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.

摘要 在青年中预防和治疗2型糖尿病(T2D)存在时间敏感的机会之窗 新的分子靶点的发现可用于疾病的预防和控制。主要目标 这项提议有两个方面。首先，这一建议提供了一种授课培训和辅导相结合的策略 培训：(A)测量单细胞染色质可及性和单细胞转录因子 (B)生物信息学，包括机器学习，用于 整合多种经济学、临床和社会人口学数据，以分类T2D的表型；和(C)领导力 以及高质量临床研究所需的管理技能。联合导师将提供综合培训 在单细胞表观基因组和转录实验室技术、数据分析和与四个人的协调培训中 咨询委员会专家。这项建议的第二个关键目标是实施假设- 驱动型研究旨在围绕具有促炎和抗炎功能的免疫细胞亚型展开研究 功能。单细胞测序将克服大量表观遗传学和RNA研究的局限性并改进 基因调控在个体细胞类型中的归属。我们利用KL2母公司的招聘平台 研究招募年轻人并检测与T2D相关的单细胞染色质可及性。在这个十字架上 横断面研究，我们将从两组10-20岁的青年中采集新的外周血液样本：新- 发病的T2D病例参与者(来自24名参与者的96,000个细胞)和健康的正常血糖对照组 参与者(n=96,000个细胞，来自24名参与者)，在一次研究访问期间通过口服葡萄糖耐量获得 测试。我们的具体目标包括(A)检验T辅助细胞(Th)-17细胞将在 与健康对照组参与者相比，T2D和调节性T细胞(Treg)在对照组中更加丰富 参与者，(B)检验决定T辅助细胞类型的基因RORC和Foxp3将具有 临床分组中染色质可及性和基因表达的不同水平，以及(C)机器 基于高通量单细胞表观基因组、转录组、社会人口学和临床数据的学习 对T2D的表型进行分类。总而言之，这项建议汇集了一支由多名导师和顾问组成的团队 科学学科，提供与单细胞表观遗传学，基因表达， 生物信息学、机器学习和临床研究的领导力，重点是发展 美国国立卫生研究院未来研究经费支持。所提出的分析的创新之处，即整合 单细胞表观遗传和单细胞基因表达，将使基因调控网络的构建成为可能 可能会提供新的战略，以保护青少年免受T2D和相关并发症的影响。