Comparative genomics and epigenomics of aging

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SUMMARY: The aging process can be naturally accelerated and decelerated during evolution leading to significant diversity in lifespan among related species. Mammals represent a particularly convenient system to examine this diversity at the molecular level, because these animals are characterized by a nearly hundred-fold difference in lifespan and their tissues and cultured cells are readily available. Unbiased characterization of genes and processes that are associated with natural changes in lifespan within mammals may lead to the development of approaches that target the aging process and possibly delay it. We hypothesize that mammalian lifespan is adjusted through a combination of common and lineage-specific processes and provide preliminary data in support of this idea. In the ongoing phase of the PPG we generated exciting data that support our general approach to lifespan control. We generated comprehensive molecular profiles across mammals, including species of exceptional longevity. These datasets include RNAseq, metabolite profiling, and chemical element profiling as well as the genomes of long-lived naked mole rat and beaver. We also generated a DNA methylation clock for mice and found that it correctly reports the effects of longevity interventions. We propose to utilize these tools and approaches to address, in close collaboration with other Projects and Cores, critical questions in our understanding of natural control of mammalian lifespan. Specifically, we propose to examine: (1) Molecular features underlying longevity in mammals. We will utilize the profiles we generated to identify molecular features and their combinations, with a focus on gene expression and metabolites, linked with longevity, ultimately building molecular signatures of long-lived species (with Core C). We will also carry out gene expression and metabolite profiling analyses of beaverized SIRT6 mice (with Project 1 and Core B), naked mole rat HAS2 transgenic mice, and mice treated with hyaluronidase inhibitors (with Project 2 and Core B), providing critical molecular insights into the mechanisms by which these genes promote longevity. (2) Genomics of long-lived rodents. We will carry out comprehensive annotation of new, much improved assemblies of naked mole rat and beaver genomes (with Core C), in turn providing critical resources for Projects, 1, 2 and 3. We will also focus on the evolution of DNA repair and chromatin remodeling genes and characterization of gene loss and gain in these species. (3) Applications of the epigenetic clock to mouse models of longevity. We have recently developed a mouse DNA methylation clock, which we will apply to the animal and cell culture models examined in the PPG (with Projects 1, 2, and 3, and Cores B and C). (4) Development and application of the naked mole rat epigenetic clock. We will utilize naked mole rats differing in age (with Project 2 and Core B), quantify age-dependent patterns of DNA methylation, and develop and apply a molecular marker of biological age.