GSE132730
Design logic of hypothalamus development mapped by single-cell RNA-seq
Purpose: We aimed to reconstruct the development formation of cellular identities' heterogeneity in the hypothalamus with single-cell RNA sequencing. We planned to track branching process of neurogenesis and follow the formation of cell identities. Results: We integrate single-cell RNA-seq data on 51,199 cells of ectodermal origin, representing critical stages of pre- and postnatal hypothalamus development, supported by anatomical lineage reconstruction to show that bulk neurogenesis in the hypothalamus, dominated by Notch signalling and its interaction with Ascl1, persists until the neonatal period to produce molecularly distinct astrocytes, ependyma, tanycytes and 30 protoclusters of neurons. Alike in adults, the assignment of neurotransmitters and neuropeptides together with transcription factors as positional marks for each neuronal cluster is sufficient to establish the spatially-resolved taxonomy of hypothalamic neurons. By deducing gene regulatory networks, exemplified by hierarchical gene clusters driven by Onecut2/Onecut3 transcription factors for dopamine neurons, we resolve how neuronal lineages diverge into functionally non-overlapping endocrine subtypes. Dopamine neurons are used to illustrate molecular convergence with their shared neurotransmitter identity representing a mismatch to their molecular distances on multidimensional vector spaces. We demonstrate the existence of non-canonical chemotropic axes in the hypothalamus, particularly sequential ligand-receptor switching in the unexpectedly abundant Slit/Robo cassette. Slit2 is identified in ventricular ependymocytes and implicated in repulsing new-born neurons that sequentially express Robo1 and Robo2 receptors for migration and differentiation. Conclusions: Overall, our unbiased map of hypothalamic cell types and extracellular guidance cues uncovers molecular principles shaping the developmental architecture of the mammalian hypothalamus and rationalise how hypothalamic neuronal heterogeneity is transformed into a multimodal neural unit that retains a virtually infinite adaptive potential throughout life. Overall design: To follow the developmental progress in the hypothalamus we obtained 10X Genomics single cell samples of the mouse hypothalamus from several developmental timepoints: E15.5 (n=8), E17.5 (n=7), P0 (n=4), P2 (n=4), P10 (n=3), P23 (n=3).