Mouse Retinal Cell Atlas: Molecular Identification of over Sixty Amacrine Cell Types

Abstract

Amacrine cells (ACs) are a diverse class of interneurons that modulate input from photoreceptors to retinal ganglion cells (RGCs), rendering each RGC type selectively sensitive to particular visual features, which are then relayed to the brain. While many AC types have been identified morphologically and physiologically, they have not been comprehensively classified or molecularly characterized. We used high-throughput single-cell RNA sequencing to profile .32,000 ACs from mice of both sexes and applied computational methods to identify 63 AC types. We identified molecular markers for each type and used them to characterize the morphology of multiple types. We show that they include nearly all previously known AC types as well as many that had not been described. Consistent with previous studies, most of the AC types expressed markers for the canonical inhibitory neurotransmitters GABA or glycine, but several expressed neither or both. In addition, many expressed one or more neuropeptides, and two expressed glutamatergic markers. We also explored transcriptomic relationships among AC types and identified transcription factors expressed by individual or multiple closely related types. Noteworthy among these were Meis2 and Tcf4, expressed by most GABAergic and most glycinergic types, respectively. Together, these results provide a foundation for developmental and functional studies of ACs, as well as means for genetically accessing them. Along with previous molecular, physiological, and morphologic analyses, they establish the existence of at least 130 neuronal types and nearly 140 cell types in the mouse retina.

Cell Atlas of the Chick Retina: Single Cell Profiling Identifies 136 Cell Types

“…ACs are a diverse class of interneurons, most of which form inhibitory (GABAergic or glycinergic) synapses on BCs, RGCs and other ACs. In mammals ACs are the most heterogeneous retinal class (Yan et al 2020a, 2020b; Peng et al,2019). Similarly, ACs formed the most heterogeneous class in chicks, with 59 putative types (Figure 1G, 6A), ranging in frequency from 0.4 to 7.2% of all ACs (Figure 6—figure supplement 1A).…”

“…We asked whether this morphological conservation is accompanied by transcriptomic conservation. To this end, we combined data from the E18/E16 chick atlas with those from our previously published retinal atlases of mouse (Macosko et al, 2015; Shekhar et al, 2016; Tran et al, 2019; Yan et al, 2020a), macaque (Peng et al, 2019) and human (Yan et al, 2020b), and submitted the entire group for clustering. This procedure generated 9 clusters, all of which contained cells from all species (Figure 10A,B).…”

“…Recently, this enterprise has been greatly enhanced by the introduction of methods for high throughput single cell transcriptomic profiling (scRNA-seq), which enable comprehensive and minimally biased sampling of cell types. To date, however, these methods have been applied only to mice and primates (Macosko et al, 2015, Shekhar et al, 2016, Rheaume et al, 2018, Peng et al, 2019, Tran et al, 2019, Yan et al, 2020a,b), restricting use of non-mammalian models and making it difficult to draw evolutionary relationships among species at the molecular level . Here, we address this limitation by using scRNA-seq to generate a cell atlas of the chick retina.…”

“…The retina also contains glial cells: Müller glia in the INL, and in many species, astrocytes and oligodendrocytes in and beneath the GCL (Reichenbach and Bringmann, 2013; Vecino et al, 2016). Altogether, transcriptomic and morphological studies have identified a total of >130 neural (neuronal and glial) cell types in mice and ∼70 in primates (Yan et al, 2020a,b; Peng et al, 2019)…”

Subpopulations of Projection Neurons in the Olfactory Bulb

“…For example, we can acquire various types of object information, such as size and shape, color, brightness, location, and motion, through the visual system ( Wandell, 1995 ). A strategy to process multiple visual submodalities is to enhance the functional diversity of the neuronal circuit by expanding the neuronal heterogeneity in the retina ( MacNeil and Masland, 1998 ; Masland, 2012 ; Baden et al, 2016 ; Yan et al, 2020 ). In the primate visual system, strong evidence suggests that the color and motion of an object are differentially processed through parallel pathways ( Nassi and Callaway, 2009 ).…”