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Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate
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Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate

Jingwen W. Ding, Chang N. Kim, Megan S. Ostrowski +5 more
September 2025
 ·
bioRxiv
 ·
DOI 
10.1101/2025.09.23.678137
94
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Why this is interesting

Functional genomics of human cortical development was limited to iPSC models; this study adapts CRISPRi Perturb-seq to primary tissue, revealing TF circuits—including opposing NR2E1/ARX roles—that govern radial glia lineage plasticity and neuropsychiatric risk.

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Summary

Systematic CRISPRi screening in primary human cortical radial glia combined with single-cell transcriptomics and lineage tracing reveals that transcription factors NR2E1 and ARX have opposing roles in regulating excitatory versus inhibitory neuron production through modulation of individual radial glia lineage plasticity and developmental progression, while ARX additionally safeguards postmitotic interneuron subtype specification through transcriptional repression of LMO1, with these regulatory mechanisms conserved across primates and convergent effector genes enriched in neurodevelopmental disorders.

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Main Claim 1 –

Primary human cortical culture enables CRISPRi Perturb-seq TF screening

Supporting evidence

  • Convergent TF effector genes are enriched for neuropsychiatric risk
  • Flow cytometry validates CRISPRi screen-detected fate phenotypes
Main Claim 2 –

NR2E1 and ARX oppositely regulate RG lineage plasticity

Supporting evidence

  • NR2E1/ARX temporal lineage effects are conserved across primates
Main Claim 3 –

ARX maintains postmitotic interneuron identity by repressing LMO1

Supporting evidence

  • LMO1 knockdown partially rescues ARX-loss ectopic interneuron programs

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. Complex genetic programs orchestrated by transcription factor (TF) circuits govern the balance between self-renewal and differentiation, and between different cell fates. Despite progress in measuring gene regulatory network activity during human cortical development, 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 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.

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