Comparative Single Cell Profiling of Retinal Development

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Project Summary Age-related macular degeneration (AMD) affects the central region of the retina important for high-acuity daytime vision, causing blindness or severe vision impairment as a result of the loss of photoreceptors from the cone-dominant fovea. Directed differentiation of retinal progenitor cells into cone photoreceptors shows promise as a therapy for AMD and other retinal dystrophies. However, commonly used model organisms such as the mouse have rod-dominant retinas, which makes them poor models for the human fovea. 13-lined ground squirrel retinas, however, have a cone/rod ratio and cone subtype composition that closely matches that of the human fovea. This project will use the 13-lined ground squirrel as a model to identify gene regulatory networks that drive development of retinal cones and test whether gain of function of candidate genes can promote cone development in mice. I hypothesize that differential activation of gene regulatory networks controlling photoreceptor development underlie the differences in the cone/rod ratio between the mouse and 13-lined ground squirrel and between the peripheral human retina and the cone- dominant fovea. To address this hypothesis, I propose two Aims. Aim 1: Comprehensively profile retinal development in the 13-lined ground squirrel at single-cell resolution using both scRNA-seq and scATAC-seq to identify candidate gene regulatory networks that control evolutionary changes in the cone/rod photoreceptor ratio. This data will allow me to identify key gene regulatory networks that control development of the 13-lined ground squirrel retina and will identify plausible causes for the difference in the production of photoreceptor subtypes between 13-lined ground squirrel and mouse and between the fovea and peripheral human retina. Aim 2: Test the functional consequences of overexpression of candidate genes in mice that are predicted to promote cone specification in 13-LGS. This will identify which changes are necessary to control the cone/rod ratio in the developing mouse retina. By understanding the gene regulatory networks that control photoreceptor proportions in the retina, I will be able to direct mouse retinal progenitors to generate a cone-dominant retina, ultimately providing an improved animal model for AMD progression and cell therapy.