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Valenzano, D. R.

Publications and source records attributed to Valenzano, D. R..

18 recordsLinked to original sources

Sexually Dimorphic Response to Dietary Restriction-induced Longevity and Muscle Rejuvenation in Nothobranchius furzeri.

Age-related skeletal muscle decline (sarcopenia) is a major contributor to frailty and mortality during aging, yet the extent to which sex shapes muscle aging and its response to dietary interventions remains poorly understood. Here, we use the short-lived vertebrate Nothobranchius furzeri (African turquoise killifish; ATK) to investigate how sex and intermittent fasting (IF) interact to regulate lifespan and skeletal-muscle aging. We establish and optimize an IF regimen that significantly extends lifespan in both male and female killifish, albeit with classical trade-offs including reduced growth and reproductive output. Despite these costs, IF markedly improves swimming performance in aged animals of both sexes. Structural analyses of killifish on a normal diet reveal pronounced sexual dimorphism in muscle aging. Males exhibit age-associated myofiber hyperplasia, whereas females maintain fiber number but undergo hypertrophic remodeling. IF partially reverses both phenotypes, restoring a more youthful fiber size distribution in both males and females. Single-nucleus RNA sequencing uncovers sex-specific remodeling of muscle-fiber composition in killifish on a normal diet, with females displaying an age-associated shift toward oxidative slow-twitch fibers that is reversed by IF, while males show relatively stable fiber-type proportions under normal and IF feeding regimens. Cell-cell communication analyses further reveal a global decline in intercellular signaling with age, alongside sex-specific restoration of distinct pathways under IF, including axon guidance and IGF signaling in females and metabolic ANGPTL signaling in males. Finally, bulk transcriptomic profiling demonstrates that aging follows largely sexually dimorphic molecular trajectories, whereas IF induces both sex-specific and shared responses. Notably, under IF, both sexes exhibit upregulation of ribosome biogenesis and genes supporting myofibrillar organization and contraction, likely underlying preserved muscle function. Together, these findings demonstrate that IF promotes longevity and muscle health through conserved anabolic mechanisms alongside sex-specific cellular and molecular rejuvenation strategies. Our work highlights the importance of incorporating sex as a biological variable when designing dietary interventions to promote healthy aging.

physiology↗

Early-life reproduction predicts male lifespan in turquoise killifish (Nothobranchius furzeri)

Individuals of the same species often display extensive lifespan heterogeneity. However, the factors underlying such heterogeneity remain largely elusive. Here, we examined whether lifespan variation in the naturally short-lived turquoise killifish (Nothobranchius furzeri) is caused by reproductive trade-offs. We found that lifespan and reproduction do not trade off: early-life reproductive success positively predicts male lifespan and reflects intrinsic quality. A causal-informed model, where intrinsic quality affects both survival and reproduction, fully recapitulates the empirical data. Together, our results show inter-individual variation in intrinsic quality explains lifespan heterogeneity in a short-lived vertebrate, challenging the view that reproductive costs drive inter-individual lifespan variation.

evolutionary biology↗

AEGIS: individual-based modeling of life history evolution

Nature presents a staggering diversity of life history strategies, ranging from rapid to slow onset of sexual maturity, short or long life, low or high number of offspring, and much more. Each species-specific life history trait reflects on the one hand specific adaptations to unique environments, e.g., nutrient availability, predation, parasite load, seasonality; and on the other hand, depends on past demographic constraints, such as population bottlenecks, migrations, etc. Studying life history diversity in nature and in the laboratory ultimately aims to identify the ecological, demographic, and intrinsic causes contributing to species-specific growth rate distributions, lifetime reproductive outcomes, as well as lifespans. However, for most species, we cannot rewind the evolutionary and demographic past to identify the causal chain of events leading to the present life history traits. We can infer past events only by sampling extant populations. In silico evolution has the advantage of providing complete time resolution for the events driving life history evolution and enables to directly test the impact of ecological and demographic variables on the evolution of life history traits. We developed AEGIS (Aging of Evolving Genomes In Silico), a software for individual-based modeling of life history trait evolution at the genotype and phenotype level. AEGIS models life history traits evolution in response to a set of factors, including resource availability, extrinsic mortality induced by predators or parasites, different levels of germline mutation rates, population size, sexual vs. asexual reproduction, and more. AEGIS serves as a powerful tool to model life history evolution and allows for parameter inference against ground truths. AEGIS can help generate estimates for the evolution of different life history traits, such as age-dependent mortality and reproduction, in response to different selective pressures and intrinsic genetic constraints.

evolutionary biology↗

Amyloid Beta Precursor Protein contributes to brain aging and learning decline in short-lived turquoise killifish (Nothobranchius furzeri)

Brain aging is a key risk factor for many neurodegenerative diseases, yet its molecular and cellular mechanisms remain elusive. Amyloid-beta precursor protein (APP) is among the most studied proteins linked to brain pathology; however, its role in non-pathological brain aging remains poorly characterized. Here, we investigate the natural impact of APP on normal brain aging using the short-lived turquoise killifish (Nothobranchius furzeri), which exhibits rapid and spontaneous age-related decline. We found that a pyroglutamated APP derivative (APPpE11) accumulates intra-neuronally in an age-dependent manner, co-localizing with a marker of cell death. We found that intraneuronal APPpE11 is also present in brains from healthy elderly humans, suggesting deep evolutionary conservation. To determine APPs role in spontaneous brain aging, we knock-out "amyloid precursor protein a" (appa) in killifish via CRISPR/Cas9. The lack of appa mitigated brain aging from a proteome-wide perspective, reduced age-related cell death and inflammation, and improved neuronal activity and learning capacity in aged individuals. Our findings show an ancestral and previously unrecognized role of amyloid-beta precursor protein in non-pathological brain aging, making it an ideal target for anti-aging interventions.

neuroscience↗

Sperm quality and function deteriorate in old males of the naturally short-lived turquoise killifish

Maximizing the life-long reproductive output would lead to the prediction that short-lived and fast aging species would undergo no - if any - reproductive senescence. Turquoise killifish (Nothobranchius furzeri) are naturally short-lived teleosts, and undergo extensive somatic aging, characterized by molecular, cellular, and organ dysfunction following the onset of sexual maturation. Here, we tested whether naturally short-lived and fast aging turquoise killifish males maximize reproduction and display minimal - if any, reproductive senescence. We analysed age-related changes in sperm traits, the proportion of fertilized eggs, as well as embryo survival. Contrary to the expectation of no reproductive aging, we found that turquoise killifish males undergo extensive reproductive aging, consisting in the age-dependent decline in sperm quality, decreased proportion of fertilized eggs and lower embryo survival. Our results indicate that male turquoise killifish do not trade-off age-dependent soma decline with life-long sustained reproductive fitness. Instead, somatic and reproductive aging appear to occur simultaneously. Our findings question generalized soma vs. reproductive senescence trade-off models and highlight the importance of integrating species-specific ecological and demographic constraints to explain observed life history traits.

evolutionary biology↗

Assessing Age-Related Decline in Anti-Bacterial Immune Responses Using an Ex-vivo Assay in African Turquoise Killifish (Nothobranchius furzeri)

Ex-vivo immune functional assays serve as essential tools for uncovering the intricate molecular mechanisms behind immune responses, both intrinsic and extrinsic, across a diverse spectrum of conditions and interventions. In this study, we devised an innovative assay aimed at quantifying anti-bacterial responses in immune cells from the primary immune organ of small teleosts. Our model of choice is the the African turquoise killifish (Nothobranchius furzeri), which has emerged as a prominent model system in the field of biology of aging, because of its natural short lifespan and the broad range of aging-related dysfunctions. Using our novel ex vivo assay, we tested age-associated differences in immune cell functionality, measured as anti-bacterial responses in young and aged turquoise killifish. Our results show that the ability to inhibit bacterial growth declines in cells extracted from aged killifish, compared to young killifish. This ex-vivo assay, designed for rapid measures of immune effector responses, holds the potential to be a scalable tool for assessing the cellular and molecular basis for anti-microbial immune responses under a range of interventions.

immunology↗

Transcriptional profiling of aging tissues from female and male African turquoise killifish

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 using RNA-seq 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.

genomics↗

Spontaneous onset of cellular markers of inflammation and genome instability during aging in the immune niche of the naturally short-lived turquoise killifish (Nothobranchius furzeri)

Turquoise killifish (Nothobranchius furzeri) are naturally short-lived vertebrates, recapitulating several aspects of human aging, including protein aggregation, telomere shortening, cellular senescence, and declined antibody diversity. The mechanistic causes of systemic aging in killifish are still poorly understood. Here we ask whether killifish undergo significant age-dependent changes in the main hematopoietic organ, which together could contribute to systemic aging. To characterize immune aging in killifish, we employed single-cell RNA sequencing, proteomics, cytometry and a functional in vitro assay. Our data indicate how old killifish display increased inflammatory markers, and while immune cells from adult killifish display increased markers of proliferation and replication-independent DNA repair in progenitor-like cell clusters, progenitors from old killifish display extensive markers of DNA double-strand breaks. In less than 10 weeks, killifish undergo several dramatic spontaneous aging-related changes in the immune niche, which could be functionally linked with its extensive systemic aging and serve as targets for anti-aging interventions.

immunology↗

Population size shapes the evolution of lifespan

Biological aging results from the age-dependent change in the force of natural selection, which increases the probability of germline variants that limit survival to accumulate in genes acting predominantly in late life1. The evolutionary mechanisms underlying the accumulation of neutral mutations and antagonistically pleiotropic gene variants that cause biological aging have been analyzed to date under the assumption of infinitely large population size. However, even though population size importantly shapes genetic and phenotype variation via drift and selection2,3, we still have a limited understanding of how finite population size impacts the evolution of mortality at the population level. Here, we study the impact of population size on lifespan evolution under mutation accumulation and antagonistic pleiotropy. We found that larger population size leads to lower age-independent, as well as age-dependent mortality under mutation accumulation, due to more effective purifying selection against deleterious germline variants. Strikingly, large population size can lead to extended lifespan under antagonistic pleiotropy, due to more effective positive selection on gene variants increasing survival in early-life, while leading to increased post-maturation mortality. Our findings provide a comprehensive numerical framework for the two major evolutionary genetic theories of aging and reveal a fundamental and yet non-appreciated role for population size in the evolution of mortality trajectories.

evolutionary biology↗

Large-scale characterization of sex pheromone communication systems in Drosophila

Insects use sex pheromones as a reproductive isolating mechanism to attract conspecifics and repel heterospecifics. Despite the profound knowledge of sex pheromones, little is known about the coevolutionary mechanisms and constraints on their production and detection. Using whole-genome sequences to infer the kinship among 99 drosophilids, we investigate how phylogenetic and chemical traits have interacted at a wide evolutionary timescale. Through a series of chemical syntheses and electrophysiological recordings, we identify 51 sex-specific compounds, many of which are detected via olfaction. Behavioral analyses reveal that many of the 42 male-specific compounds are transferred to the female during copulation and mediate female receptivity and/or male courtship inhibition. Measurement of phylogenetic signals demonstrates that sex pheromones and their cognate olfactory channels evolve rapidly and independently over evolutionary time to guarantee efficient intra- and inter-specific communication systems. Our results show how sexual isolation barriers between species can be reinforced by species-specific olfactory signals.

evolutionary biology↗

Antibody repertoire sequencing reveals systemic and mucosal immunosenescence in the short-lived turquoise killifish

Aging individuals exhibit a pervasive decline in adaptive immune function, with important implications for health and lifespan. Previous studies have found a pervasive loss of immune-repertoire diversity in human peripheral blood during aging; however, little is known about repertoire aging in other immune compartments, or in species other than humans. Here, we perform the first study of immune-repertoire aging in an emerging model of vertebrate aging, the African turquoise killifish (Nothobranchius furzeri). Despite their extremely short lifespans, these killifish exhibit complex and individualized heavy-chain repertoires, with a generative process capable of producing millions of distinct productive sequences. Whole-body killifish repertoires decline rapidly in within-individual diversity with age, while between-individual variability increases. Large, expanded B-cell clones exhibit far greater diversity loss with age than small clones, suggesting important differences in how age affects different B cell populations. The immune repertoires of isolated intestinal samples exhibit especially dramatic age-related diversity loss, related to an elevated prevalence of expanded clones. Lower intestinal repertoire diversity was also associated with transcriptomic signatures of reduced B-cell activity, supporting a functional role for diversity changes in killifish immunosenescence. Our results highlight important differences in systemic vs. organ-specific aging dynamics in the adaptive immune system. Significance StatementImmune function declines dramatically with age, with important consequences for health in the elderly. Changes in the diversity and composition of the bodys antibody repertoire are an important contributor to this age-related dysfunction. However, studying repertoire aging at high spatial and temporal resolution is hampered by the long lifespans of humans and other vertebrate models, and the difficulty of acquiring human samples other than peripheral blood. Here, we characterize the aging of the antibody repertoire in a naturally short-lived vertebrate, the turquoise killifish (Nothobranchius furzeri). We found that aging killifish undergo rapid loss of repertoire diversity in both whole-body and intestinal samples within four months of hatching. Loss of repertoire diversity in the gut was also associated with broader gene-expression changes indicative of reduced B-cell activity. As such, killifish represent a powerful laboratory model to study adaptive immune aging.

immunology↗

Genomics of a killifish from the Seychelles islands supports transoceanic island colonization and reveals relaxed selection of developmental genes

How freshwater fish colonize remote islands remains an evolutionary puzzle. Tectonic drift and trans-oceanic dispersal models have been proposed as possible alternative mechanisms. Integrating dating of known tectonic events with population genetics and experimental test of salinity tolerance in the Seychelles islands golden panchax (Pachypanchax playfairii), we found support for trans-oceanic dispersal being the most likely scenario. At the macroevolutionary scale, the non-annual killifish golden panchax shows stronger genome-wide purifying selection compared to annual killifishes from continental Africa. Reconstructing past demographies in isolated golden panchax populations provides support for decline in effective population size, which could have allowed slightly deleterious mutations to segregate in the population. Unlike annual killifishes, where relaxed selection preferentially targets aging-related genes, relaxation of purifying selection in golden panchax affects genes involved in developmental processes, including fgf10.

evolutionary biology↗

Intra-Species Differences in Population Size shape Life History and Genome Evolution

The evolutionary forces shaping life history trait divergence within species are largely unknown. Killifish (oviparous Cyprinodontiformes) evolved an annual life cycle as an exceptional adaptation to life in arid savannah environments characterized by seasonal water availability. The turquoise killifish (Nothobranchius furzeri) is the shortest-lived vertebrate known to science and displays differences in lifespan among wild populations, representing an ideal natural experiment in the evolution and diversification of life history. Here, by combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among turquoise killifish populations. We generate an improved reference assembly for the turquoise killifish genome, trace the evolutionary origin of the sex chromosome, and identify genes under strong positive and purifying selection, as well as those evolving neutrally. We find that the shortest-lived turquoise killifish populations, which dwell in fragmented and isolated habitats at the outer margin of the geographical range of the species, are characterized by small effective population size and accumulate throughout the genome several small to large-effect deleterious mutations due to genetic drift. The genes most affected by drift in the shortest-lived turquoise killifish populations are involved in the WNT signalling pathway, neurodegenerative disorders, cancer and the mTOR pathway. As the populations under stronger genetic drift are the shortest-lived ones, we propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by causing the genome-wide accumulation of deleterious mutations, cumulatively contribute to the short adult lifespan in turquoise killifish populations.

evolutionary biology↗

Extreme genomic volatility characterises the evolution of the immunoglobulin heavy chain locus in teleost fishes

The evolution of the adaptive immune system has provided vertebrates with a uniquely sophisticated immune toolkit, enabling them to mount precise immune responses against a staggeringly diverse range of antigens. Like other vertebrates, teleost fishes possess a complex and functional adaptive immune system; however, our knowledge of the complex antigen-receptor genes underlying its functionality has been restricted to a small number of experimental and agricultural species, preventing a systematic investigation of how these crucial gene loci evolve. Here, we analyse the genomic structure of the immunoglobulin heavy chain (IGH) gene loci in the cyprinodontiforms, a diverse and important group of teleosts present in many different habitats across the world. We reconstruct the complete IGH loci of the turquoise killifish (Nothobranchius furzeri) and the southern platyfish (Xiphophorus maculatus) and analyse their in vivo gene expression, revealing the presence of species-specific splice isoforms of transmembrane IGHM. We further characterise the IGH constant regions of ten additional cyprinodontiform species, including guppy, amazon molly, mummichog and mangrove killifish. Phylogenetic analysis of these constant regions reveals multiple independent rounds of duplication and deletion of the teleost-specific antibody class IGHZ in the cyprinodontiform lineage, demonstrating the extreme volatility of IGH evolution. Focusing on the cyprinodontiforms as a model taxon for comparative evolutionary immunology, this work provides novel genomic resources for studying adaptive immunity and sheds light on the evolutionary history of the adaptive immune system.

immunology↗

Circular RNAs in the ageing African turquoise killifish

CircRNAs are a subgroup of RNAs which form a circular molecule. During the splicing process the 3 splice donor loops back to form a covalent bond with an upstream 5 splice acceptor instead of the downstream 5 acceptor. The majority of circRNAs are non-coding splice isoforms of protein coding genes showing tissue and time specific expression. Because circRNAs have no 5 cap nor 3 poly-A tail, they degrade slower than their linear host genes. Only few studies were able to show a specific function for circRNAs.\n\nIn this work we sequenced 23 samples from three tissues (brain, muscle, and gut) at three (two for gut) time points throughout the life of the naturally short-lived African turquoise killifish (Nothobranchius furzeri). We identified 1810 unique circRNAs, half of which are conserved with humans and mice. With this study we provide a comprehensive atlas to the circRNA landscape in the ageing African turquoise killifish, which serves as a novel resource to the circRNA as well as the ageing community.

genomics↗

AEGIS: An In Silico Tool to Model Genome Evolution in Age-Structured Populations

AEGIS (Ageing of Evolving Genomes In Silico) is a versatile population-genetics numerical-simulation tool that enables the evolution of life history trajectories under sexual and asexual reproduction and a wide variety of evolutionary constraints. By encoding age-specific survival and reproduction probabilities as discrete genomic elements, AEGIS allows these probabilities to evolve freely and independently over time. Simulation of population evolution with AEGIS demonstrates that ageing-like phenotypes evolve in stable environments under a wide range of conditions, that life history trajectories depend heavily on mutation rates, and that sexual populations are better able to accumulate high levels of beneficial mutations affecting early-life survival and reproduction. AEGIS is free and open-source, and aims to become a standard reference tool in the study of life-history evolution and the evolutionary biology of ageing.

evolutionary biology↗

Cell cycle dynamics during diapause entry and exit in an annual killifish revealed by FUCCI technology

BackgroundAnnual 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 quiescence, delaying hatching until 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).\n\nDevelopmental transitions associated with diapause entry and exit can be linked with cell cycle events. Here we set to image this transitions in living embryos.\n\nResultsTo 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 M phase (diapause I).\n\nThereafter, 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.\n\nConclusionsOur 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.\n\nList of AbbreviationsIn this paper, we will refer to several developmental stages or morphological structures using abbreviations. To make the reading easier, we resume here a list of all the abbreviations, to which the reader can refer at any time.

developmental biology↗

Regulation of Life Span by the Gut Microbiota in The Short-Lived African Turquoise Killifish

Gut bacteria occupy the interface between the organism and the external environment, contributing to homeostasis and disease. Yet, the causal role of the gut microbiota during host aging is largely unexplored. Here, using the African turquoise killifish (Nothobranchius furzeri), a naturally short-lived vertebrate, we show that the gut microbiota plays a key role in modulating vertebrate life span. Recolonizing the gut of middle-age individuals with bacteria from young donors resulted in life span extension and delayed behavioral decline. This intervention prevented the decrease in microbial diversity associated with host aging and maintained a young-like gut bacterial community, characterized by overrepresentation of the key genera Exiguobacterium, Planococcus, Propionigenium and Psychrobacter. Our findings demonstrate that the natural microbial gut community of young individuals can causally induce long-lasting beneficial systemic effects that lead to life span extension in a vertebrate model.

genomics↗