Using DNA Methylation Analysis As a Tool to Develop in Vitro Models for Aging Studies

Aging is the leading risk factor for neurodegenerative diseases. To develop better therapeutics and treatment strategies for these disorders, it is important to understand the aging process as well as to develop models of aged organisms, tissues, and cells. However, due to ethical reasons and long timescales, this is challenging in a human context. Human pluripotent stem cells (hPSCs) can be differentiated to neural tissues and cells but often reflect fetal states. Our aim is to develop an in vitro model for accelerated aging using hPSC-derived neurons and cerebral organoids. Prior work has investigated the use of various perturbations to induce neurotoxicity or aging related phenotypes like heterochromatin reorganization. Here we exposed human neurons and organoids to progerin overexpression and oxidative stress and assessed phenotypic changes relevant to aging. To assess induction of aging in as unbiased a manner as possible, without relying on proxy cellular phenotypes that could arise directly from the perturbations themselves, we will measure whole genome DNA methylation profiles (DNAm). Whole genome DNAm profiling has been used to develop age-predicting algorithms called Epigenetic Clocks. We plan to apply the novel Fetal Brain Clock (FBC), to predict the chronological age of our perturbed samples. In parallel, we are developing a comparative analysis of modified 2D neurons, organoids, and human brain tissues. These studies will contribute to developing a standard aging technique for in vitro models like cerebral organoids. Furthermore, this model may be used to examine biomarkers and molecular processes relevant to neurodegenerative disorders.