A single cell transcriptomic analysis of human neocortical development

Abstract

Defining the number, proportion, or lineage of distinct cell types in the developing human brain is an important goal of modern brain research. We defined single cell transcriptomic profiles for 40,000 cells at mid-gestation to identify cell types in the developing human neocortex. We define expression profiles corresponding to all known major cell types at this developmental period and identify multiple transcription factors and co-factors expressed in specific cell types, providing an unprecedented resource for understanding human neocortical development including the first single-cell characterization of human subplate neurons. We characterize major developmental trajectories during early neurogenesis, showing that cell type differentiation occurs on a continuum that involves transitions that tie cell cycle progression with early cell fate decisions. We use these data to deconvolute regulatory networks and map neuropsychiatric disease genes to specific cell types, implicating dysregulation of specific cell types, as the mechanistic underpinnings of several neurodevelopmental disorders. Together these results provide an extensive catalog of cell types in human neocortex and extend our understanding of early cortical development, human brain evolution and the cellular basis of neuropsychiatric disease.One Sentence Summary: Comprehensive single cell transcriptomes in developing human cortex inform models of cell diversity, differentiation and disease risk. Main text:The human cortex is composed of billions of cells estimated to encompass hundreds or thousands of distinct cell types each with unique functions (1, 2). It is reasonable to assume that to understand a system as complex as the human cortex, it is necessary to understand its components (3,4). Ground breaking work in mouse revealed the power of single-cell transcriptomics for providing a framework for understanding the complexity and heterogeneity of cell types in the brain (5-10). The availability of high quality tissue and advances in single-cell transcriptomic technologies now permit us to catalog the cell type diversity of the human cortex in a comprehensive and unbiased manner (11). Despite the enormous progress that has been made in characterizing early cortical development (1,(12)(13)(14)(15)(16), many of the molecular mechanisms underpinning the generation, differentiation, and development of the diverse types of cells remain largely unknown (17). Molecular taxonomies of cortical cell types from developing human brains enable us to understand the mechanisms of neurogenesis and how the remarkable cellular diversity found in the human cortex is achieved (18-22). Developing knowledge of neocortical cell types and their transcriptional programs during this epoch is a key step in understanding mechanistic dysregulation in neurodevelopmental disorders with cell type resolution. Several recent studies have taken a first step in this direction, analyzing several hundred, or a few thousand cells from developing human brain (18-22). However, advances in te...

Defining the Genetic, Genomic, Cellular, and Diagnostic Architectures of Psychiatric Disorders

“…Two general approaches are used to determine cell-type or stage specificity. The first assigns genes implicated by risk variants directly to cell types based on transcriptomics (Polioudakis et al, 2018;Skene et al, 2018). The second partitions genetic risk across non-coding regions and compares the predicted activity of these regions across cell types and developmental stages, which to date have been primarily based on tissue-level open chromatin rather than single cells (de la .…”

“…A recent study of single-nuclei RNA-seq from human fetal and adult brain has validated the enrichment of genes harboring large-effect de novo mutations associated with ASD in fetal glutamatergic neurons (Polioudakis et al, 2018). These detailed transcriptomic profiles provide nuance, especially for individual genes, identifying genes expressed broadly across neurons or with relative specificity for inhibitory neurons, neural progenitors, or non-neural cells (Polioudakis et al, 2018).…”

“…A recent study of single-nuclei RNA-seq from human fetal and adult brain has validated the enrichment of genes harboring large-effect de novo mutations associated with ASD in fetal glutamatergic neurons (Polioudakis et al, 2018). These detailed transcriptomic profiles provide nuance, especially for individual genes, identifying genes expressed broadly across neurons or with relative specificity for inhibitory neurons, neural progenitors, or non-neural cells (Polioudakis et al, 2018). The importance of the fetal period for ASD is supported by GWAS results integrated with regulatory chromatin interactions and gene expression, which show enrichment of enhancer marks in the fetal brain and higher expression of ASD target genes during fetal corticogenesis (Grove et al, 2019).…”

Genetic control of gene expression and splicing in the developing human brain

“…We found 68% of overlapping eQTLs tag the same regulatory region, even if the top SNP differed (Figure 4E). To further examine the differences in eGenes at the different developmental time points, eGenes were annotated based on fetal cell type markers, identified through differential expression of single cell sequencing identified cell clusters (Methods; Polioudakis et al, 2018). We find many more fetal eGenes are in fact fetal cell type markers compared to eGenes that either overlap with adult, or are adult specific (Figure 4F), which is expected given the expected cellular composition of each epoch.…”

Single cell atlas of trisomy 21 cerebral cortex

“…scRNAseq has been widely used to explore the heterogeneity of human cerebral cortex for several years [3][4][5][6] and neuron generation 7 . Additionally, brain cellular compositions under pathological conditions have also been studied using scRNA including PD, AD and ASD, revealing cell type and molecular alteration related to pathology [8][9][10][11] .…”