The role of epigenetics in RPE heterogeneity with early AMD

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Summary The NEI AMD Pathobiology group concluded that identifying all of the pathogenic signals, prioritizing their contribution relative to one another, and establishing when these signals are pathogenic will lead to effective treatment for each AMD stage. Because preventing or curing early AMD will eliminate the burdens of advanced AMD and reduce its financial burden, this proposal will focus on early AMD. Cellular heterogeneity is a well- recognized phenomenon. While ordered heterogeneity is protective, stress causes disordered heterogeneity that induces disease by aggressive subclones, even if comprised of a limited number of cells. Retinal pigment epithelium (RPE) heterogeneity is well recognized in early AMD, but its pathogenic role is unexplored. The epigenome mechanistically links environmental exposures with the transcriptome to influence biological processes, and epigenetic changes vary across individual cells to cause pathogenic cellular heterogeneity. Smoking, the highest environmental risk factor for AMD, is a powerful epigenetic inducer in part, due to the altered expression of chromatin modification enzymes that can reprogram the transcriptome to disrupt multiple cytoprotective pathways, a fundamental characteristic of a complex disease like AMD. Using ATAC-seq and RNA-seq, we previously linked reduced chromatin accessibility in promoter regions of genes with the RPE transcriptome in early AMD eyes, implicating the RPE as a driver of early AMD. Furthermore, iPSC-RPE cells treated with smoke had chromatin accessibility profiles similar to the RPE from early AMD eyes. While valuable, this global approach does not define RPE heterogeneity or the impact of heterogeneity on RPE functions related to AMD pathobiology. The objective is to define RPE heterogeneity in early AMD due to reduced chromatin accessibility from smoking by addressing the hypothesis that pathologic RPE subsets contribute to early AMD through transcriptome changes induced by epigenetic or genetic alterations. SA1. Define pathogenic RPE heterogeneity by regional location in aging and early AMD by chromatin accessibility and transcriptome modifications. ScRNA-seq and scATAC-seq will be used on the RPE from the macula and periphery from aging and early AMD genotyped globes, and chromatin accessibility and pathologic pathways from cellular subsets will be visualized by ATAC-see and immunohistochemistry. SA2. Determine the extent that RPE heterogeneity i) develops due to chromatin accessibility and transcriptional heterogeneity with aging or smoking, and ii) impacts RPE function in a model of early AMD. ScATAC-seq and scRNA-seq will be used to assess chromatin accessibility and transcriptional RPE heterogeneity in wild-type (littermates), HDAC11-/-, and WT mice treated with HDAC11 inhibitor Mocetinostat exposed to chronic cigarette smoke. The spatial distribution of RPE heterogeneity will be identified using immunofluorescence of biomarkers of cellular subsets and ATAC-see and impact on RPE function will be assessed.