Gene expression dynamics of human and mouse craniofacial development at the single-cell level

Craniofacial development is a complex process that involves the specification of diverse and transient cell types. However, our understanding of these processes and the cell-types present during human craniofacial developmental remains limited. We address this gap in knowledge through single-nucleus RNA sequencing of human craniofacial development spanning 4 to 8 post-conception weeks. This resource identifies multiple subtypes of mesenchyme, epithelium, and cranial neural crest, among other functionally distinct cell types. Extensive comparisons to single-nucleus gene expression and spatial transcriptomics of comparable mouse developmental stages reveal functional conservation of most cell types and identification of anatomically distinct cell subtypes. We find distinct contributions of cellular subtypes to normal facial morphology and common risk factors for orofacial clefts. Additionally, we find specific ectodermal and epithelial subtypes whose gene expression networks are most significantly affected by rare de novo protein-altering variants from orofacial cleft patients. Together our data provide an extensive resource for understanding human craniofacial development at the cellular level.