Single-cell spatial transcriptomics of inherited retinal degeneration reveals broad and focal organization of disease responses

Abstract Inherited retinal degenerations are largely monogenic disorders characterized by progressive photoreceptor dysfunction and death. Although the transcriptomic responses to inherited degeneration are well-characterized, how these responses are spatially organized across the retinal axis has not been mapped. Here, we used seqFISH to spatially profile 173 cell identity and degeneration-associated genes with single-cell, single-transcript resolution in male wild-type and LCA5 gt/gt mouse retinas at early, intermediate, and advanced disease stages. In early disease, rod injury and stress response markers were enriched in the superior retina, while rod function and identity markers were enriched in the inferior retina. Nested within the broader superior-inferior organization, a coordinated rod injury response comprising Edn2 , Fgf2 , Socs3 , and Stat3 was organized into focal regions on the order of 100 μm in width, with high-response regions directly adjacent to low-response regions. These focal regions were locally enriched for markers of Müller reactive gliosis and rod stress responses. Our single-cell spatiotemporal map reveals that transcriptional responses to degeneration vary at both the broad and focal scales, and offers a framework for investigating how local tissue properties and interactions among neighboring cells may contribute to disease progression.