A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

Abstract

The mammalian prefrontal cortex comprises a set of highly specialized brain areas containing billions of cells and serves as the centre of the highest-order cognitive functions, such as memory, cognitive ability, decision-making and social behaviour. Although neural circuits are formed in the late stages of human embryonic development and even after birth, diverse classes of functional cells are generated and migrate to the appropriate locations earlier in development. Dysfunction of the prefrontal cortex contributes to cognitive deficits and the majority of neurodevelopmental disorders; there is therefore a need for detailed knowledge of the development of the prefrontal cortex. However, it is still difficult to identify cell types in the developing human prefrontal cortex and to distinguish their developmental features. Here we analyse more than 2,300 single cells in the developing human prefrontal cortex from gestational weeks 8 to 26 using RNA sequencing. We identify 35 subtypes of cells in six main classes and trace the developmental trajectories of these cells. Detailed analysis of neural progenitor cells highlights new marker genes and unique developmental features of intermediate progenitor cells. We also map the timeline of neurogenesis of excitatory neurons in the prefrontal cortex and detect the presence of interneuron progenitors in early developing prefrontal cortex. Moreover, we reveal the intrinsic development-dependent signals that regulate neuron generation and circuit formation using single-cell transcriptomic data analysis. Our screening and characterization approach provides a blueprint for understanding the development of the human prefrontal cortex in the early and mid-gestational stages in order to systematically dissect the cellular basis and molecular regulation of prefrontal cortex function in humans.

Multi-hit autism genomic architecture evidenced from consanguineous families with involvement of FEZF2 and mutations in high-risk genes

“…To further test the multiple-hit hypothesis in FEZF2 allele-linked families 2, 6, 18 and 23, we investigated whether in all FEZF2 allele-linked families at least one of those second hits was also expressed in FEZF2-expressing cells. For this analysis, we took advantage of single-cell and single-nuclei data from fetal and adult human frontal cortex (49,50). In these datasets, FEZF2 is expressed in neural progenitor cells (NPC) and excitatory neurons (L5 in adult).…”

“…2018 and Lake et al 2017, respectively (49,50). Counts were log-normalized using Seurat V3 (Stuart et al 2019) and a scale factor of 10,000.…”

“…Co-expression of FEZF2, other mutated genes from the high-risk ensemble and genes displaying de novo SNVs in FEZF2 allele-linked families.Barplots indicating the proportion FEZF2-expressing (red), "putative second hit"-expressing (green), and both FEZF2/second gene-expressing (blue) cells in frontal cortex single cell datasets derived from human fetal(Zhong et al 2018) and adult (Lake et al 2017) brains. High FEZF2 expression is found in progenitor cells and excitatory neurons in the fetal brain, and in cell cluster Ex6a in the adult brain, corresponding to a layer 5 subpopulation, as described in Lake et al 2017.…”

Dissecting the human immune system with single cell RNA sequencing technology

“…In contrast, scRNA‐seq, a revolutionary technology developed in 2009, offers an entirely unbiased strategy to characterize single cell. ScRNA‐seq has great potentials on all aspects of biological science, including microbiology, neurobiology, oncology, and especially immunology . It has already revealed exciting molecular insights into the complexity of the immune system by identifying novel cell subsets based on transcriptional profiles.…”

“…ScRNA-seq has great potentials on all aspects of biological science, including microbiology, neurobiology, oncology, and especially immunology. 4,5 It has already revealed exciting molecular insights into the complexity of the immune system by identifying novel cell subsets based on transcriptional profiles. The application of scRNA-seq in disease conditions is leading to new level of understanding of pathogenesis.…”