Studying the Epigenetic Regulation of Stem Cell Aging and Rejuvenation

Abstract

Across nearly all organisms, aging is considered a multifactorial process characterized by a loss of molecular, cellular, and tissue integrity, resulting in age-associated disorders and ultimately death. The specific mechanisms that underlie this dysfunction include intra- and extra-cellular changes, but regardless of their origin, the majority of them converge on the aging cell’s epigenome. In addition to being a central node in aging pathologies, the epigenome has the potential to be modified, presenting a particularly appealing target for intervention. Therefore, a better understanding of the epigenetic underpinnings of aging is necessary, and the two studies that make up this dissertation seek to better understand this topic. In the first study, we sought to examine the cellular determinants of DNA methylation age predictors, also known as epigenetic clocks, which are among the most widely used and accurate aging biomarkers currently available. Importantly, these age predictors are built on DNA methylation profiles of bulk tissues. Therefore, our understanding of the influence of particular cell types on these clocks is limited. To address this question, we analyzed various cellular subpopulations including stem versus differentiated cells as well as proliferative versus quiescent cells throughout lifespan across multiple tissues in mice. Interestingly, we observed a previously unappreciated variability in epigenetic age among adult stem cell populations that appeared to correlate with tissue turnover. Fittingly, we were able to verify that forced stem cell proliferation led to increases in epigenetic age. Moreover, we experimentally demonstrated that age-associated changes in cell type composition within aging tissues have the potential to skew epigenetic clocks. Collectively, the insights into some of these cellular drivers will inform how results from these clocks are used and interpreted in the future. In our second study, we examined the functional roles of histone post-translational modifications (PTMs) in hematopoietic stem cell (HSC) aging. With age, HSCs exhibit defects including but not limited to biased differentiation and aberrant self-renewal, which contribute to various age-associated pathologies including blood cancers and increased susceptibility to infection. Yet, the molecular drivers of this process are largely unknown. While others have correlated epigenetic changes, specifically histone PTMs, with aging hallmarks, little has been done to systematically test the function of these marks in aging HSCs. Intriguingly, we show that selective down regulation of the repressive mark, histone 3 lysine 9 (H3K9) methylation, in HSCs ameliorates multiple aging hallmarks and also leads to functional improvements in HSC self-renewal. Overall, this work identifies a novel regulator of HSC aging and describes a strategy to functionally perturb H3K9 methylation to alleviate age-associated defects in the HSC compartment. Taken together, the work in this dissertation provides novel mechanistic insights into epigenetic processes integral to aging biology. We hope the findings from these projects will help inform the creation of (i) more robust tools that measure aging and (ii) more tractable interventions to ameliorate age-associated pathologies.