Human neurogenesis: single-cell sequencing and in vitro modeling

Abstract The brain contains immense cellular diversity. Early neuroanatomists identified broad structural brain features and used a variety of stains to characterize, draw, and name a number of constituent cell types. However, our granular understanding of what defines cellular identity, and how this relates to human neurogenesis, has been transformed by the sequencing of the human genome and subsequent technological advances. The genome enabled a translation of single gene level studies to genome-wide, unbiased characterization of gene expression patterns. Rapidly developing gene sequencing technology has revolutionized our understanding of cellular diversity, first based on microarray technology, then RNA-sequencing of 3′ fragments, to more recent whole-transcriptome sequencing, and ultimately single-cell sequencing. Single-cell sequencing allows for a heterogeneous tissue, like the brain, to be broken down into its component cell types based on fundamentally relevant single cell level gene programs. The advent of single-cell sequencing has been transformative for many fields, but using single-cell sequencing in the study of the brain and specifically brain development has enabled a convergence of the understanding of gene expression with features such as area, layer, age, connectivity, morphology, and ultimately cellular function, to achieve a core foundational understanding of cell type identity. While a number of these approaches are now being applied to human development, they have already been widely applied to rodent models, especially the mouse. Due to limitations of accessibility of human brain tissue, in vitro model systems such as the cerebral organoid have been developed to further our understanding of cellular and molecular developmental programs and to functionally test hypotheses gathered from sequencing studies. Here, we focus on established and emerging single-cell technologies, how they have enabled discovery in human brain development, and how organoid models recapitulate cellular developmental trajectories.