Δ4-p63 Enhances Epithelial Stem Cell Clonogenicity and Cooperates with Oncogenic KRAS to Promote Squamous Dysplasia

p63 is a critical transcription factor for the development and maintenance of stratified epithelia and is essential for the proliferative capacity of epithelial stem cells. Here, we investigated the biological significance of a Δ4-p63 isoform generated by deletion of exon 4 of the p63 gene. Although Δ4-p63 is undetectable in normal epithelia, its expression is positively associated with human squamous cell carcinoma (SCC). Mice heterozygous for the p63 exon 4 deletion developed normally, whereas homozygous mutants were neonatal lethal. Although no overt histological abnormalities were detected in the skin of heterozygous mice, epithelial cells isolated from these animals exhibited markedly enhanced clonogenic potential compared with cells from wild-type (WT) mice. This phenotype persisted during prolonged culture and serial passage, suggesting an intrinsic increase in epithelial stem cell proliferative or self-renewal capacity rather than transient expansion associated with differentiation. Furthermore, heterozygosity for the p63 exon 4 deletion markedly enhanced epithelial dysplasia in mice expressing oncogenic Kras ^G12D , revealing a genetic interaction between p63 exon 4 deficiency and oncogenic KRAS signaling. ChIP-seq analysis demonstrated that p63 in WT mice and the p63/Δ4-p63 complex in heterozygous mice retain highly similar genome-wide DNA-binding profiles, indicating that exon 4 deletion does not abolish p63 chromatin occupancy. However, p63 and p63/Δ4-p63 showed preferential association with distinct subsets of regulatory regions. p63 in WT mice preferentially occupied regions associated with epithelial transcriptional regulators, whereas p63/Δ4-p63 in heterozygous mice preferentially associated with regulatory regions linked to Klf14, Elk4, Npas/Bmal1, Arnt, and Ar. Together, these findings suggest that Δ4-p63 is not simply a loss-of-function isoform, but instead alters the p63-dependent transcriptional landscape and epithelial stem cell state, creating a cellular context that cooperates with oncogenic KRAS to promote squamous epithelial dysplasia.