Loss of PAX6 alters the excitatory/inhibitory neuronal ratio in human cerebral organoids

The transcription factor PAX6 is a crucial regulator of multiple aspects of embryonic forebrain development. Its well-known roles in mice include regulating differentiation of excitatory and inhibitory neurons in the embryonic cortex. PAX6's roles during human forebrain development are less well understood. Using human cerebral organoids, we investigated PAX6's roles in human neurodevelopment. Homozygous PAX6 mutant (PAX6-/-) organoids were larger than controls and contained inhibitory cell types not found in PAX6+/+ controls. These inhibitory cells exhibited clear transcriptomic similarties and comparable distribution to analogous inhibitory cells previously described in Pax6-/- mice. Differentiation trajectory inferencing showed that the inhibitory cells were generated from both radial glia and neuroectodermal progenitor populations. Inferring cell-cell communication using CellChat showed that loss of PAX6 in cerebral organoids increased the probability of cells engaging with inappropriate signalling pathways. Our findings indicate that while PAX6's role in controlling excitatory versus inhibitory neural differentiation is conserved, there are alterations in the activities of intercellular signalling pathways in human PAX6-/- cortical progenitors that have not been described in mice, indicating potential species-specific mechanistic differences.