OVERVIEW.
Why demographic aging – i.e., the onset, rate, and duration of adult mortality trajectories – often differs between males and females is not understood. Equally perplexing is how sex-specific demographic aging is underpinned by sex-specific organismal senescence – i.e., the deterioration of biochemical and physiological processes leading to declining function with advancing age. Stated simply, the why and how of sex-specific aging are questions without unifying answers – answers that have broad implications for conservation, agriculture, and human health.
Thus, IISAGE will address a significant knowledge gap in understanding how sex-specific aging arises from mechanisms at the genomic, cellular, organismal, and population levels. So far, progress towards this goal has been made largely by researchers working independently within different biological domains. However, to fully comprehend how sex-specific aging occurs and how it manifests across populations and species, it is essential to integrate these disciplines. Achieving a broadly integrated understanding of sex-specific aging will require interdisciplinary research cutting across molecular, organismal, population, and evolutionary biology. IISAGE will bring together researchers from these diverse, often siloed disciplines to investigate the question: Why do males and females age differently?
THEMES.
For each species, we are measuring a set of cellular aging phenotypes using IISAGE shared methods, and measuring mortality trajectories where possible, and analyzing data via shared deep learning pipelines that incorporate phylogeny. For a subset of species, we are manipulating sex-specific genome architecture, physiology, and sexual-size dimorphism. Phenotypic plasticity in aging phenotypes is being measured in wild populations along thermal clines or in laboratory populations in reciprocal temperature transplants and sex reversal experiments. Together, measurements from diverse species and manipulations analyzed with a unified pipeline will allow us to test contributions of sex determination (Theme 1), organismal biology (Theme 2), and phenotypic plasticity (Theme 3) to sex-specific aging phenotypes. Integrating across themes 1-3, we will test the generalizability of these findings across evolutionary timescales, and test for repeated evolutionary patterns, constraints, and lineage specific phenotypes (Theme 4).
PROJECTS.
The core research activities of IISAGE focus on novel insights into the major mechanisms driving sex differences in aging across animal species. We organize our pursuit of this goal into our four themes, each with three specific projects.
THEME I: How do sex chromosomes and sex determining mechanisms contribute to sex-specific aging?
These projects measure age-specific molecular, cellular, and organismal phenotypes in males and females across animal species that vary in their type of sex chromosomes, genome size, and epigenetic features. Study species range from those without sex chromosomes, where the genomes of males and females are identical at fertilization, to species with fully differentiated heteromorphic sex chromosomes and dosage compensation, and species between these two extremes. These comparative data will be integrated with measures from animals in which we have manipulated heterochromatin and dosage compensation.
Project 1.1 – Exploiting natural variation in sex determination
Co-Investigator(s): Jamie Walters, Richard Meisel, Gerald Wilkinson, Anne Bronikowski, Tony Gamble, Peggy Biga
Project Summary:
Our first approach to identifying how sex chromosomes, sex determination mechanisms, and genome architecture impact sex differences in aging is to measure species across the full range of natural variation in sex determination mechanisms. In amniotes, contrasts of interest include mammals to reptiles, and, within reptiles, genetic versus temperature sex determination. In Lepidoptera, species contrasts between those with old and new Z chromosomes will be undertaken. In flies, species with new sex chromosomes of various ages (including neo-X chromosomes, or proto-sex chromosomes, and ZW chromosomes) will be contrasted with species that bear the ancestral X chromosomes. Quantifying our aging phenotypes in these diverse species will establish how variation in sex determination and sex-specific genome architecture associates with sex-specific aging.
Project 1.2 – Manipulating heterochromatin
Lead-investigator: Nicole Riddle
Project Summary:
Heterochromatin content decreases with age and often differs between sexes. Therefore, in this project, we will alter heterochromatin content, genome size, and transposable element content in D. melanogaster to test the hypothesis that these aspects of genome organization are responsible for sex-differences in age-associated chromatin changes and therefore contribute to sex-specific aging. For all manipulations, we will carry out lifespan assays .
Project 1.3 – Manipulating dosage compensation
Co-investigator(s): Rich Meisel, Erica Larschan, Ashley Webb
Project Summary:
We will manipulate dosage compensation in three species (mouse, D. melanogaster, and blow fly) to test the hypothesis that sex-specific gene regulation of sex chromosomes is responsible for sex differences in aging. Mice, like humans, use an XY chromosome system for sex determination, and dosage compensation occurs through the inactivation of one of the two X chromosomes in females. Most flies also use an XY chromosome system for sex determination, but dosage compensation occurs through the upregulation of the single X chromosome in males.
THEME II: How does variation in physiology and morphology contribute to sex-specific aging?
These projects focus on the role of mitochondrial function, DNA repair efficiency, and size dimorphism in generating sex-specific aging. Each of these factors has been associated with sex differences in aging, but their causal relationships are not yet resolved. Study species include amniotes, fish, and insects, with a focus on closely related species showing differences in sexual size dimorphisms (SSD) and/or sex-specific aging.
Project 2.1 – Exploiting natural variation in SSD and physiology
Co-investigator(s): Jamie Walters, Rich Meisel, Gerald Wilkinson, Peggy Biga, Anne Bronikowski, Tony Gamble
Project Summary:
Our first approach is to define the contribution of mitochondrial function, DNA repair, and SSD to sex- specific aging using IISAGE shared aging phenotypes. Using the set of focal amniote, fish, and insect species, we will determine how mitochondrial function and DNA repair relate to sex-specific aging across species. Species represent naturally occurring biased and unbiased size dimorphism, and endo- vs. ectothermic physiology. Quantifying cellular aging phenotypes in these diverse species will establish how variation in size dimorphism and thermoregulatory mode associate with sex specific aging. Specifically, we will test the hypotheses that the faster aging sex has lower mitochondrial function, more free radical production, and lower DNA repair efficiency.
Project 2.2 – Manipulating cellular stress responses
Co-investigator(s): Nicole Riddle, Ashley Webb
Project Summary:
We will manipulate cellular stress physiology in mouse and D. melanogaster to test the hypothesis that sex-specific responses to cellular stress are responsible for sex differences in aging.
Project 2.3 – Selective Breeding
Co-investigator(s): Nicole Riddle, Richard Meisel
Project Summary:
To explicitly test the impact of sexual size dimorphism (SSD) on sex-specific aging, we will carry out selective breeding experiments in D. melanogaster and D. pseudoobscura. This work in insect species will be complemented by data mining of existing quantitative genetics results from Drosophila and agricultural species (chicken, swine, cattle, fish), where size selection is common and has been ongoing for decades. Samples from young and aged adults of both sexes will be requested for size-selection breeding experiments. The data from insects and agricultural species will show how SSD impacts our aging phenotypes and reveal its role in generating sex-specific aging.
THEME III: How does sex-by-environment plasticity contribute to sex-specific aging?
Interactions between sex and environment, particularly if there are some environments that lack sex-specific aging, suggest that phenotypic plasticity contributes to sex-specific aging. In a few extraordinary species, sex-reversal occurs despite genotypic sex determination. These projects use a quantitative genetic framework to construct sex-specific norms of reaction for aging phenotypes across a range of temperatures.
Project 3.1 – Exploiting natural variation
Co-investigator(s): Gerald Wilkinson, Anne Bronikowski, Tony Gamble
Project Summary:
We will sample wild populations along thermal clines – using either elevational or altitudinal gradients – to determine if certain environmental conditions alter sex differences in aging within each of the following species: big brown bats (Eptesicus fuscus); western terrestrial garter snakes (Thamnophis elegans) ; house geckos (Hemidactylus turcicus); and painted turtles (Chrysemys picta).
Project 3.2 – Laboratory manipulations
Co-investigator(s): Jamie Walters, Rich Meisel, Peggy Biga
Project Summary:
To quantify the extent to which sex differences in aging phenotypes depend on the environment, the following laboratory species will be reared at various temperatures: meal moths (Plodia interpunctella), Apple codling moths (Cydia pomonella), house flies (M. domestica), and southern platyfish (Xiphophorous maculatus).
Project 3.3 – Species with sex reversal
Co-investigator(s): Ashley Webb, Rich Meisel, Peggy Biga
Project Summary:
Both water temperature and early life food intake result in female-to male sex reversal in medaka fish (Oryzias latipes), which will be tested to assess how sex differences in aging are influenced by phenotypic or genetic sex. A similar experiment using “four core genotypes” in mice and sex reversal in house flies will be conducted to determine the impact of genotype versus phenotype on aging.
THEME IV: How repeatable, fixed, and/or labile are sex-specific mechanisms of aging across animal diversity?
These projects will identify the macroevolutionary patterns and processes that govern the evolution of sex-specific aging. These efforts will employ an evolutionary systems biology approach to synthesize the data collected by Themes 1-3 and test hypotheses that require integration across all themes, made possible by carefully selected species for comparative analyses and targeted laboratory manipulations. The analyses will reveal the relationships among sex-specific aging, age-associated genome instability and cellular stress physiology, environmental and genetic variation, and SSD to quantify the constraint and flexibility of sex-specific aging across varying evolutionary timescales.
Project 4.1 – Integrate multi-omics data to identify regulatory evolution of sex-specific aging
Lead-investigator: Ellie Duan
Project Summary:
Regulatory evolution plays an essential role in establishing new traits. Thus, we will identify the gene regulatory basis of sex differences in aging. We will also identify genes and regulatory networks controlling sex-specific aging that are evolutionarily conserved and those that are taxon-specific. The results of these analyses will feed into machine learning (ML) and phylogenetic comparative approaches, with the physiological aging phenotypes, to identify evolutionarily conserved and taxon-specific drivers of sex-specific aging.
Project 4.2 – Implement ML approaches to predict cellular pathways which drive sex-specific aging
Lead-investigator: Ritambhara Singh
Project Summary:
We will interrogate the integrated multi-omics and physiological data by using ML models to develop hypotheses for which cellular pathways drive sex differences in aging. Specifically, we will implement neural networks, which are adept at identifying structures in noisy, nonlinear data automatically. Models like Convolutional Neural Networks have been used successfully to predict gene expression or chromatin accessibility across thousands of genomic sites. Our goal is to extract candidate genomic signals that could drive changes in gene expression, chromatin accessibility, and cellular physiology across sexes and ages – disentangling the complex relationships among the datasets collected by IISAGE.
Project 4.3 – Integrate sex-specific aging with evolutionary phylogenetic constraints
Lead-investigator: Tony Gamble
Project Summary:
Comparative phylogenetic methods, such as phylogenetic generalized least squares analysis, will be used to identify the processes that govern the evolution of sex-specific aging and test existing hypotheses regarding how differences in sex-specific genome architecture across species impact sex differences in aging. We will build on existing approaches that model the evolution of quantitative genomics traits using an Ornstein–Uhlenbeck process (i.e., Brownian motion with a pull toward an optimum value). To those ends, we will incorporate the functional elements identified by the ML approaches (relevant sequences associated with genes, pathways, conservation, etc.) and data from other experiments (mitochondrial function, SSD, etc.) into a phylogenetic model to identify conservation and lineage-specific change. By accommodating phylogeny, we will test for associations between functional genomic data, genome architecture (e.g., sex chromosomes, dosage compensation, genome size), organismal phenotypes, and sex differences in aging.
