Hypoxia impedes differentiation of cranial neural crest cells into derivatives relevant for craniofacial development

Orofacial clefts are the second-most prevalent congenital malformation. Risk factors are multifactorial and include genetic components but also environmental factors. One environmental factor is hypoxia during pregnancy, caused for instance by tobacco smoking, medication or living at high altitudes. Knowledge about the molecular link between hypoxia and orofacial clefts is at large. We here show that hypoxia has only modest effects on proliferating cranial neural crest cells, but dramatically influences their differentiation potential. We detected massive perturbations in their differentiation to chondrocytes, osteoblasts and smooth muscle cells. The transcriptional induction of the majority of regulated genes during each of these processes was grossly impaired by hypoxic conditions, as evidenced by genome-wide transcriptomic analyses. Bioinformatic analyses pointed to cytoskeletal organization and amino acid metabolism as two main processes compromised during all three differentiation pathways, and several orofacial cleft risk genes were among the genes with impaired induction during hypoxia. Our analyses reveal a drastic influence of hypoxia on the differentiation potential of cranial neural crest cells as a possible source for the occurrence of orofacial clefts.