Cerebral organoids display dynamic clonal growth with lineage replenishment

During development tissue stem cells expand by symmetrical divisions while asymmetric divisions self-renew a tissue stem cell and produce differentiating cell types that assemble into functional organs. In brain development this process is variable for individual neural stem cells, resulting in differentially sized stem cell clones, but it is unclear how overall brain size is reproducibly generated during neurogenesis. Imaging-based lineage tracing allows for lineage analysis at high cellular resolution but systematic approaches to analyze clonal relationships in an entire tissue are currently lacking. Here we implement whole-tissue lineage tracing by genomic DNA barcoding in 3D human cerebral organoids and show that individual stem cell clones produce progeny on a vastly variable scale. We find that symmetrically dividing cells in a subpopulation of lineages continuously resides within the developing human tissue and drive the variable lineage size distribution. We show that stem cell output is tunable to tissue demands by chemical ablation or genetic fate restriction in chimeric organoids in which perturbed organoid development is completely compensated for by unaffected lineages. This data reveals adaptive plasticity of stem cell populations in developing human brain tissue dependent on tissue needs to ensure normal development.