Cell Atlas Of The Chick Retina: Single Cell Profiling Identifies 150 Cell Types

Retinal structure and function have been studied in many vertebrate orders, but molecular characterization has been largely confined to mammals. Here, we used single-cell RNA sequencing (scRNA-seq) to generate a cell atlas of the chick retina. From ~40000 single cell transcriptomes, we identified ~150 cell types distributed among the six classes conserved across vertebrates – photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and glial cells. To match molecular profiles to morphology, we adapted a method for CRISPR-based integration of reporters into selectively expressed genes. For Müller glia, we found that transcriptionally distinct cells were regionally localized along the anterior-posterior, dorsal-ventral and central-peripheral retinal axes. We also identified immature photoreceptor, horizontal cell and oligodendrocyte types that persist into late embryonic stages. Finally, we analyzed relationships among chick, mice and primate retinal cell types. Taken together, our results provide a foundation for anatomical, physiological, evolutionary, and developmental studies of the avian visual system. Overall design: We used scRNA-seq to profile cells from the chick retina. From ~40,000 single cell transcriptomes, we identified cells of all 6 classes named above (PR, HC, BC, AC, RGC and glia) and used unsupervised methods to divide them into ~150 clusters. We show that 136 of the groups represent putative cell types, with others corresponding to developmental intermediates. We then devised a method for CRISPR-based somatic cell integration of fluorescent reporters into genes shown by scRNA-seq to be expressed by specific types. Using this technique along with other histological methods, we matched molecular profiles to morphology for many neuronal types. We also found a positional signature in Mu¨ller glia, with distinct expression patterns based on their location along the anterior-posterior, dorsal-ventral and central-peripheral retinal axes. Finally, we compared the cell classes and types of chick retina with those of three mammalian species – mouse, macaque and human – demonstrating conserved molecular features of all classes and some types, along with multiple differences between chick and mammals. Together, our results provide new insights into retinal structure and evolution generally, as well as a foundation for anatomical, physiological, and developmental studies of avian retina. GEO series of mammalian data used for comparison: Mouse rods: GSE63472 Mouse Bipolar cells: GSE81904 Mouse all other classes: GSE149715 Macaque all classes: GSE118852 Human all classes: GSE148077