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The African Turquoise Killifish: a Model for Exploring Vertebrate Aging and Diseases in the Fast Lane

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The African Turquoise Killifish: a Model for Exploring Vertebrate Aging and Diseases in the Fast Lane Downloaded from symposium.cshlp.org on June 11, 2016 - Published by Cold Spring Harbor Laboratory Press The African Turquoise Killifish: A Model for Exploring Vertebrate Aging and Diseases in the Fast Lane 1 1,2 ITAMAR HAREL AND ANNE BRUNET 1Department of Genetics, Stanford University, Stanford, California 94305 2Glenn Laboratories for the Biology of Aging at Stanford, Stanford, California 94305 Correspondence: [email protected] Why and how organisms age remains a mystery, and it defines one of the biggest challenges in biology. Aging is also the primary risk factor for many human pathologies, such as cancer, diabetes, cardiovascular diseases, and neurodegenerative diseases. Thus, manipulating the aging rate and potentially postponing the onset of these devastating diseases could have a tremendous impact on human health. Recent studies, relying primarily on nonvertebrate short-lived model systems, have shown the importance of both genetic and environmental factors in modulating the aging rate. However, relatively little is known about aging in vertebrates or what processes may be unique and specific to these complex organisms. Here we discuss how advances in genomics and genome editing have significantly expanded our ability to probe the aging process in a vertebrate system. We highlight recent findings from a naturally short-lived vertebrate, the African turquoise killifish, which provides an attractive platform for exploring mechanisms underlying vertebrate aging and age-related diseases. MODELING AGING IN THE ing vertebrate aging and age-related diseases (Harel et al. LABORATORY 2015). Aging research has greatly benefited from investigating short-lived nonvertebrate models (Fig. 1A), specifically THE AFRICAN TURQUOISE KILLIFISH yeast (Saccharomyces cerevisiae), worm (Caenorhabdi- tis elegans), and fly (Drosophila melanogaster). These First collected in 1968 in the Gonarezhou National studies have revealed that some pathways, such as the Park (Zimbabwe), the turquoise killifish is currently the TOR (target of rapamycin) and insulin/IGF (insulin- shortest-lived vertebrate that can be bred in captivity like growth factor), can regulate the aging process in an (Genade et al. 2005; Valenzano et al. 2006b; Cellerino evolutionary conserved manner (Kenyon 2010). Howev- et al. 2015; Harel et al. 2015), with a life span of 4–6 er, some crucial aspects of human aging and related pa- mo in optimal laboratory conditions (six- to 10-fold thologies cannot be faithfully modeled in nonvertebrates. shorter-lived than mice and zebrafish, respectively). These aspects include features unique to vertebrate phys- This fish species has likely evolved a compressed life iology (such as blood, bones, and an adaptive immune cycle (30–40 d from an egg to a sexually mature adult) system), and “vertebrate-specific” genes (such as APOE to adapt to its transient habitat—seasonal water ponds and p15INK4B). On the other hand, the use of classical present only during a brief rainy season (Fig. 1B). Impor- vertebrate models (namely, the mouse and zebrafish) for tantly, despite its short life span, this fish recapitulates this purpose has been drastically limited by their life stereotypical age-dependent phenotypes and pathologies span, which is relatively long for experimental approach- such as decline in fertility, cognitive functions, muscle es (up to 3.5 and 5 yr, respectively; Tacutu et al. 2013). mass (sarcopenia), and regenerative capacity, as well as Insights into the mechanisms of aging have also been increase in senescence, neurodegeneration, and cancer- provided by the study of exceptionally long-lived verte- ous lesions (Genade et al. 2005; Valenzano et al. 2006b; brates (Fig. 1A), such as the naked mole rat (30 yr), the Di Cicco et al. 2011; Wendler et al. 2015). Importantly, Brandt’s bat (30 yr), and the bow-headed whale (200 the turquoise killifish also displays a conserved response yr) (Tacutu et al. 2013). These species represent a unique to environmental stimuli known to affect aging in other resource for understanding the mechanisms behind ex- species, such as dietary restriction (Terzibasi et al. 2009), treme longevity using comparative genomics, proteo- resveratrol (Valenzano et al. 2006b), and temperature mics, and cellular approaches (Austad 2010; Gorbunova (Valenzano et al. 2006a). et al. 2014). However, these long-lived species are less Overall, fish offer several advantages as laboratory an- suited for genetic manipulation, life span, or longitudinal imals (Schartl 2014). External fertilization provides a studies. What could be the ideal model system for study- clear window for developmental process and increased ing vertebrate aging in the laboratory? An exciting ap- accessibility for manipulation. Other advantages include proach would be to choose a naturally short-lived a remarkable regenerative capacity and compatibility vertebrate to systematically probe the principles govern- with high-throughput approaches, specifically genetic Copyright # 2015 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/sqb.2015.80.027524 Cold Spring Harbor Symposia on Quantitative Biology, Volume LXXX 1 Downloaded from symposium.cshlp.org on June 11, 2016 - Published by Cold Spring Harbor Laboratory Press 2 HAREL AND BRUNET A Genetic aging models B The African turquoise killifish Yeast/Worm/Fly Turquoise killifish Mouse Zebrafish (~1-3 months) (~ 6 months) (~ 3.5 years) (~ 5 years) 12 34 5 Short-lived models Long-lived species 40 80 120 160 200 Figure 1. (A) Life span of nonvertebrate and vertebrate genetic model systems used for experimental aging and disease research (top). Life span of long-lived model systems used primarily for cellular and comparative genomic approaches (bottom). (B) The turquoise killifish originates from ephemeral ponds in Zimbabwe and Mozambique (top). Example of a young and old male turquoise killifish (bottom). (Modified from Harel et al. 2015.) and drug screens. The turquoise killifish has additional nomics and evolutionary studies of aging and longevity. advantages, such as an XY-based sexual determination Importantly, the annotated genome also set the foundation system (Valenzano et al. 2009); this is in contrast to many for developing the second part of this platform—a stream- other fish, including zebrafish. Furthermore, the exis- lined genome-editing pipeline (Fig. 2). tence of highly inbred and wild-derived strains (Terzibasi The CRISPR/Cas9 (clustered regularly interspaced et al. 2008) provides an important advantage for genetic short palindrome repeats associated Cas9 nuclease) sys- studies and mapping of complex traits such as color and tem (Jinek et al. 2012; Cong et al. 2013; Mali et al. life span (Valenzano et al. 2009; Kirschner et al. 2012). 2013), has emerged as an effective approach for intro- Together, these characteristics make this fish an attractive ducing targeted mutations in a variety of organisms (for model organism uniquely fit to study vertebrate aging, a detailed list, see Hsu et al. 2014), providing a great physiology, and age-dependent diseases throughout or- promise for genetic studies in both model and nonmodel ganismal life span. Although many tools have been de- systems. A recent review has defined the main nine “hall- veloped for the turquoise killifish, including genetic marks of aging” (Lo´pez-Otı´n et al. 2013), including telo- linkage maps and Tol2-based transgenesis (Reichwald mere attrition, deregulated nutrient sensing, and stem cell et al. 2009; Valenzano et al. 2009, 2011; Hartmann and exhaustion (Fig. 3A). Several genes within these hall- Englert 2012; Kirschner et al. 2012), the lack of a marks, such as IGF1R and RPS6KB1, are evolutionary sequenced genome and the ability to manipulate endog- conserved regulators of longevity (Kenyon 2010), where- enous genes has drastically limited the use of this organ- as others, such as APOE and TERT, have been implicated ism. Thus, for the turquoise killifish to become a widely in human age-associated diseases (Alzheimer’s disease used vertebrate model, genomic and genome editing ap- [Rhinn et al. 2013] and dyskeratosis congenita [Arma- proaches had to be generated. nios 2009], respectively). However, the vast majority of candidate genes and gene variants have not been system- atically evaluated in the context of vertebrate aging and A RAPID GENOME-TO-PHENOTYPE age-related diseases. We recently proposed that the tur- PLATFORM FOR VERTEBRATE AGING quoise killifish might be uniquely fit for the challenge This challenge was recently addressed by developing a (Harel et al. 2015). This study used the CRISPR/Cas9 comprehensive genome-to-phenotype platform for this genome-editing system to mutate multiple aging-related naturally short-lived fish (Fig. 2; Harel et al. 2015). The genes (Fig. 3A), thus providing a promising approach to genomic aspect of this platform included the de novo rapidly explore the genetics of vertebrate aging and age- assembled turquoise killifish genome, RNA sequencing related diseases. (RNA-seq) in several organs, H3K4me3 (trimethylation of lysine 4 on histone H3) chromatin landscape, and de- TELOMERASE-DEFICIENT FISH DISPLAY tailed protein homology (Fig. 2). Integrating these geno- THE FASTEST ONSET OF RELATED mic data sets made it possible to fully annotate the genome HUMAN PATHOLOGIES of the turquoise killifish, as well as analyze expression patterns for key aging candidate genes. This genomic plat- Telomeres, the protective end of chromosomes, shorten form represents an exciting resource
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