Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

Abstract

Somatic stem cells contribute to tissue ontogenesis, homeostasis, and regeneration through sequential processes. Systematic molecular analysis of stem cell behavior is challenging because classic approaches cannot resolve cellular heterogeneity or capture developmental dynamics. Here we provide a comprehensive resource of single-cell transcriptomes of adult hippocampal quiescent neural stem cells (qNSCs) and their immediate progeny. We further developed Waterfall, a bioinformatic pipeline, to statistically quantify singe-cell gene expression along a de novo reconstructed continuous developmental trajectory. Our study reveals molecular signatures of adult qNSCs, characterized by active niche signaling integration and low protein translation capacity. Our analyses further delineate molecular cascades underlying qNSC activation and neurogenesis initiation, exemplified by decreased extrinsic signaling capacity, primed translational machinery, and regulatory switches in transcription factors, metabolism, and energy sources. Our study reveals the molecular continuum underlying adult neurogenesis and illustrates how Waterfall can be used for single-cell omics analyses of various continuous biological processes.

Fine processes of Nestin-GFP–positive radial glia-like stem cells in the adult dentate gyrus ensheathe local synapses and vasculature

“…Single-cell RNA sequencing as well as subsequent electrophysiological analyses have recently shown that NGP RGL stem cells express functional glutamate receptors (ref. 57; but see also ref. 58 for contrast and ref.…”

Molecular profiling of aged neural progenitors identifies Dbx2 as a candidate regulator of age‐associated neurogenic decline

“…This hypothesis is consistent with the previously described alterations in the cell cycle of aged NSPCs (Apostolopoulou et al., 2017; Daynac et al., 2014, 2016; Stoll et al., 2011). Dbx2 is part of a cohort of transcription factor genes that are enriched in quiescent NSPCs of the SGZ and SVZ and are downregulated in NSPCs actively engaged in cell proliferation and neurogenesis (Codega et al., 2014; Shin et al., 2015), thus suggesting that Dbx2 may negatively regulate NSPC proliferation in both adult neurogenic niches. Elevated Dbx2 expression in adult NSPCs also phenocopied several of the molecular effects of aging, including the altered expression of key genes such as Sox2 and p21 that are associated with proliferation and differentiation.…”

Direct neuronal reprogramming: learning from and for development

“…A possible explanation is that their gradual differentiation, through successive rounds of proliferation and often an intermediate progenitor state, could allow them to acquire the most appropriate metabolism slowly. Indeed, recent RNA-seq data revealed that adult NSCs start to change their metabolism when they become activated and enter cell cycle (Llorens-Bobadilla et al, 2015;Shin et al, 2015). Even the recent identification of NSCs turning into neurons in the adult zebrafish forebrain without any apparent division seems to occur rather slowly (Barbosa et al, 2015), over the course of weeks, which would allow time for metabolic transition.…”

“…For example, maintenance of progenitors requires de novo lipogenesis (Knobloch et al, 2013), while commitment and differentiation are associated with reduced expression of glycolytic genes (Llorens-Bobadilla et al, 2015;Shin et al, 2015). This in turn is influenced by the activity of mTOR (Amiri et al, 2012;Kim et al, 2009), a metabolic rheostat involved in the integration of nutrients and regulation of growth factor signalling (Mihaylova et al, 2014).…”