Mapping Integrated Single-Cell Chromatin Accessibility with the Single-Cell Transcriptional Landscape in Pediatric Type 2 Diabetes

绘制儿科 2 型糖尿病中单细胞染色质可及性与单细胞转录景观的整合图谱

• 批准号: 10664557
• 负责人: Lisa Rachel Staimez
• 金额: $ 15.34万
• 依托单位: EMORY UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2027-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10664557
• 关键词: 21 year old; ATAC-seq; Adult; Advisory Committees; Anti-Inflammatory Agents; Apoptosis; Artificial Intelligence; Automobile Driving; Beta Cell; Bioinformatics; Biological Markers; Blood; Blood specimen; Cell Death; Cells; Cellular Assay; Cessation of life; Childhood; Chromatin; Circulation; Classification; Clinical; Clinical Data; Clinical Research; Clinical Sciences; Complication; Cross-Sectional Studies; DNA Methylation; Data; Data Analyses; Deterioration; Development; Diabetes Mellitus; Diabetic Nephropathy; Discipline; Disease; Distress; Epidemiology; Epigenetic Process; FOXP3 gene; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Grant; Helper-Inducer T-Lymphocyte; Immunophenotyping; Individual; Inflammation; Inflammatory; Infrastructure; Insulin; Insulin Resistance; Investigation; Laboratories; Leadership; Life Cycle Stages; Life Style Modification; Machine Learning; Malignant Neoplasms; Maps; Measurement; Measures; Mentors; Metabolic Diseases; Methods; Methylation; Molecular; Molecular Profiling; Molecular Target; Non-Insulin-Dependent Diabetes Mellitus; OGTT; Obesity; Organ Transplantation; Parents; Participant; Peripheral Nervous System Diseases; Phenotype; Predisposition; Prevention; RNA; Regulatory T-Lymphocyte; Reporting; Research; Research Personnel; Retinal Diseases; Site; Source; Specificity; Structure of beta Cell of islet; Symptoms; T-Lymphocyte; Techniques; Testing; Time; Tissue-Specific Gene Expression; Training; Translations; Transposase; United States National Institutes of Health; Visit; Youth; aged; aspirate; cell free DNA; cell type; diabetes pathogenesis; disorder control; disorder prevention; epigenetic regulation; epigenomics; experience; gene regulatory network; glycemic control; improved; indexing; innovation; inter-individual variation; islet; multiple omics; novel marker; peripheral blood; pharmacologic; prenatal testing; preservation; prevent; recruit; risk stratification; single cell sequencing; single cell technology; skills; sociodemographics; success; systemic inflammatory response; transcription factor; transcriptome sequencing; transcriptomics; translational applications

ABSTRACT A time-sensitive window of opportunity exists in preventing and treating type 2 diabetes (T2D) in youth where the identification of new molecular targets could be used for disease prevention and control. The key objectives of this proposal are twofold. First, this proposal provides a combined strategy of didactic training and mentored training for (a) the measurement of single-cell chromatin accessibility and single-cell transcription factors associated with T2D using innovative wet-lab techniques; (b) bioinformatics, including machine learning, for the integration of multi-omic, clinical, and sociodemographic data to classify phenotypes of T2D; and (c) leadership and management skills required of high-quality clinical studies. The co-mentors will provide integrated training in single-cell epigenomic and transcriptomic lab techniques, data analyses, and coordinated training with four advisory committee experts. The second key objective of this proposal is the implementation of hypothesis- driven research aims around subtypes of immune cells that have pro-inflammatory vs. anti-inflammatory function. Single-cell sequencing will overcome the limitations of bulk epigenetic and RNA studies and improve attribution of gene regulation in individual cell types. We leverage the recruitment platform from our KL2 parent study to recruit youth and examine single-cell chromatin accessibility associated with T2D. In this cross sectional study, we will collect new peripheral blood samples from two groups of youth aged 10-20-years: new- onset T2D case participants (n=96,000 cells from 24 participants) and healthy, normoglycemia control participants (n=96,000 cells from 24 participants), obtained during a single study visit by oral glucose tolerance test. Our specific aims include (a) testing the hypothesis that T helper (Th)-17 cells will be more abundant in T2D compared to healthy control participants and regulatory T cells (Treg) more abundant in control participants, (b) testing the hypothesis that genes determining T Helper cell type, Rorc and Foxp3, will have different levels of chromatin accessibility and different gene expression in clinical groups, and (c) machine learning based on high-throughput single-cell epigenomic, transcriptomic, sociodemographic, and clinical data to classify phenotypes of T2D. In summary, this proposal assembles a team of mentors and advisors across scientific disciplines to provide thorough training in research related to single-cell epigenetics, gene expression, bioinformatics, machine learning, and leadership in clinical studies, with emphasis on the development of future research for NIH grant support. The innovations of the proposed analyses, namely the integration of single cell epigenetic and single cell gene expression, will enable construction of gene regulatory networks that may inform new strategies to protect youth from T2D and related complications.

抽象的 预防和治疗青少年 2 型糖尿病 (T2D) 存在一个时间敏感的机会窗口，其中 新分子靶标的鉴定可用于疾病预防和控制。主要目标 这项建议有两个方面。首先，该提案提供了教学培训和指导的综合策略 (a) 单细胞染色质可及性和单细胞转录因子测量的培训 使用创新的湿实验室技术与 T2D 相关； (b) 生物信息学，包括机器学习， 整合多组学、临床和社会人口学数据对 T2D 表型进行分类； (c) 领导力 高质量临床研究所需的和管理技能。共同导师将提供综合培训 单细胞表观基因组和转录组实验室技术、数据分析以及与四个人的协调培训 咨询委员会专家。该提案的第二个关键目标是假设的实施 - 驱动性研究的目标是围绕具有促炎性和抗炎性的免疫细胞亚型 功能。单细胞测序将克服大量表观遗传学和 RNA 研究的局限性并改善 个体细胞类型中基因调控的归因。我们利用 KL2 母公司的招聘平台 研究招募年轻人并检查与 T2D 相关的单细胞染色质可及性。在这个十字 截面研究，我们将从两组10-20岁的青少年中采集新的外周血样本：新- 发病 T2D 病例参与者（n=24 名参与者的 96,000 个细胞）和健康、血糖控制正常的参与者 参与者（n = 24 名参与者的 96,000 个细胞），通过口服葡萄糖耐量进行单次研究访问期间获得 测试。我们的具体目标包括 (a) 检验以下假设：辅助性 T (Th)-17 细胞在 与健康对照参与者相比，T2D 参与者的调节性 T 细胞 (Treg) 更丰富 参与者，(b) 检验决定 T 辅助细胞类型的基因 Rorc 和 Foxp3 的假设 临床组中不同水平的染色质可及性和不同的基因表达，以及（c）机器 基于高通量单细胞表观基因组、转录组、社会人口统计学和临床​​数据的学习 对 T2D 表型进行分类。总之，该提案组建了一支由各个领域的导师和顾问组成的团队 科学学科提供单细胞表观遗传学、基因表达、 生物信息学、机器学习和临床研究的领导力，重点是开发 NIH 拨款支持的未来研究。所提出的分析的创新点，即整合 单细胞表观遗传和单细胞基因表达，将能够构建基因调控网络 可能会为保护青少年免受 T2D 及相关并发症的新策略提供信息。