Summary
The development of the human neocortex is a highly dynamic process and involves complex cellular trajectories controlled by cell-type-specific gene regulation1. Here, we collected paired single-nucleus chromatin accessibility and transcriptome data from 38 human neocortical samples encompassing both the prefrontal cortex and primary visual cortex. These samples span five main developmental stages, ranging from the first trimester to adolescence. In parallel, we performed spatial transcriptomic analysis on a subset of the samples to illustrate spatial organization and intercellular communication. This atlas enables us to catalog cell type-, age-, and area-specific gene regulatory networks underlying neural differentiation. Moreover, combining single-cell profiling, progenitor purification, and lineage-tracing experiments, we have untangled the complex lineage relationships among progenitor subtypes during the transition from neurogenesis to gliogenesis in the human neocortex. We identified a tripotential intermediate progenitor subtype, termed Tri-IPC, responsible for the local production of GABAergic neurons, oligodendrocyte precursor cells, and astrocytes. Remarkably, most glioblastoma cells resemble Tri-IPCs at the transcriptomic level, suggesting that cancer cells hijack developmental processes to enhance growth and heterogeneity. Furthermore, by integrating our atlas data with large-scale GWAS data, we created a disease-risk map highlighting enriched ASD risk in second-trimester intratelencephalic projection neurons. Our study sheds light on the gene regulatory landscape and cellular dynamics of the developing human neocortex.
Competing Interest Statement
A.R.K. is a co-founder, consultant, and director of Neurona Therapeutics. The remaining authors declare no competing interests.
Footnotes
(1)Validating Neuronal Interactions: To validate the predicted interactions between excitatory and inhibitory neurons by NCEM and CellChat, we manipulated somatostatin (SST) signaling in human cortical slice cultures and performed single-cell RNA sequencing. We found that SST receptor activation inhibited excitatory neuron maturation across multiple subtypes, indicating regulation by IN-MGE-SSTs. (2)Validating Gene Regulatory Networks: We validated SCENIC+-inferred gene regulatory networks by comparing the predicted eRegulons with ChIP-seq and 3D enhancer-promoter interaction data from the human brain, finding significant overlap. (3)Confirming Tri-IPC Tripotency: To confirm the tripotency of Tri-IPC (previously IPC-IAO), we transplanted them into early postnatal mouse cortex. Tri-IPCs differentiated into inhibitory neurons, oligodendrocytes, and astrocytes, confirming their tripotency in vivo. (4)Mapping Glioblastoma Multiforme Cells: Mapping glioblastoma multiforme (GBM) cells using our atlas revealed that over half of these cells resemble Tri-IPCs, with many others resembling descendant cell types from Tri-IPCs. This supports the role of Tri-IPCs as cancer stem cells and suggests that their multipotency and proliferative capacity contribute to GBM heterogeneity and growth.
