Modeling p63-associated human birth defects with systems developmental biology approaches

The overarching goal of the proposed research is to understand how point mutations in the DNA binding domain (DBD) of p63 cause different phenotypes in Ectrodactyly, Ectodermal Dysplasia, and Cleft lip/palate (EEC) syndrome. The transcription factor p63 is the most critical regulator governing epithelial fate specification and the maintenance of stemness in adult epithelial tissues. Loss of p63 expression during mouse embryonic development leads to widespread failure of epithelial and limb development. In humans, heterozygous p63 mutations causes birth defects that include ectodermal dysplasia, orofacial clefting and hand/foot malformation. Interestingly, p63 mutations in the DBD often cause different phenotypes in the skin of human patients. This suggest the existence of p63 DBD mutation-sensitive enhancers and their regulated genes. Our preliminary studies have revealed that: 1) p63 profoundly changes transcriptome, chromatin accessibility and signaling competence of epithelial cells during skin development; 2) signaling pathways that are directly relevant to hair morphogenesis, including Wnt and EDAR signaling, are direct targets of p63. This establishes a molecular basis to examine the mechanism of hair defects observed in EEC; 3) our novel R279C and R280C het and homo mutant mice show different defects than p63 KO, revealing distinct biological functions of each mutation; 4) R279C and R280C het mutations differentially affect critical genes involved in epidermal fate specification and induction of hair follicles; 5) R279C het mutation affects the H3K27Ac levels of a subset of p63 bound enhancers. Our hypothesis is that a subset of p63 enhancers is sensitive to p63 DBD mutations, and their dysregulated genes underlie the defects in the skin of p63 mutants. To investigate this hypothesis, we propose to use systems developmental biology tools including scRNA-seq, scATAC-seq and their associated computational tools, combining with a high-fidelity CRISPR-mediated knockin approach, to examine p63-controlled enhancers and gene regulatory networks (GRNs) in murine skin. We propose to 1) investigate the role of EEC-associated p63 mutations in epidermal fate specification; 2) Investigate the role of EEC-associated p63 mutations in hair morphogenesis; 3) elucidate the impact of p63 DBD mutations on open chromatin accessibility, enhancer activity and genome organization. Success of these aims will provide genetic, genomic and molecular insights into the etiology of birth defects caused by p63 mutations. Our preliminary studies have revealed that: 1) p63 profoundly changes transcriptome, chromatin accessibility and signaling competence of epithelial cells during skin development; 2) signaling pathways that are directly relevant to hair morphogenesis, including Wnt and EDAR signaling, are direct targets of p63. This establishes a molecular basis to examine the mechanism of hair defects observed in EEC; 3) our novel R279C and R280C het and homo mutant mice show different defects than p63 KO, revealing distinct biological functions of each mutation; 4) R279C and R280C het mutations differentially affect critical genes involved in epidermal fate specification and induction of hair follicles; 5) R279C het mutation affects the H3K27Ac levels of a subset of p63 bound enhancers. Our hypothesis is that a subset of p63 enhancers is sensitive to p63 DBD mutations, and their dysregulated genes underlie the defects in the skin of p63 mutants. To investigate this hypothesis, we propose to use systems developmental biology tools including scRNA-seq, s