Ferniani, M. | Search bioRxiv

bioRxiv2026

p63 and p73 regulate convergent and factor-specific transcriptional programs in cutaneous squamous cell carcinoma

Aberrant transcriptional regulation is a defining feature of squamous cell carcinoma (SCC), yet how lineage transcription factors coordinate shared and factor-specific oncogenic programs remains poorly understood. Although TP63 (p63) is frequently amplified in SCC, the contribution of its paralog TP73 (p73) has remained unclear. Here we show that p73, together with p63, is upregulated in skin SCC and is required for tumorigenesis. Mechanistically, p63 and p73 form heteromeric complexes and co-occupy distal enhancer elements, establishing a shared chromatin regulatory framework. Integration of chromatin and transcriptomic profiling reveals that this common enhancer landscape supports both convergent and divergent transcriptional outputs. Both factors cooperatively sustain core proliferation but also exert regulatory biases, with p63 preferentially reinforcing epithelial lineage circuits and p73 contributing to DNA replication and stress-associated pathways. Among shared downstream targets, p63/p73 co-regulation of multiple epidermal growth factor receptor (EGFR) ligands establishes a feed-forward signaling module that amplifies mitogenic signaling. Amphiregulin emerges as a dominant functional mediator, and its depletion phenocopies key aspects of p63/p73 loss, including impaired proliferation and tumor formation. Together, these findings support a model in which shared enhancer occupancy by p63 and p73 drives cooperative and factor-specific transcriptional programs, linking chromatin regulation to signaling and tumor maintenance.

molecular biology↗

bioRxiv2025

Targeted p63 isoform switch corrects dominant mutations in AEC syndrome without disrupting epidermal homeostasis

The transcription factor p63 is a master regulator of stratified epithelial development, and its disruption causes severe congenital defects affecting the skin, limbs, and craniofacial structures in both humans and mice. Among p63-related disorders, Ankyloblepharon-Ectodermal Defects-Cleft Lip/Palate (AEC) syndrome is caused by dominant mutations primarily affecting the Sterile Alpha Motif (SAM) domain and the Transactivation Inhibitory Domain (TID) of the TP63 gene, which are unique to the p63 isoform. These mutations promote protein aggregation and transcriptional dysregulation, ultimately leading to debilitating skin erosions, suggesting that isoform-specific strategies could be therapeutically relevant. To explore a therapeutic strategy based on isoform switching, we generated a conditional mouse model with deletion of exon 13, resulting in replacement of p63 by the shorter p63{beta} isoform, which is expressed in the skin at lower levels. Although we found that p63 is required for limb and palate development, p63{beta} proved sufficient to support epidermal formation, postnatal skin homeostasis, and wound healing. At the molecular level, the switch from p63 to p63{beta} preserved chromatin binding and global transcriptional programs in keratinocytes. We next used genome editing to delete exon 13 in human primary keratinocytes, inducing a switch from p63 to p63{beta}. This isoform switch maintained normal proliferation and global gene expression. Importantly, p63{beta} expression in AEC patient-derived keratinocytes rescued protein aggregation, restored mechanical integrity, and normalized epidermal gene expression. Together, these findings demonstrate that p63{beta} can functionally compensate for p63 in the skin and establish and indicate that isoform switching could offer a new treatment option for AEC syndrome.

molecular biology↗