Splicing Defects and Cell Death Cause SF3B2-Linked Craniofacial Microsomia

Craniofacial microsomia (CFM) is a genetically and phenotypically heterogeneous disorder characterized by hypoplasia of facial tissue that is often asymmetric. Affected tissues typically include the ears (external and internal), mandible, and maxilla, but various extracranial anomalies have also been reported. Loss-of-function variants in the SF3B2 gene have recently been reported in 8 cases of CFM, representing one of the more common genetic causes identified to date. To better define the full phenotypic spectrum associated with variants in SF3B2, we report novel loss-of-function variants in SF3B2 in 5 new families with CFM. Furthermore, to determine the mechanism by which SF3B2 loss-of-function perturbs craniofacial development, we established sf3b2-null mutant zebrafish, which exhibited severe deficiencies in craniofacial cartilage and bone progenitors due to elevated apoptosis and reduced proliferation of cranial neural crest cells. In addition, we generated a heterozygous truncating variant of SF3B2 in human induced pluripotent stem cells using CRISPR/Cas9 gene editing. Differentiation of these cells into neural crest cells was accompanied by increased cell death and reduced proliferation. RNA sequencing of sf3b2 mutant zebrafish revealed widespread disruption of mRNA splicing, including mdm2, a key regulator of Tp53-mediated apoptosis. Genetic inhibition of tp53 in sf3b2 mutants demonstrated that tp53 inhibition reduces early cell death but does not improve proliferation or craniofacial cartilage development. Therefore, our functional studies indicate that widespread mRNA splicing disruption, in addition to Tp53-dependent cell death, contributes to the craniofacial features observed in SF3B2-related CFM.