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

> **NIH NIH R01** · NORTHWESTERN UNIVERSITY · 2022 · $463,032

## Abstract

Project Summary:
 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.

## Key facts

- **NIH application ID:** 10539094
- **Project number:** 1R01HD107841-01A1
- **Recipient organization:** NORTHWESTERN UNIVERSITY
- **Principal Investigator:** Rui Yi
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $463,032
- **Award type:** 1
- **Project period:** 2022-09-16 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10539094

## Citation

> US National Institutes of Health, RePORTER application 10539094, Modeling p63-associated human birth defects with systems developmental biology approaches (1R01HD107841-01A1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10539094. Licensed CC0.

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