The role of the Foxi3 transcription factor in craniofacial microsomia

Craniofacial abnormalities are some of the most common birth defects. Although cleft lip and/or palate and craniosynostosis are the most common craniofacial defects, craniofacial microsomia (CFM) is estimated to be the third most prevalent cranial anomaly, occurring at between 1 in 3000 – 1 in 6000 live births. Although the symptoms of CFM can vary widely in severity, they share a variety of features consistent with abnormal development of first and second pharyngeal arches, including a shortening of the mandible, microtia, preauricular tags and epibulbar dermoids. These defects are typically, but not exclusively unilateral, and although some families presenting with CFM have been identified, most are considered sporadic and have no genetic diagnosis. Difficulties in understanding the origins of CFM include its heterogeneity, the lack of clear underlying molecular mechanisms and the paucity of good animal models for these disorders. We have identified a transcription factor, Foxi3, that is expressed early and broadly in pharyngeal ectoderm and endoderm, and is later restricted to the pharyngeal pouches and clefts. Foxi3 mutant mice show severe defects in most pharyngeal arch derivatives – for example, the mutants lack much of the lower jaw, and have a complete loss of the middle ear ossicles and the external ear. Recently, our colleagues found over 20 human variants in Foxi3 associated with craniofacial defects including CFM and microtia, and our preliminary data suggests these defects can be modeled in mice carrying some of these variants. Moreover, the Gata3 transcription factor, which has been associated with CFM in genome-wide association studies, is co-expressed with Foxi3 in several developing cranial tissues and has also recently been shown to cause CFM phenotypes when mutated in mice. This raises the possibility that Foxi3 and Gata3 interact genetically during craniofacial development. In this proposal, we will first attempt to create a mouse model of CFM using Foxi3 mutant alleles created in our lab and Gata3 mutant alleles characterized by our collaborators. Second, we will perform a bioinformatic analysis of the gene regulatory networks controlled by Foxi3 and Gata3, by analyzing gene expression in pharyngeal tissue from Foxi3 homozygous mutants, heterozygous mutant and wild type mice, and by performing CUT&RUN on pharyngeal tissue to identify direct targets of Foxi3 and Gata3. Finally, we will address the role of Foxi3 during early craniofacial development by performing conditional deletions of Foxi3 in pharyngeal ectoderm and endoderm and determining its contribution to normal craniofacial development in each tissue. Project Number: 7R01DE032244-04 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Dental and Craniofacial Research (NIDCR) | Principal Investigator: Andrew Groves | Institution: WASHINGTON UNIVERSITY, SAINT LOUIS, MO | Award Amount: $573,768 | Activity Code: R01 | Study Section: Skeletal Biology Development and Disease Study Section[SBDD] View on NIH RePORTER: https://reporter.nih.gov/project-details/11379649