Disentangling neural cell diversity using single-cell transcriptomics

Abstract

Cellular specialization is particularly prominent in mammalian nervous systems, which are composed of millions to billions of neurons that appear in thousands of different 'flavors' and contribute to a variety of functions. Even in a single brain region, individual neurons differ greatly in their morphology, connectivity and electrophysiological properties. Systematic classification of all mammalian neurons is a key goal towards deconstructing the nervous system into its basic components. With the recent advances in single-cell gene expression profiling technologies, it is now possible to undertake the enormous task of disentangling neuronal heterogeneity. High-throughput single-cell RNA sequencing and multiplexed quantitative RT-PCR have become more accessible, and these technologies enable systematic categorization of individual neurons into groups with similar molecular properties. Here we provide a conceptual and practical guide to classification of neural cell types using single-cell gene expression profiling technologies.

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).…”

Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq

“…In addition, the 5HT3a EGFP mouse labels a large population of striatal interneurons that, together with the previously mentioned markers (with some overlap), make up 5% of the striatal neurons, arguing that we have mouse genetic tools to target all interneurons in the striatum (Muñoz-Manchado et al., 2016). Large-scale efforts using transcriptome sequencing of thousands of single cells in neuronal tissue hold promise to revolutionize our understanding of the neuronal diversity in the mammalian brain (Poulin et al., 2016). Previous striatal single-cell RNA sequencing (scRNA-seq) studies have focused on the SPNs, excluding interneurons from their analysis (Gokce et al., 2016).…”

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

“…By applying a battery of statistical tools to cluster cells based on their similarities in gene expression, it is then possible to identify, group and classify discrete cell types and cell stages within a heterogeneous population. Accordingly, over the last several years the advent of such single cell transcriptome profiling – also referred to as single-cell RNA-sequencing or single-cell RNA-seq – has fueled an explosion of new information on the complexity of cell types in the nervous system based on genes expressed by individual cells (Poulin et al, 2016; Zeng and Sanes, 2017). However, since a cell’s transcriptome represents just one aspect of its identity, additional work is needed to integrate other structural and functional features – distribution, morphology, connectivity and physiology – in order to devise a principled framework with which to create a taxonomy of cell types in the brain.…”