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Genetic underpinnings of craniofacial disorders explored with spatial sequencing

通过空间测序探索颅面疾病的遗传基础

基本信息

批准号：
10712635
负责人：
Robert Aaron Cornell
金额：
$ 72.79万
依托单位：
UNIVERSITY OF WASHINGTON
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-08-01 至 2028-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10712635
关键词：
ATAC-seq Address Affect Artificial Intelligence Atlases Candidate Disease Gene Cell Differentiation process Cells Cleft Lip Code Computational algorithm Conceptions Conceptus Congenital Abnormality DNA Data Set Dental Development Disease Embryo Engineering Epithelium Etiology Face Fetus Fishes Gastrula Gene Expression Gene Mutation Genes Genetic Genetic Counseling Goals Growth Factor Heritability Heterogeneity Human Hypodontia In Vitro Individual Inherited Knowledge Learning Ligands Linkage Disequilibrium Location Medial Mesenchymal Mesenchyme Methods Modeling Morphogenesis Multiomic Data Mus Mutation Neural Crest Newborn Infant Oral Oral cavity Palate Pathogenicity Patients Periderm Preventive therapy Protocols documentation Resolution Risk Rodent Salivary Glands Secondary Palate Structure TGFB3 gene Testing Therapeutic Intervention Time Tissues Tooth structure Untranslated RNA Variant Zebrafish cell type craniofacial development craniofacial disorder design disorder risk effectiveness testing experimental study fetal gene regulatory network genome wide association study human fetus tissue human tissue improved induced pluripotent stem cell loss of function malformation member model organism multiple omics network models oral cavity epithelium oral ectoderm orofacial cleft outcome prediction paralogous gene permanent tooth scaffold single cell sequencing single nucleus RNA-sequencing single-cell RNA sequencing spatiotemporal stem cell therapy transcription regulatory network transcriptome sequencing transcriptomics virtual

项目摘要

Malformations of the oral cavity, which include dental anomalies (hypodontia, hyperdontia), cleft lip and or cleft plate (orofacial cleft, OFC), and salivary gland anomalies (ectopic or aplasia), are among the most common birth defects in the US. The design of preventative therapies for these disorders will require a precise understanding of the transcriptional regulatory networks (TRNs) governing development of the relevant tissues. Studies in model organisms have been invaluable, for instance revealing that mesenchyme in these structures derives from neural crest and epithelia in them derives largely from oral ectoderm. However, it is unclear how these TRNs are deployed over developmental time and within spatial domains of the mouth. Moreover, aspects of these TRNs are likely to be human specific, for instance those regulating the development of secondary dentition, which does not occur in rodents. Finally, all of the disorders mentioned above have a genetic basis, in none has all of the heritable risk been fully explained. Knowledge of the TRNs in human tissue is the surest way to find candidate genes to harbor such risk. Recent advances in our spatial transcriptomics (sciSpace), and access to donated human fetal tissue, permit these important questions to be addressed in a precise spatio-temporal manner. Here we propose, in Aim 1, to conduct sciSpace over the entire human face at four critical developmental timepoints (7-9, 10-12, 13-15, and 16-18 weeks post conception). We will then focus on the secondary palate and the genetic underpinnings of OFC. We will use computational algorithms to deduce the membership and regulatory hierarchy of TRNs regulating differentiation of distinct domains of palate epithelium and palate mesenchyme; top ranking members of these TRNs are strong candidates to harbor the missing heritability for OFC. In Aim 2, we will use the results of the first aim to develop protocols for converting induced pluripotent stem cells (iPSC) into palate epithelium and mesenchymal cells. We will engineer iPSC with 2 coding and 2 non-coding variants associated with OFC, differentiate the engineered iPSC into palate cell types, and subject the differentiated cells to single cell RNA-seq. This will reveal the specific cell types, and the step in their development, that is affected by the variants, illuminating the pathogenic mechanisms of OFC. These experiments will identify strong candidates for the missing heritability for orofacial cleft, improve functional tests of DNA variants associated with it, and provide the datasets to similarly analyze other inherited craniofacial disorders.

口腔畸形，包括牙齿畸形（牙下、牙多）、唇裂和/或唇裂