Uncovering the molecular identity of retinal cell types, and their responses to nerve injury using single-cell transcriptomics

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ABSTRACT Neurons of the central nervous system (CNS) have been historically categorized into discrete "types" based on structure, physiological responses, connectivity patterns, and molecular profiles. Heterogeneity can have other consequences- e.g. recent studies have found that some neuronal types in the retina are more resilient than other types to optic nerve injury, an event that leads to irrecoverable damage in vision. My project combines cutting-edge single-cell genomic technologies, advanced computational data analysis and molecular tools to define heterogeneity of neuronal types comprehensively, to connect molecular definitions to histology, and explore the functional consequences of this heterogeneity during nerve injury. I will focus on a tractable system, the mouse retina, which communicates visual responses to the brain. It is as complex as any other region of the brain (containing ~120 neuronal types), but benefits from having a compact, accessible structure, and experimental tools make it especially suited for detailed analyses. Building on my previous postdoctoral work, this project will, 1) Complete the census of the mouse retina, which will the first for any CNS region, by inferring molecular taxonomies of two of its most heterogenous classes (amacrines and ganglion cells) from data collected using high-throughput single-cell RNA-sequencing. Using the mouse census, initiate a similar mapping of the macaque retina, which is harder to access experimentally, but shares important features with humans that are absent in mice. 2) Conduct a systematic investigation of cell-type specific responses in the retina to optic nerve injury. This usually leads to a rapid, stereotypic death of retinal ganglion cells (RGCs), but a recent study by my colleagues reported that some RGC types are more resilient than others. Here, using 1) as a resource, I will identify factors, cell intrinsic and extrinsic, that make these RGC types resilient. 3) Selective resilience of cell types is now recognized as a feature of diseases like glaucoma and stroke. Therapies therefore need to cater to different cell types. To learn more, and derive general principles, I will examine the impact of known therapeutic interventions on the survival of different RGC types, and the underlying molecular responses, within the optic nerve injury model. Taken together, my project will derive substantial molecular information underlying neuronal heterogeneity in the mouse and macaque retina and general principles for cell-type selective resilience following CNS injury in mice. The lessons from this work will provide valuable guidance for similar studies in less accessible regions of the brain (e.g. cerebral cortex).