Single cell profiling of non-neuronal retinal cells reveals dynamic multicellular responses to central nervous system injury

Non-neuronal cells play key roles in the complex cellular interplay that follows central nervous system (CNS) insult. To assess this interplay, we generated single-cell atlases of immune, glial and epithelial cells from adult mouse retina before and at multiple times after axonal transection (optic nerve crush; ONC), delineating changes in their composition, expression, and interactions. After injury, glial reactivation was coupled with chemokine upregulation and a unique retinal pigment epithelial (RPE) cell state. We resolved dynamic trajectories of mononuclear phagocytes, identified resident Ms4a7+MHC-IIhi and Ms4a7+MHC-IIlo subsets, and demonstrated that CCR2+ monocytes give rise to macrophages with overlapping signatures. We documented synchronized multicellular programs and interactions among neurons, glia, RPE and immune cells, highlighting coordinated gliosis, immune activation, and an interferon-response program. Finally, we mapped expression of human retinal disease-related genes by retinal and eyecup cells. Our atlas helps decipher the cellular circuitry, spatial relationships and molecular interactions following CNS injury. In these experiments, we FACS sorted for immune cells (CD45), Müller glia (GLAST), astrocytes (CD140a) and retinal pigment epithelial cells from dissociated retinas and eyecups of adult (6-8 wk old) mice, including uninjured controls, and at 6 time points following optic nerve crush (12h, 1d, 2d, 4d, 1w, 2w). Single cells were subjected to 10X Chromium library prep and RNA sequencing.