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

利用系统发育生物学方法对 p63 相关人类出生缺陷进行建模

• 批准号: 10705852
• 负责人: Rui Yi
• 金额: $ 46.36万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-16 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10705852
• 关键词: Address; Adult; Affect; Alleles; Basement membrane; Binding; Biological Process; CRISPR/Cas technology; Cell Adhesion; Cell Lineage; Cells; Child; Chromatin; Cleft Palate; Clustered Regularly Interspaced Short Palindromic Repeats; Competence; Congenital Abnormality; DNA Binding Domain; Data; Defect; Development; Developmental Biology; Dryness; Ectodermal Dysplasia; Embryonic Development; Enhancers; Epithelial Cells; Epithelium; Etiology; Event; Extracellular Matrix; Failure; Gene Expression; Genes; Genetic; Genetic Models; Genetic Transcription; Genome; Genomics; Goals; Growth; Hair; Hair follicle structure; Hand; Heterozygote; Homo; Human; Human Development; Hypopigmentation; Impairment; Individual; Knock-in; Knowledge; Limb Development; Maintenance; Mediating; Mesenchymal; Messenger RNA; Mission; Modeling; Molecular; Morphogenesis; Mus; Mutant Strains Mice; Mutation; National Institute of Child Health and Human Development; Natural regeneration; Neonatal; Patients; Phenotype; Point Mutation; Reporting; Research; Role; Scalp structure; Signal Pathway; Signal Transduction; Skin; Specific qualifier value; Structural Congenital Anomalies; Syndrome; System; Systems Biology; Testing; Tissues; WNT Signaling Pathway; appendage; cleft lip and palate; computerized tools; ectrodactyly-ectodermal dysplasia-clefting syndrome; epithelial stem cell; foot; gene regulatory network; genetic analysis; in vivo; insight; loss of function; malformation; mouse model; mutant; novel; novel therapeutics; orofacial cleft; precise genome editing; promoter; single cell analysis; single cell technology; single-cell RNA sequencing; skin organogenesis; stemness; success; tool; transcription factor; transcriptome

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.

项目概要： 这项研究的首要目标是了解基因组中的点突变是如何发生的。 p63 DNA结合域（DBD）在缺指、外胚层畸形中引起不同表型 发育不良和唇腭裂（EEC）综合征。转录因子p63是最关键的 调节上皮细胞命运特化和成人干性维持的调节因子 上皮组织小鼠胚胎发育过程中p63表达的缺失导致 上皮和肢体发育的广泛失败。在人类中，杂合子p63突变 导致出生缺陷，包括外胚层发育不良，口面裂和手/脚 畸形有趣的是，DBD中的p63突变通常会导致不同的表型。 人类患者的皮肤。这表明存在p63 DBD突变敏感性增强子 和它们的调控基因。 我们的初步研究表明：1）p63深刻地改变了转录组， 皮肤发育过程中上皮细胞的染色质可及性和信号传导能力; 2） 与毛发形态发生直接相关的信号通路，包括Wnt和EDAR 信号传导，是p63的直接靶点。这建立了一个分子基础来研究机制 3）我们的新型R279 C和R280 C het和homo突变小鼠显示， 与p63 KO不同的缺陷，揭示了每种突变的不同生物学功能; 4）R279 C 和R280 C het突变差异影响表皮命运特化中涉及的关键基因 和毛囊诱导; 5）R279 C het突变影响一个子集的H3 K27 Ac水平 p63结合增强子。我们的假设是，p63增强子的子集对p63 DBD敏感 突变和它们失调的基因是p63突变体皮肤缺陷的基础。到 为了研究这一假设，我们建议使用系统发育生物学工具，包括 scRNA-seq、scATAC-seq及其相关的计算工具，结合高保真的 CRISPR介导的敲入方法，以检查p63控制的增强子和基因调控 网络（GRNs）在小鼠皮肤。我们建议：1）研究EEC相关的p63的作用 表皮命运特化中的突变; 2）研究EEC相关的p63突变的作用 3）阐明p63 DBD突变对开放染色质的影响 可接近性、增强子活性和基因组组织。这些目标的实现将提供 对p63引起的出生缺陷病因学的遗传、基因组和分子见解 突变。