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

基本信息

批准号：
10310856
负责人：
Emma Wentworth Winchester
金额：
$ 4.2万
依托单位：
UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-08-01 至 2023-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10310856
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

项目摘要

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.

项目摘要龋齿是一种常见的口腔疾病，一生中会影响美国90％的成年人。狂热的病变当牙齿表面上的微生物通过产生酸对碳水性反应时，牙齿发育的时间随着时间的流逝那降低了搪瓷。除了饮食和卫生等生活方式因素外，研究表明了可遗传的龋齿风险的成分，假设位于牙齿中制成的搪瓷蛋白中发展。基因组广泛的关联研究（GWAS）已经鉴定了52个基因座，其中包含常见变体与汽车风险相关，其中大多数都在增强器。增强子是非编码序列包含募集转录因子并循环到靶基因的启动子以增强的结合基序它以时间，组织和细胞类型特异性方式转录，以控制时空基因表达发展。增强子功能障碍会影响靶基因在表达结构域中的靶基因的表达人体导致组织分离的疾病，类似于汽车表现。我们已经观察到了来自卡内基阶段的颅面组织中的增强剂中的Caries SNP 13-17，其中包含发展齿。我们观察到在小鼠颅面区域组成的增强子中，汽车SNP的类似增强从类似的发育阶段，包括孤立的小鼠牙齿芽。这些结果表明了进化上构成早期牙齿的活跃增强子。虽然我们已经关联过具有龋齿风险的特定牙齿增强剂，其靶基因，最终可能是龋齿的原因易感性，保持不明状态。此外，这些结果没有区分潜水员细胞类型包括牙釉质结，牙齿上皮细胞和牙齿间质细胞的牙齿。给定生产发育过程中牙齿上皮细胞的搪瓷基质蛋白的蛋白质，我们假设失调的失调发育牙齿的上皮细胞中的搪瓷基质基因，由非编码中的变体驱动基因组，容易带来发展。在此提案中，我们将确定特定于细胞类型的进化上的增强子构成与龋齿风险相关的局部局部，并预测其目标基因早期发育的牙齿。 AIM 1将通过在芽级小鼠切牙上执行scatac-seq并使用功能性染色质注释来识别细胞类型特定的增强剂，然后应用基于连锁dissequage dissequage的计算方法来查找子集与龋齿风险相关的增强剂。 AIM 2将确定牙齿中与龋齿相关的基因通过将多个“ OMIC”数据集整合到通过接触中的活动中，早期发育的牙齿上皮计算模型。通过这项研究，我们将确定与汽车相关的增强子及其靶基因，即这将促进本提案范围之外的定量和功能性龋齿风险分析。这该奖学金中提出的实验将为扩展我的基因组和单身技能提供机会作为牙科发育和疾病领域的临床科学家职业的细胞技术。