Continuous and discrete neuron types of the adult murine striatum

The striatum is a large brain region containing two major cell types: D1 (dopamine receptor 1) and D2 (dopamine receptor 2) expressing spiny projection neurons (SPNs). We explored neuronal heterogeneity in the adult murine striatum using single-cell RNA-seq of SPNs combined with quantitative RNA in situ hybridization (ISH). We developed a novel computational algorithm that distinguishes discrete versus continuous cell identities in scRNA-seq data, and used it to show that SPNs in the striatum can be classified into four major discrete types with little overlap and no implied spatial relationship. Within these discrete classes, we find continuous variation along multiple spatial gradients axes of expression; these gradients define anatomical location by a combinatorial mechanism. These gradients correlate well to previously-mapped gradients of connectivity. Using these insights, we discovered novel spatially localized regions of the striatum, one of which contains patch-D2 SPNs that express Tac1, Htr7, and Th. Intriguingly, we found one subtype that strongly co-expresses both D1 and D2 dopamine receptors, and uniquely expresses a rare D2 receptor splice variant. Our results elucidate the hierarchy of neuronal identity and suggest that neuronal circuitry has a substructure at far higher resolution than is typically interrogated which is defined by the precise identity and location of a neuron.