GSE116970
CRISPR-Cas9 Screens Reveal Genes Regulating a G0-like State in Human Neural Progenitors [Bulk RNA-seq]
The coordination of developmental potential and proliferation in stem and progenitor cells is essential for mammalian development and tissue homeostasis. To better understand this coordination in human neural progenitor cells (hNPCs), we performed CRISPR-Cas9 screens and identified genes that limit their expansion. These screens revealed that knockout of growth-limiting genes, including CREBBP, NF2, PTPN14, TAOK1, or TP53, caused increased hNPC expansion via skipping of a transient G0-like state, accompanied by transcriptional reprogramming of G1 subpopulations. Hallmarks of the G0-like state included expression of genes associated with quiescent neural stem cells and neural development and molecular features found in quiescent cells (e.g., hypo-phosphorylated Rb, CDK2low activity, and p27high). Further, G0-skip genes act through both distinct and convergent downstream effectors, including cell cycle, Hippo-YAP, and novel targets. The results suggest that hNPC expansion is constrained by a transient G0-like state, regulated by multiple pathways, that facilitates retention of neurodevelopmental identity. Overall design: 33 samples in total were analyzed for gene expression using RNA-sequencing including either the entire population, sorted for G0/G1 (mCherry-CDT1(aa30/120)-positive), or partial differentiation following removal of growth factors for 7 days. Bulk RNA-seq include 2-3 replicates and controls include wild-type NPCs, non-targeting CRISPR-Cas9 NPCs, and unsorted/undifferentiated NPCs.