Poster #16 - Alexandra Manchel

Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk.

Alexandra Manchel 1, Nagham Khouri-Farah 2, Emma Wentworth Winchester 2, Brian M. Schilder 3,4, Kelsey Robinson 5, Sarah W. Curtis 5, Nathan G. Skene 3,4, Elizabeth J. Leslie-Clarkson 5, Justin Cotney 1,6 Affiliations: 1 Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 2 Graduate Program in Genetics and Developmental Biology, UConn Health 3 Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK 4 UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK 5 Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA 6 Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA

Craniofacial development gives rise to the complex structures of the face and involves the interplay of diverse cell types. Despite its importance, our understanding of human-specific craniofacial developmental mechanisms and their genetic underpinnings remains limited. Here, we present a comprehensive single-nucleus RNA sequencing (snRNA-seq) atlas of human craniofacial development from craniofacial tissues of 24 embryos that span six key time points during the embryonic period (4-8 post-conception weeks). This resource resolves eight major cell types and their transcriptional dynamics, including muscle progenitors and SOX10+ cranial neural crest cells (CNCCs), as well as dozens of subtypes of ectoderm and mesenchyme. Comparative analyses reveal substantial conservation of major cell types, alongside human biased variations in gene expression programs. SOX10+ cells, which play a crucial role in craniofacial morphogenesis, exhibit the lowest marker gene conservation, underscoring their evolutionary plasticity. Integrating spatial transcriptomics data from both human and mouse craniofacial development allowed for annotation of cell-type clusters with anatomical features. This allowed us to link common variants associated with facial morphology and rare de novo variants identified in orofacial cleft patients to anatomically distinct cellular subtypes. These data also gave us the opportunity to investigate evolutionary distinctions between modern humans, ancient hominins, and non-human primates. Intriguingly, Neanderthal-introgressed sequences are enriched near genes with biased expression in the maxillary process and specialized ectodermal subtypes, suggesting their contribution to modern human craniofacial features. This atlas offers unprecedented insights into the cellular and genetic mechanisms shaping the human face, highlighting conserved and distinctly human aspects of craniofacial biology. Our findings illuminate the developmental origins of craniofacial disorders, the genetic basis of facial variation, and the evolutionary legacy of ancient hominins. This work provides a foundational resource for exploring cellular and genetic mechanisms shaping the modern human face, with implications for clinical research into congenital anomalies.