Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects underlying impaired adult neurogenesis

Abstract

Neural stem cells (NSCs) contribute to plasticity and repair of the adult brain. Niches harboring NSCs are crucial for regulating stem cell self-renewal and differentiation. We used single-cell RNA profiling to generate an unbiased molecular atlas of all cell types in the largest neurogenic niche of the adult mouse brain, the subventricular zone (SVZ). We characterized > 20 neural and non-neural cell types and gained insights into the dynamics of neurogenesis by predicting future cell states based on computational analysis of RNA kinetics. Furthermore, we apply our single-cell approach to mice lacking LRP2, an endocytic receptor required for SVZ maintenance. The number of NSCs and proliferating progenitors was significantly reduced. Moreover, Wnt and BMP4 signaling was perturbed. We provide a valuable resource for adult neurogenesis, insights into SVZ neurogenesis regulation by LRP2, and a proof-of-principle demonstrating the power of single-cell RNA-seq in pinpointing neural cell type-specific functions in loss-of-function models. KEYWORDSadult neurogenesis, neurogenic niche, single-cell RNA sequencing, adult neural stem cells, subventricular zone, LDL-receptor related protein, RNA velocity HIGHLIGHTS  unbiased single-cell transcriptomics characterizes adult NSCs and their niche  cell type-specific signatures and marker genes for 22 SVZ cell types  Free online tool to assess gene expression across 9,804 single cells  cell type-specific dysfunctions underlying impaired adult neurogenesis

Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis

“…Our analyses provide a molecular characterization of the NSC transition to and from dormancy. Consistent with other studies of quiescent stem cells (reviewed in van Velthoven and Rando, 2019), including quiescent adult NSCs (Llorens-Bobadilla et al, 2015;Mizrak et al, 2019;Kalamakis et al, 2019;Zywitza et al, 2018;Basak et al, 2018;Dulken et al, 2017;Shin et al, 2015;Berg et al, 2019;Hochgerner et al, 2018;Artegiani et al, 2017), our data indicate that dormancy involves a broad dampening of cell biological processes associated with an active state. As embryonic RPs transitioned to postnatal dNSCs, they shut down processes associated with cell division, transcription, RNA metabolism and protein translation, processing, and trafficking.…”

Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics

“…To further analyze the epidermal differentiation dynamics in UW skin, we performed RNA velocity analysis, in which the direction of state transitions and the extent of change in RNA dynamics are indicated by the vectors (arrows) and their lengths, respectively (La Svensson and Pachter, 2018). The Col17a1 Hi and SP1 states showed small RNA velocities (short or no arrows), known to associate with both quiescent and terminally differentiated cells (Svensson and Pachter, 2018;Zywitza et al, 2018), whereas the ER, GA, and SP2 states exhibited large RNA velocities (Figure 7F). Transition from the Col17a1 Hi state to the ER state was associated with increasing arrow lengths, which may reflect a rapid activation in RNA dynamics (e.g., increased RNA splicing efficiency; see below).…”

A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury

“…Astrocytes close to the lesion form Ascl1-expressing transit-amplifying cells before generating proliferative clusters of doublecortin (Dcx) + neuroblasts and mature neurons. Single-cell RNA sequencing (scRNA-seq) revealed that conditional knockout of Rbpj-k drives induction of a neural stem cell program in cortical astrocytes that resembles canonical neurogenic processes, as observed in transcriptome analyses of the germinal niche (Llorens-Bobadilla et al, 2015;Zywitza et al, 2018). However, only after a stab wound injury can the neurogenic program be instigated, and Notch-deficient cortical astrocytes are able to progress through amplifying cell divisions to generate GABAergic interneurons.…”