Single-cell analysis of diversity in human stem cell-derived neurons

Abstract

Neural stem and progenitor cells produce one of the most remarkable organs in nature, the human brain. Among neural stem cell progeny, post-mitotic neurons are likewise remarkably diverse. Single-cell transcriptomic approaches are now cataloging a long-sought-after molecular taxonomy of neuronal diversity in the brain. Contemporary single-cell omic classifications of neuronal diversity build from electrophysiological approaches that for decades have measured and cataloged diverse biophysical properties of single neurons. With the widespread application of human pluripotent stem cell-based models of neurogenesis to investigate disease pathology and to develop new drugs, a high-resolution understanding of neuronal diversity in vivo is essential to benchmark the state of in vitro models of human neurological disease.

Keywords: Neural development; Neural stem cells; Neuronal diversity; Pluripotent stem cells; Single-cell analysis.

Figure 1.. Single cell approaches are essential to measure neuronal diversity.

(A) In a morphologically diverse population of neurons (left), transcriptomic diversity present only in a rare population of neurons is lost in bulk measurement. Schematized gene expression measurements from bulk tissue and from single cells (right) are used for illustration. Bulk analysis indicates that all neurons express high levels of gene A (orange), and low levels of gene B (green); whereas, single cell measurement identifies neuronal diversity. (B) Diversity among morphologically similar neurons (left) is also obscured by bulk measurement. As in (A, right), bulk measurement indicates that all neurons express equal levels of genes A and B; whereas, single cell measurement can reveal distinct subpopulations.

Figure 2.. Genomic diversity may be greater within single neuronal subtypes, than among clonally-related neurons.

The molecular taxonomy of excitatory cortical neurons is based on laminar residence. Morphological, physiological, and transcriptomic diversity is catalogued by comparing layer VI neurons, to layer V neurons, for example. However, genomic diversity is expected to expand in an orthogonal direction. Radial cortical columns contain neurons of each subtype that were born from the same NPC, these clonally related progeny are expected to share somatic mutations. Tangentially distributed columns, on the other hand, arise from different NPCs and are expected to accumulate distinct mutational profiles from other columns.