SummaryThe mammalian nervous system executes complex behaviors controlled by specialized, precisely positioned, and interacting cell types. Here, we used RNA sequencing of half a million single cells to create a detailed census of cell types in the mouse nervous system. We mapped cell types spatially and derived a hierarchical, data-driven taxonomy. Neurons were the most diverse and were grouped by developmental anatomical units and by the expression of neurotransmitters and neuropeptides. Neuronal diversity was driven by genes encoding cell identity, synaptic connectivity, neurotransmission, and membrane conductance. We discovered seven distinct, regionally restricted astrocyte types that obeyed developmental boundaries and correlated with the spatial distribution of key glutamate and glycine neurotransmitters. In contrast, oligodendrocytes showed a loss of regional identity followed by a secondary diversification. The resource presented here lays a solid foundation for understanding the molecular architecture of the mammalian nervous system and enables genetic manipulation of specific cell types.

The primary sensory system requires the integrated function of multiple cell types, although its full complexity remains unclear. We used comprehensive transcriptome analysis of 622 single mouse neurons to classify them in an unbiased manner, independent of any a priori knowledge of sensory subtypes. Our results reveal eleven types: three distinct low-threshold mechanoreceptive neurons, two proprioceptive, and six principal types of thermosensitive, itch sensitive, type C low-threshold mechanosensitive and nociceptive neurons with markedly different molecular and operational properties. Confirming previously anticipated major neuronal types, our results also classify and provide markers for new, functionally distinct subtypes. For example, our results suggest that itching during inflammatory skin diseases such as atopic dermatitis is linked to a distinct itch-generating type. We demonstrate single-cell RNA-seq as an effective strategy for dissecting sensory responsive cells into distinct neuronal types. The resulting catalog illustrates the diversity of sensory types and the cellular complexity underlying somatic sensation.

Oligodendrocytes have been considered as a functionally homogenous population in the central nervous system (CNS). We performed single-cell RNA-Seq on 5072 cells of the oligodendrocyte lineage from ten regions of the mouse juvenile/adult CNS. Twelve populations were identified, representing a continuum from Pdgfra+ oligodendrocyte precursors (OPCs) to distinct mature oligodendrocytes. Initial stages of differentiation were similar across the juvenile CNS, whereas subsets of mature oligodendrocytes were enriched in specific regions in the adult brain. Newlyformed oligodendrocytes were found to be resident in the adult CNS and responsive to complex motor learning. A second Pdgfra+ population, distinct from OPCs, was found along vessels. Our study reveals the dynamics of oligodendrocyte differentiation and maturation, uncoupling them at a transcriptional level and highlighting oligodendrocyte heterogeneity in the CNS. *Correspondence to: sten.linnarsson@ki.se, goncalo.castelo-branco@ki.se. Additional Author notes: SM, AZ, HL, WDR, SL and GC-B designed the experiments. PE, EA, JH-L, TH, WDR, SL and GC-B, senior authors, obtained funding. SM, AZ, SC, HH, RAR, DG, MH, AMM, GLM, FR, HL, LX, EF performed experiments. LX, HL and WDR have priority of observation of the rapid differentiation of oligodendrocytes in the complex motor wheel paradigm. SM, AZ, DvB, AMF, GLM, PL analysed data. SM, AZ, SL and GC-B wrote the paper, with the assistance and proofreading of all authors. Oligodendrocytes ensheath axons in the CNS, allowing rapid saltatory conduction and providing metabolic support to neurons. While a largely homogeneous oligodendrocyte population is thought to execute these functions throughout the CNS (1), these cells were originally described as morphologically heterogeneous (2). It is thus unclear if oligodendrocytes become morphologically diversified during maturation through interactions within the local environment, or if there is intrinsic functional heterogeneity (3-5). We analyzed 5072 transcriptomes of single cells expressing markers from the oligodendrocyte lineage, isolated from ten distinct regions of the anterior-posterior and dorsal-ventral axis of the mouse juvenile and adult CNS (Fig. 1A and 1B). Biclustering analysis (6) ( Fig. S1B and S15), hierarchical clustering ( Fig. 1C) and differential expression analysis (Supporting File Supplementary Excel S1 and S2) led to the identification of thirteen distinct cell populations. t-Distributed Stochastic Neighbour Embedding (t-SNE) projection ( Fig. 2A) indicated a narrow differentiation path connecting OPCs and myelinforming oligodendrocytes, diversifying into six mature states, which was supported by pseudo-time analysis (Fig. S2A-B). Europe PMC Funders GroupOPCs co-expressed Pdgfra and Cspg4 (Figs. 2B, S1B and S10) and 10% co-expressed cell cycle genes ( Fig. S2E-F), consistent with a cell division turnover of 19 days in the juvenile cortex (7). Several genes identified in OPCs were previously associated with astrocytes/ radial glia (6) (Fabp7 an...

During vertebrate development, neuronal survival depends on target-derived neurotrophic factors. Brain-derived neurotrophic factor (BDNF), a member of the neurotrophin family, can prevent the death of particular peripheral sensory neurons in vitro, and of central motor neurons as well as dopaminergic and cholinergic neurons of the basal forebrain during development. It also prevents the death of motor neurons and midbrain dopaminergic neurons induced by lesions. Here we show that mutant mice lacking BDNF have severe deficiencies in coordination and balance, associated with excessive degeneration in several sensory ganglia including the vestibular ganglion. The few remaining vestibular axons fail to contact the vestibular sensory epithelia, and terminate in the adjacent connective tissue. Survival of sympathetic, midbrain dopaminergic and motor neurons is not affected. These results indicate that BDNF is required for the survival and target innervation of particular neuronal populations.