and low cost of maintenance, the African turquoise killifish has emerged as an attractive model organism that combines the scalability of invertebrate models with the unique features of vertebrate organisms. A growing community of researchers is using the African turquoise killifish for studies in diverse fields, including aging, organ regeneration, development, "suspended animation," evolution, neuroscience, and disease. A wide range of techniques is now available for killifish research, from genetic manipulations and genomic tools to specialized assays for studying life span, organ biology, response to injury, etc. This protocol collection provides detailed descriptions of the methods that are generally applicable to all killifish laboratories and those that are limited to specific disciplines. Here, we give an overview of the features that render the African turquoise killifish a unique fast-track vertebrate model organism.
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Affiliation(s)
- Felix Boos
- Department of Genetics, Stanford, California 94305, USA
| | - Jingxun Chen
- Department of Genetics, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford, California 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, California 94305, USA
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4
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Teefy BB, Lemus AJJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. Cell Rep 2023; 42:113237. [PMID: 37837621 PMCID: PMC10842523 DOI: 10.1016/j.celrep.2023.113237] [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: 05/05/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, and spleen. We annotate 22 cell types, define marker genes, and infer differentiation trajectories. We find pervasive sex-dimorphic gene expression across cell types. Sex-dimorphic genes tend to be linked to lipid metabolism, consistent with clear differences in lipid storage in female vs. male turquoise killifish livers. We use machine learning to predict sex using single-cell gene expression and identify potential markers for molecular sex identity. As a proof of principle, we show that our atlas can be used to deconvolute existing bulk RNA sequencing (RNA-seq) data to obtain accurate estimates of cell type proportions. This atlas can be a resource to the community that could be leveraged to develop cell-type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J J Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA; Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA; Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA.
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Xu A, Teefy BB, Lu RJ, Nozownik S, Tyers AM, Valenzano DR, Benayoun BA. Transcriptomes of aging brain, heart, muscle, and spleen from female and male African turquoise killifish. Sci Data 2023; 10:695. [PMID: 37828039 PMCID: PMC10570339 DOI: 10.1038/s41597-023-02609-x] [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: 06/21/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
The African turquoise killifish is an emerging vertebrate model organism with great potential for aging research due to its naturally short lifespan. Thus far, turquoise killifish aging 'omic' studies have examined a single organ, single sex and/or evaluated samples from non-reference strains. Here, we describe a resource dataset of ribosomal RNA-depleted RNA-seq libraries generated from the brain, heart, muscle, and spleen from both sexes, as well as young and old animals, in the reference GRZ turquoise killifish strain. We provide basic quality control steps and demonstrate the utility of our dataset by performing differential gene expression and gene ontology analyses by age and sex. Importantly, we show that age has a greater impact than sex on transcriptional landscapes across probed tissues. Finally, we confirm transcription of transposable elements (TEs), which are highly abundant and increase in expression with age in brain tissue. This dataset will be a useful resource for exploring gene and TE expression as a function of both age and sex in a powerful naturally short-lived vertebrate model.
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Affiliation(s)
- Alan Xu
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, 90089, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ryan J Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, USA
| | - Séverine Nozownik
- Unit of Forensic Genetics, University Center of Legal Medicine, Lausanne, Switzerland
| | - Alexandra M Tyers
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Strasse 9b, 50931, Cologne, Germany
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
| | - Dario R Valenzano
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Strasse 9b, 50931, Cologne, Germany
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, 90089, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, 90089, USA.
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA.
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6
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Bedbrook CN, Nath RD, Nagvekar R, Deisseroth K, Brunet A. Rapid and precise genome engineering in a naturally short-lived vertebrate. eLife 2023; 12:e80639. [PMID: 37191291 PMCID: PMC10188113 DOI: 10.7554/elife.80639] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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.
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Affiliation(s)
- Claire N Bedbrook
- Department of Genetics, Stanford UniversityStanfordUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Ravi D Nath
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Rahul Nagvekar
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Karl Deisseroth
- Department of Bioengineering, Stanford UniversityStanfordUnited States
- Department of Psychiatry and Behavioral Sciences, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Anne Brunet
- Department of Genetics, Stanford UniversityStanfordUnited States
- Glenn Laboratories for the Biology of Aging at StanfordStanfordUnited States
- Wu Tsai Neurosciences Institute, Stanford UniversityStanfordUnited States
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7
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Teefy BB, Lemus AJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex-dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539616. [PMID: 37214847 PMCID: PMC10197525 DOI: 10.1101/2023.05.05.539616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism to study vertebrate aging. Here we describe the first multi-tissue, single-cell gene expression atlas of female and male turquoise killifish tissues comprising immune and metabolic cells from the blood, kidney, liver, and spleen. We were able to annotate 22 distinct cell types, define associated marker genes, and infer differentiation trajectories. Using this dataset, we found pervasive sex-dimorphic gene expression across cell types, especially in the liver. Sex-dimorphic genes tended to be involved in processes related to lipid metabolism, and indeed, we observed clear differences in lipid storage in female vs. male turquoise killifish livers. Importantly, we use machine-learning to predict sex using single-cell gene expression in our atlas and identify potential transcriptional markers for molecular sex identity in this species. As proof-of-principle, we show that our atlas can be used to deconvolute existing liver bulk RNA-seq data in this species to obtain accurate estimates of cell type proportions across biological conditions. We believe that this single-cell atlas can be a resource to the community that could notably be leveraged to identify cell type-specific genes for cell type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B. Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J.J. Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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MacArthur MR, Mitchell SJ. Sex differences in healthspan and lifespan responses to geroprotective dietary interventions in preclinical models. CURRENT OPINION IN PHYSIOLOGY 2023. [DOI: 10.1016/j.cophys.2023.100651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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9
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Mathuru AS. The holy grail of longevity research. eLife 2022; 11:e85001. [PMID: 36562603 PMCID: PMC9788805 DOI: 10.7554/elife.85001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A new technology to study physiology and cognition elevates African turquoise killifish as a model organism for studies of aging in vertebrates.
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Affiliation(s)
- Ajay S Mathuru
- Yale-NUS CollegeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Institute of Molecular and Cell Biology, A*STARSingaporeSingapore
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