Context-dependent Foxa2 activity maintains floor plate fate and tunes Sonic hedgehog signaling to regulate neural progenitor differentiation

The developing spinal cord contains both neural and non-neural tissues that arise within a shared morphogen signaling environment, raising the question of how distinct lineage identities are established and maintained. A striking example of this is the floor plate (FP), a mesoderm-derived, non-neural midline structure that functions as a critical signaling center adjacent to neural progenitor domains. Here, using zebrafish, we show that the pioneer transcription factor foxa2 is expressed in the FP, adjacent p3 neural progenitors, and p3-derived Kolmer-Agduhr” (KA”) interneurons. Loss of foxa2 results in a complete loss of canonical FP identity and an expansion of p3 progenitors. Lineage tracing reveals that, in the absence of foxa2 , FP cells undergo a fate transformation into neuron-producing p3-like cells, indicating that Foxa2 functions as a lineage barrier to preserve non-neural FP identity. In contrast, within the neural lineage, loss of foxa2 leads to elevated Sonic hedgehog (Shh) pathway activity and impaired KA” differentiation, suggesting that Foxa2 negatively regulates Shh responsiveness. Conversely, Foxa2 overexpression induces ectopic FP and KA” marker expression in a stage-dependent manner. Together, our findings reveal a dual role for Foxa2 in maintaining the non-neural FP lineage while fine-tuning morphogen responsiveness in neighboring neural progenitors during spinal cord development.