Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate.
Publication Year:
2025
PubMed ID:
41040362
Public Summary:
During cortical development, neural stem cells generate the different types of neurons and glia that form the neocortex. Genetic and environmental factors that alter the cell fate decisions of neural stem cells can result in disorders of the nervous system. In this study, we sought to systematically identify gene regulating neural stem cell decisions using CRISPR-based approaches to repress transcription factors, the major regulators of networks of genes. We found that genes linked to neurodevelopmental disorders are more likely to be downstream of many transcription factors (well connected) and we identified specific transcription factors regulating the cell fate decisions of neural stem cells by controlling their rate of maturation. We further identified transcription factors that regulate how neurons, once produced, safeguard their identity. For one disease-linked gene, ARX, we identified a candidate modifier gene that when also repressed could partially restore the normal gene expression pattern of inhibitory neurons.
Scientific Abstract:
Human cortical neurogenesis involves conserved and specialized developmental processes during a restricted window of prenatal development. Radial glia (RG) neural stem cells shape cortical cell diversity by giving rise to excitatory neurons, oligodendrocytes, and astrocytes, as well as olfactory bulb interneurons (INs) and a recently characterized population of cortical INs(1,2). Complex genetic programs orchestrated by transcription factor (TF) circuits govern the balance between self-renewal and differentiation, and between different cell fates(3-8). Despite progress in measuring gene regulatory network activity during human cortical development(9-12), functional studies are required to evaluate the roles of TFs and effector genes in human RG lineage progression. Here we establish a human primary culture system that allows sensitive discrimination of cell fate dynamics and apply single cell clustered regularly interspaced short palindromic repeats interference (CRISPRi) screening(13,14) to examine the transcriptional and cell fate consequences of 44 TFs active during cortical neurogenesis. We identified multiple TFs, with novel roles in cortical neurogenesis, including ZNF219, previously uncharacterized, that represses neural differentiation and NR2E1 and ARX that have opposing roles in regulating RG lineage plasticity and progression across developmental stages. We also uncovered convergent effector genes downstream of multiple TFs enriched in neurodevelopmental and neuropsychiatric disorders and observed conserved mechanisms of RG lineage plasticity across primates. We further uncovered a postmitotic role for ARX in safeguarding IN subtype specification through repressing LMO1. Our study provides a framework for dissecting regulatory networks driving cell fate consequences during human neurogenesis.
