Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage

Abstract

Summary Neural stem cells (NSCs) in the adult mammalian brain serve as a reservoir for the generation of new neurons, oligodendrocytes, and astrocytes. Here we use single cell RNA-sequencing to characterize adult NSC populations and examine the molecular identities and heterogeneity of in vivo NSC populations. We find that cells in the NSC lineage exist on a continuum through the processes of activation and differentiation. Interestingly, rare intermediate states with distinct molecular profiles can be identified and experimentally validated, and our analysis identifies putative surface markers and key intracellular regulators for these subpopulations of NSCs. Finally, using the power of single cell profiling, we conduct a meta-analysis to compare in vivo NSCs and in vitro cultures, distinct fluorescent-activated cell sorting strategies, and different neurogenic niches. These data provide a resource for the field and contribute to an integrative understanding of the adult NSC lineage.

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

“…With the advent of scRNA-seq, elegant work has been done to identify cell subtypes in mixed populations (Jaitin et al 2014;Patel et al 2014;Treutlein et al 2014;Zeisel et al 2015;Olsson et al 2016;Poulin et al 2016;Dulken et al 2017). However, it remains a major challenge to understand the mechanisms and dynamics by which distinct cell subtypes arise during development (Trapnell 2015).…”

Single‐cell transcriptomics reveals distinct inflammation‐induced microglia signatures

“…In recent years, single-cell RNA sequencing investigations have emerged as a remarkable method to depict heterogeneous cell populations and measure cell-to-cell expression variability of thousands of genes [23][24][25]. In the murine and human brains, single-cell RNA sequencing analyses have revealed neural and glial cell heterogeneity [26][27][28][29][30]. Similarly, the complexity of immune cell types has been recently unravelled [31].…”

Concurrent cell type–specific isolation and profiling of mouse brains in inflammation and Alzheimer’s disease

“…Further studies have noted additional artifacts in the form of preparation-induced transcriptomic changes (26), such as artificial inflammatory signals due to endotoxin-contaminated reagents like Percoll. Single-cell transcriptional analysis has been increasingly used to profile specific cell types, providing a great deal of information related to cell type subpopulations (29)(30)(31)(32)(33)(34). However, single-cell RNA sequencing does not result in high coverage of the transcriptome, and the results obtained are often unable to be integrated for systems biology applications designed to analyze cellular crosstalk in the CNS in health and disease (29,35).…”