Uncovering Caries Risk in the Noncoding Genome of the Developing Tooth

揭示发育中牙齿非编码基因组中的龋齿风险

• 批准号: 10401809
• 负责人: Emma Wentworth Winchester
• 金额: $ 4.33万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10401809
• 关键词: Acids; Adult; Affect; Ameloblasts; Binding; Biological Assay; Candidate Disease Gene; Carbohydrates; Cells; Cellular Assay; Chromatin; Clinical; Code; Computer Models; Computing Methodologies; Coupled; Data; Data Set; Dental; Dental Enamel; Dental Hygiene; Dental Pulp; Dental Sac; Dental caries; Dentin; Development; Diet; Disease; Embryo; Enamel Formation; Enhancers; Epithelial; Epithelial Cells; Exons; Fellowship; Functional disorder; Gene Expression; Genes; Genetic; Genetic Transcription; Genome; Genomics; Health; Heritability; Human; Human Genome; Hygiene; Immune; Incisor; Investigation; Lesion; Link; Linkage Disequilibrium; Mesenchymal; Microbe; Modeling; Molecular Conformation; Mouth Diseases; Multiomic Data; Mus; Nature; Odontoblasts; Odontogenesis; Patients; Predisposition; Prevention; Production; Proteins; Public Health; Quality of life; Risk; Role; Saliva; Scientist; Signal Transduction; Single Nucleotide Polymorphism; Supporting Cell; Surface; Systemic disease; Techniques; Time; Tissues; Tooth Diseases; Tooth Germ; Tooth structure; Transposase; Untranslated RNA; Variant; Work; base; career; cell type; craniofacial; craniofacial development; craniofacial tissue; enamel matrix proteins; experimental study; genome annotation; genome wide association study; human tissue; insight; lifestyle factors; microbiome; multiple datasets; negative affect; oral microbiome; promoter; recruit; response; scaffold; skills; spatiotemporal; tooth surface; transcription factor

Project Summary Caries is a common oral disease that will affect 90% of US adults in the course of their lifetime. Carious lesions of the tooth develop over time when microbes on the tooth surface respond to carbohydrates by producing acids that degrade enamel. In addition to lifestyle factors like diet and hygiene, studies have shown a heritable component of caries risk, which is hypothesized to lie in the enamel proteins made during tooth development. Genome wide association studies (GWAS) have identified 52 loci containing common variants associated with caries risk, the majority of which lie in enhancers. Enhancers are noncoding sequences containing binding motifs that recruit transcription factors and loop to the promoter of a target gene to enhance its transcription in a time, tissue, and cell type-specific manner to control spatiotemporal gene expression in development. Enhancer dysfunction can affect expression of target genes in a subset of expression domains in the body, resulting in tissue-isolated disease, similar to caries presentation. We have observed enrichment of caries SNPs in enhancers active in craniofacial tissue from Carnegie stages 13-17, which contain the developing tooth. We observed a similar enrichment of caries SNPs in conserved enhancers of mouse craniofacial regions from similar developmental stages, including in isolated mouse tooth buds. These results suggest a role for evolutionarily conserved active enhancers of the early tooth in caries predisposition. While we have associated specific tooth enhancers with caries risk, their target genes, which may be ultimately responsible for caries predisposition, remain unidentified. Additionally, these results do not differentiate between the diverse cell types of the tooth including the enamel knot, dental epithelial cells, and dental mesenchymal cells. Given the production of enamel matrix proteins by dental epithelial cells during development, we hypothesize that dysregulation of enamel matrix genes in epithelial cells of the developing tooth, driven by variants in the non-coding genome, predisposes one to caries development. In this proposal, we will identify cell type-specific enhancers at evolutionarily conserved loci associated with caries risk and predict their target genes in the early developing tooth. Aim 1 will identify cell type specific enhancers associated with caries, by performing scATAC-seq on bud stage mouse incisors and using functional chromatin annotations to identify cell type-specific enhancers, then applying linkage disequilibrium-based computational methods to find the subset of enhancers associated with caries risk. Aim 2 will determine caries-associated genes in the dental epithelium of the early developing tooth by integrating multiple “omics” data sets into an activity by contact computational model. With this investigation we will identify caries-associated enhancers and their target genes, which will facilitate quantitative and functional caries risk assays outside the scope of this proposal. The experiments proposed in this fellowship will provide the opportunity to expand my skills in genomics and single cell techniques for a career as a clinician-scientist in the field of dental development and disease.

项目概要 龋齿是一种常见的口腔疾病，将影响 90% 的美国成年人一生。龋损 当牙齿表面的微生物通过产生酸对碳水化合物做出反应时，牙齿的发育会随着时间的推移而发展 会降低牙釉质。除了饮食和卫生等生活方式因素外，研究还表明，遗传因素 龋齿风险的组成部分，推测其存在于牙齿生长过程中产生的牙釉质蛋白中 发展。全基因组关联研究 (GWAS) 已鉴定出 52 个包含常见变异的位点 与龋齿风险相关，其中大部分在于增强剂。增强子是非编码序列 含有结合基序，可招募转录因子并环至靶基因的启动子以增强 它以时间、组织和细胞类型特异性的方式转录，以控制时空基因表达 发展。增强子功能障碍会影响一部分表达域中靶基因的表达 身体，导致组织隔离疾病，类似于龋齿的表现。我们观察到富集 卡内基第 13-17 阶段颅面组织中活跃的增强子中的龋齿 SNP，其中包含正在发育的 齿。我们在小鼠颅面部区域的保守增强子中观察到龋齿 SNP 的类似富集 来自相似的发育阶段，包括在分离的小鼠牙芽中。这些结果表明 早期牙齿在龋齿易感性中进化上保守的活性增强剂。虽然我们有关联 具有龋齿风险的特定牙齿增强剂，其目标基因，可能最终导致龋齿 倾向，尚未确定。此外，这些结果并不能区分不同的细胞类型 牙齿的结构包括牙釉质结、牙上皮细胞和牙间充质细胞。鉴于产量 在发育过程中，牙上皮细胞对牙釉质基质蛋白的影响，我们假设 发育中牙齿上皮细胞中的牙釉质基质基因，由非编码基因的变异驱动 基因组，使人容易患龋齿。在本提案中，我们将确定特定于细胞类型的 与龋齿风险相关的进化保守位点的增强子并预测其目标基因 早期发育的牙齿。目标 1 将通过以下方式识别与龋齿相关的细胞类型特异性增强子： 对芽期小鼠门牙进行 scATAC-seq 并使用功能染色质注释来识别细胞 类型特异性增强子，然后应用基于连锁不平衡的计算方法来查找子集 与龋齿风险相关的增强剂。目标 2 将确定牙齿中与龋齿相关的基因 通过接触将多个“组学”数据集整合到活动中来研究早期发育牙齿的上皮细胞 计算模型。通过这项研究，我们将确定与龋齿相关的增强子及其目标基因， 这将有助于本提案范围之外的定量和功能性龋齿风险测定。这 该奖学金中提出的实验将提供扩展我在基因组学和单细胞学方面的技能的机会 细胞技术作为牙科发育和疾病领域的临床科学家的职业生涯。