Uncovering Coordinated Multicellular Responses to CNS Injury

Inbal Benhar ¹ Jiarui Ding ¹ Wenjun Yan ² Irene E. Whitney ² Anne Jacobi ^2,3 Malika Sud ¹ Grace Burgin ¹ Karthik Shekhar ¹ Nicholas M. Tran ² Chen Wang ³ Zhigang He ³ Joshua R. Sanes ² Aviv Regev ¹

¹Klarman Cell Observatory, Broad Institute of MIT and Harvard, USA
²Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, USA
³F.M. Kirby Neurobiology Center, Boston Children's Hospital, USA

Non-neuronal cells play key roles in the complex cellular interplay that follows central nervous system (CNS) insult. To understand this interplay at a tissue level, we generated a single-cell atlas of immune, glial and epithelial cells from adult mouse retina before and at multiple time points after axonal injury, identifying rare and undescribed subsets, and delineating changes in cell composition, expression programs, and interactions. Computational analysis charted an inflammatory cascade after injury with three phases. The early phase consisted of reactivation of retinal glia, providing chemotactic signals for immune infiltration, concurrent with infiltration of monocytes from the circulation. In the second phase, these differentiated to macrophage subsets resembling resident border-associated macrophages. In parallel, concurrent with the peak rate of neuronal death, a multicellular interferon program was synchronously activated across resident glia, likely driven by microglia-derived type-I interferon. Our findings provide insights regarding post-injury CNS tissue dynamics and a framework to decipher cellular circuitry, spatial relationships and molecular interactions following tissue injury.