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: 10895267
• 负责人: Emma Wentworth Winchester
• 金额: $ 5.35万
• 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/10895267
• 关键词: Acids; Adult; Affect; Ameloblasts; Binding; Biological Assay; Candidate Disease Gene; Carbohydrates; Cells; Cellular Assay; Chromatin; Clinical; Code; Computer Models; Computing Methodologies; Conceptions; Coupled; Data; Data Set; Dental; Dental Enamel; Dental Hygiene; Dental Pulp; Dental Sac; Dental caries; Dentin; Development; Diet; Disease; Embryo; Enamel Formation; Enhancers; Epithelial Cells; Epithelium; 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; candidate identification; 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.

项目摘要 龋病是一种常见的口腔疾病，90%的美国成年人在一生中都会受到影响。龋病 当牙齿表面的微生物通过产酸对碳水化合物做出反应时，牙齿就会随着时间的推移而发育 那会使牙釉质退化。除了饮食和卫生等生活方式因素外，研究表明， 龋齿风险的组成部分，假设存在于牙齿过程中产生的釉质蛋白中 发展。全基因组关联研究已经确定了52个包含常见变异的基因座 与龋齿风险有关，其中大部分存在于增强剂中。增强子是非编码序列 含有结合基序，可招募转录因子并循环到目标基因的启动子以增强 它以时间、组织和细胞类型特异的方式转录，以控制时空基因的表达 发展。增强子功能障碍可影响靶基因在表达域子集中的表达 对身体造成组织隔离的疾病，类似于龋齿的呈现。我们观察到富集物 卡内基13-17期头面部组织中活跃的促进剂中的龋病SNPs，这包含了发育中的 牙齿。我们在小鼠颅面部区域的保守增强子中观察到类似的龋病SNPs的富集性。 来自相似的发育阶段，包括分离的小鼠牙蕾。这些结果表明， 进化上保守的早期牙齿在龋病易感性中的活性增强剂。虽然我们已经将 有龋齿风险的特定牙齿增强剂，其目标基因可能是最终导致龋齿的原因 倾向性，仍然无法辨认。此外，这些结果没有区分不同的细胞类型 包括牙釉质结节、牙齿上皮细胞和牙齿间充质细胞。考虑到生产情况 牙上皮细胞在发育过程中对釉质基质蛋白的影响，我们假设 发育中牙齿上皮细胞中的釉质基质基因，由非编码变异所驱动 基因组，易患龋齿。在本提案中，我们将确定特定于细胞类型的 与龋病风险相关的进化保守基因座上的增强子和预测其目标基因 发育早期的牙齿。AIM 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 对蕾状期小鼠切牙进行scatac-seq，并使用功能性染色质注释来识别细胞 特定类型的增强子，然后应用基于连锁不平衡的计算方法来找到子集 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集成到一个活动中的早期发育牙齿上皮 计算模型。通过这项研究，我们将识别与龋齿相关的增强子及其靶基因， 这将促进本提案范围之外的定量和功能性龋病风险分析。这个 在此奖学金中提出的实验将提供机会来扩展我在基因组学和单身方面的技能 细胞技术，作为一名临床医生--牙科发育和疾病领域的科学家。