Translatomic response of retinal Muller glia to acute and chronic stress

Analysis of retina cell type-specific epigenetic and transcriptomic signatures is crucial to understanding the pathophysiology of retinal degenerations such as age-related macular degeneration (AMD) and delineating cell autonomous and cell-non-autonomous mechanisms. We have discovered that Aldh1l1 is specifically expressed in the major macroglia of the retina, Muller glia, and, unlike the brain, is not expressed in retinal astrocytes. This allows use of Aldh1l1 cre drivers and Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) constructs for temporally controlled labeling and paired analysis of Muller glia epigenomes and translatomes. As validated through a variety of approaches, the Aldh1l1cre/ERT2-NuTRAP model provides Muller glia specific translatomic and epigenomic profiles without the need to isolate whole cells. Application of this approach to models of acute injury (optic nerve crush) and chronic stress (aging) uncovered few common Muller glia-specific transcriptome changes in inflammatory pathways, and mostly differential signatures for each stimulus. The expression of members of the IL-6 and integrin-linked kinase signaling pathways was enhanced in Muller glia in response to optic nerve crush but not aging. Unique changes in neuroinflammation and fibrosis signaling pathways were observed in response to aging but not with optic nerve crush. The Aldh1l1cre/ERT2-NuTRAP model allows focused molecular analyses of a single, minority cell type within the retina, providing more substantial effect sizes than whole tissue analyses. The NuTRAP model, nucleic acid isolation, and validation approaches presented here can be applied to any retina cell type for which a cell type-specific cre is available.

Automated summary

Analysis of specific epigenetic and transcriptomic signatures in retina cell types is important for understanding retinal degenerative diseases. This study discovers a method to specifically analyze the epigenomes and translatomes of Muller glia cells. Applying this method to acute injury and chronic stress models reveals different transcriptomic changes in Muller glia cells for each stimulus.