Epigenetic Analysis of iPS Cell Models of Aging and Alzheimer's Disease

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DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (14) Stem Cells, and specific Challenge Topic, 14-AG-101: Induced Pluripotent Stem (iPS) Cells for Aging and Neurodegeneration Research. Aging is accompanied by cognitive decline in a major segment of the population and is the primary risk factor for Alzheimer's disease (AD). Despite this central role in disease pathogenesis and morbidity, the aging of the brain is not well understood at a molecular level. The overall goal of this application is to gain new insights into human aging and neurodegenerative disease by exploring the physiology and epigenetics of iPS cells and iPS cell-derived neurons generated from skin fibroblasts of individuals at different ages and with AD. Transcriptional profiling of AD fibroblasts compared with age-matched controls shows changes in the expression of cell death genes, synaptic genes and genes encoding proteins involved in epigenetic modification of chromatin. Moreover, some of these changes also appear in the expression profile of the prefrontal cortex in AD. Our working hypothesis is that epigenetic changes in synaptic and cell death regulatory genes contribute to the aging of the brain and play a role in the pathogenesis of AD. This idea is supported by our published studies which show that repression of neuronal gene expression, particularly synaptic genes, is a prominent feature of human brain aging that has evolved in long-lived primates (1, 2). Our unpublished results further suggest that these age-related gene expression changes may reflect epigenetic changes in chromatin, and exhibit an altered pattern in AD leading to altered gene expression. This project will bring together a multidisciplinary team with broad expertise in neurobiology, disease biology and genomics from Harvard Medical School, the Dana Farber Cancer Institute and the Broad Institute to characterize iPS cell lines and neurons derived from dermal fibroblasts of individuals across the adult human lifespan (age 24-90 years) and patients with sporadic AD. Differentiation of iPS cells to neurons in vitro will be characterized by immunocytochemical, electrophysiologic and genomic criteria and compared with primary human cortical neurons and neural progenitors. Of particular interest will be the ability of iPS neurons to form functional synapses and survive under stress-related conditions associated with aging and AD, such as oxidative stress and exposure to amyloid ¿-protein (A¿), and whether this changes in cells derived from AD patients. Transcriptional and epigenomic profiling of donor-derived iPS cells and iPS neurons will be performed using microarrays and by applying recent innovations in deep sequencing chromatin immunoprecipitation (ChIP- seq). This multidisciplinary approach will evaluate iPS cells as models of aging and neurodegeneration, and explore the roles of gene regulation and epigenetics. Since we have already established iPS-like cell lines from normal aged and AD donors, we anticipate that these goals can be accomplished in the two year time frame of a challenge application. PUBLIC HEALTH RELEVANCE: Presently about 4 million Americans suffer from Alzheimer's disease (AD) constituting an enormous financial, emotional and productivity burden on society. Our studies suggest that epigenetic modifications of the genome may play a major role in the aging of the human brain, and may contribute to the vulnerability of the aging brain to AD. This study will determine if neurons derived from induced progenitor stem cells can serve as a model to study the role of epigenetics in aging and AD, providing a new level of analysis of the human brain in health and disease.