Development of the African killifish as a new model for aging biology


The search for mechanisms that control aging in vertebrates has been hampered by the absence of short-lived vertebrate models, as mice live about 2-3 years and zebrafish about 4-5 years. To fill this gap, we are pioneering the development of a new model organism for aging research, the naturally short-lived African killifish Nothobranchius furzeri. This new model organism will enable the rapid interrogation of genetic and environmental factors involved in aging, and the discovery of vertebrate-specific principles for lifespan regulation.

The African killifish lives in ephemeral pools of water in Africa, and has probably evolved a short lifespan adapted to this habitat (Terzibasi et al., 2007; Valdesalici and Cellerino, 2003). Embryos can resist drought until the next wet season. In optimal laboratory conditions, N. furzeri has a maximal lifespan of about 4-6 months, and is, so far, the shortest-lived vertebrate that can be bred in captivity. In controlled conditions, different wild-derived populations of this fish can display 2-3 fold differences in their maximal lifespan (Kirschner et al., 2012; Terzibasi et al., 2008). The natural short lifespan and the significant variation in maximal lifespan among distinct populations make N. furzeri an ideal model to probe the mechanisms of aging in vertebrates.

We have started to successfully transform this natural short-lived vertebrate into a usable model organism for aging research. In 2010, we went on a field trip to Zimbabwe and Mozambique to collect different populations of N. furzeri to increase the availability of strains for this species. We have created the first microsatellite linkage map in N. furzeri (Valenzano et al., 2009). We have established the first transgenic lines in this species using the Tol2 transposase system (Valenzano et al., 2011). More recently, we have completed the first de novo assembly of N. furzeri genome using deep sequencing (Valenzano, Benayoun, Singh et al., 2015) and have successfully developed CRISPR-Cas9 mediated genome-editing in this fish (Harel et al., 2015). The collection of wild populations with differences in lifespan and the development of modern genomic tools in N. furzeri are major steps in pioneering N. furzeri as a new vertebrate model for aging research.

Our goal is to use this new model to discover new principles of aging regulation in vertebrates. We have embarked on an ambitious project to map genes involved in lifespan variation in the wild-derived populations of this fish using a quantitative trait loci analysis combined with deep sequencing analysis. We identified several loci associated with survival between the strains of N. furzeri, including vertebrate-specific ones (Valenzano et al, 2015). Using genome-editing, we have generated strains deficient for several genes in nutrient-sensing and epigenetic pathways, and want to use this approach to examine the role of these vertebrate-specific genes in aging. We will also determine if perturbing orthologs of the conserved H3K4me3 and H3K27me3 modifiers affects the lifespan of N. furzeri parents, and if so, whether this triggers transgenerational inheritance of lifespan in descendants. Finally, we are excited to combine the use of modern genomic tools with the existence of large numbers of populations and species of fish with different natural lifespans to reveal the evolutionary forces that underlie lifespan differences in the wild.



Harel I, Benayoun BA, Machado M, Singh PP, Hu CK, Pech MF, Valenzano DR, Zhang E, Sharp SC, Artandi SE and Brunet A (2015) A Platform for rapid exploration of aging and diseases in a naturally short-lived vertebrate. Cell, 160: 1013-1026. Abstract  PDF

Harel I, Valenzano DR, and Brunet A (2016) Efficient genome engineering approaches for the short-lived African turquoise killifish. Nature Protocols, 11: 2010-2028. Abstract PDF

Terzibasi, E, Valenzano DR, Benedetti M, Roncaglia P, Cattaneo A, Domenici L, and Cellerino A (2008) Large differences in aging phenotype between strains of the short-lived annual fish Nothobranchius furzeri. PLoS One 3, e3866.

Terzibasi E, Valenzano DR, and Cellerino, A. (2007). The short-lived fish Nothobranchius furzeri as a new model system for aging studies. Exp Gerontol 42, 81-89.

Valdesalici S, and Cellerino A (2003). Extremely short lifespan in the annual fish Nothobranchius furzeri. Proc Biol Sci 270 Suppl 2, S189-191.

Valenzano DR, Kirschner J, Kamber RA, Zhang E, Weber D, Cellerino A, Englert C, Platzer M, Reichwald K, and Brunet A (2009) Mapping loci associated with tail color and sex determination in the short-lived fish Nothobranchius furzeri. Genetics, 183, 1385-1395.

Valenzano, DR, Sharp S, and Brunet A (2011) Transposon-mediated transgenesis in the short-lived African killifish Nothobranchius furzeri, a vertebrate model for aging. G3 (Bethesda) 1, 531-538.

Valenzano DR, Benayoun BA, Singh PP, Zhang E, Etter PD, Hu CK, Clément-Ziza M, Willemsen D, Cui R, Harel I, Machado BE, Yee MC, Sharp SC, Bustamante CD, Beyer A, Johnson EA, and Brunet A  (2015) The African turquoise killifish genome provides insights into evolution and genetic architecture of lifespan. Cell, 163: 1539-1554. Abstract PDF African Killifish Genome Browser