Dkk2 interacts with Pax9 in palate mesenchyme to pattern and tune osteogenesis

Cleft palate is a common craniofacial disorder involving multiple genetic and environmental predisposing factors. Currently, limited insight exists into the molecular mechanisms regulating osteogenic differentiation and patterning in the palate during embryogenesis. This study utilized the Pax9-deficient mouse genetic model of cleft palate to investigate the role of Pax9 in osteogenic differentiation. Single-nucleus transcriptomics and chromatin accessibility assays validated by whole-transcriptome and single-molecule spatial transcriptomics suggest a relationship between separate Pax9+ and osteogenic populations. Loss of Pax9 resulted in premature osteogenic differentiation and bone maturation. The spatially restricted osteogenic domains in Pax9(−/−) mice are bounded by Dkk2, which normally interfaces with Pax9 in the mesenchyme. Together, these results confirm a regulatory role for the Wnt pathway in patterning of palatal bone, offering novel insights into the complex nature of developmental signaling and osteodifferentiation in the palate.