CONTROLLED MODELING REVEALS ROBUST CLONAL EXPANSION FOLLOWING CELL DEATH IN THE FETAL BRAIN

Neuronal clonal expansion during human brain development has been inferred from the presence of disproportionately large neuronal families in some individuals. However, its developmental origin remains unclear due to the lack of controlled in vivo experimental systems. Here, we establish a mouse-based experimental and computational framework to model neural stem cell clonal expansion following spatially restricted cell loss during development. To achieve selective and mosaic ablation of neural stem cells, we characterized the rat Nestin promoter and identified uniform Cre activity across neuroepithelial cells as early as embryonic day E10.5, earlier than previously reported. Using NestinCre-driven expression of diphtheria toxin A, we generate chimeric brains in which subclones of neural stem cells are selectively eliminated, thereby creating a competitive developmental environment. In all animals, surviving stem cells undergo robust compensatory clonal expansion, producing large neuronal families validated by whole-genome and single-cell RNA sequencing. Mathematical modeling shows that a modest acceleration of DNA replication in as few as 10% of stem cells is sufficient to predict dominant clones comprising up to ~40% of the brain. Clonal expansion is accompanied by depletion of the neural stem cell pool, suggesting long-term developmental trade-offs.