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. Overall design: 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.