Insights into the FOXE3 Transcriptional Network and Disease Mechanisms from the Investigation of a Regulatory Variant Driving Complex Microphthalmia

FOXE3 encodes a conserved, lens-specific transcription factor essential for eye development. Biallelic mutations in FOXE3 lead to a spectrum of ocular anomalies, from cataracts to complex microphthalmia (CM), with clinical severity correlating to genotype. In a CM case with a truncating mutation (p.Cys240*), we identified a regulatory variant (rv, rs745674596 G>A) 3 kb upstream of FOXE3 . Mouse models harboring either the rv or a frameshift mutation were generated in homozygosity ( Foxe3rv/rv, Foxe3-/- ) and compound heterozygosity ( Foxe3rv/Foxe3- ). Phenotypic analysis revealed progressive severity: Foxe3rv/rv mice exhibited cataracts and anterior segment dysgenesis, Foxe3rv/Foxe3-displayed more severe anomalies, and Foxe3-/- mice consistently developed CM. These findings align with human genotype-phenotype relationships. Notably, a direct correlation between protein levels and ocular phenotype was observed, with no association to mRNA levels. In Foxe3-/- mice, CM resulted from early disorganization of the anterior lens epithelium, leading to degeneration and ocular involution. Transcription factor binding assays identified USF2 as a key regulator of FOXE3 expression, positioning USF2 as a promising candidate in ocular development and disease, enhancing our understanding of the FOXE3-related network. This study underscores the importance of integrated approaches to identify genetic variants and cis-regulatory elements, revealing a novel mechanism for microphthalmia through degeneration and involution.