Abstract/Summary
Aging is the principal risk factor for age-related macular degeneration (AMD), a neurodegenerative disease
characterized by the irreversible loss of vision. Clinical and mouse studies indicate that consumption of diets with
higher dietary glycemic indices increase AMD risk. Atrophy of the retinal pigmented epithelium (RPE) layer is an
AMD hallmark that precedes photoreceptor cell loss. However, the mechanisms underlying RPE impairment with
aging and exacerbation by poor diet are unclear. Thus, therapeutic approaches to maintain RPE function with
aging and prevent AMD are yet to be developed. Epigenetic processes (DNA modifications and chromatin
accessibility) in the RPE may play a central mechanistic role in the pathogenesis and progression of AMD. DNA
modifications, [cytosine base methylation and hydroxymethylation (mC and hmC respectively)], are fundamental
regulators of DNA accessibility and gene regulation/expression. A barrier to progress in understanding the role
of epigenetic mechanisms in RPE aging and DNA modifications in particular, has been the lack of quantitatively
accurate, genome-wide data in this specific cell type. Without the knowledge of the specific genomic locations
of altered modifications/accessibility with aging it is impossible to design mechanistic studies that unravel the
functional effects of epigenetic reconfiguration. Therefore, the critical next step for the field is to generate these
genome-wide maps of mC and hmC in CG and CH contexts and genomic accessibility in the primary cellular
site of AMD pathogenesis, the RPE, from both sexes across the lifespan. To address this critical issue, we have
developed a cell-type specific, tamoxifen-inducible Cre, transgenic NuTRAP model to allow isolation of nucleic
acids (DNA & RNA), specifically from RPE cells. In Aim 1, changes in mC/hmC and chromatin accessibility
patterns with aging will be examined by whole genome oxidative bisulfite sequencing (WGoxBS) and ATAC-seq
in RPE. In Aim 2, the RPE-specific differential changes in the translatome will be identified as a function of aging.
In prior studies we have determined that age-related DNA modification changes can be prevented by caloric
restriction. In aim 3, we will interrogate the potential of Western and ketogenic dietary patterns, in combination
with impaired oxidative stress resolution pathways, to exacerbate or ameliorate changes in the RPE epigenome
and gene expression profiles. Paired epigenomic and transcriptomic data from the same animals will be used
to: 1) assess aging with ‘epigenetic clocks’ in RPE, 2) determine the role of altered modification patterns in age-
and dietary/oxidative stress- related changes in gene expression, 3) determine enrichment of differential
modifications/accessibility in regulatory regions of the genome, and 4) identify and refine genomic loci for
epigenome editing. These studies will determine critical genomic regions with altered DNA modification patterns
that can be manipulated in future interventional studies. The ultimate goal of the research is to develop clinical
interventions that target the RPE epigenome to maintain visual function with aging and prevent AMD.