Mitochondrial DNA, Nuclear DNA Methylation, and Cardiometabolic Disease Traits

线粒体 DNA、核 DNA 甲基化和心脏代谢疾病特征

• 批准号: 10297789
• 负责人: Chunyu Liu
• 金额: $ 64.41万
• 依托单位: BOSTON UNIVERSITY MEDICAL CAMPUS
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10297789
• 关键词: Affect; Aging; Anabolism; Applications Grants; Blood; Blood Glucose; Body mass index; CRISPR/Cas technology; Cardiometabolic Disease; Cardiovascular Diseases; Cell Line; Cells; Cellular Metabolic Process; Communities; DNA Methylation; DNA biosynthesis; DNA copy number; DNA-Directed DNA Polymerase; Databases; Development; Diagnosis; Disease; Elderly; Energy Metabolism; Etiology; European; Event; Fasting; Gene Expression; Gene Expression Regulation; Gene Proteins; Genes; Genome; Genotype; Heart; Hybrids; Impairment; Knock-out; Knowledge; Link; Maintenance; Measures; Mediating; Mediation; Metabolic syndrome; Methylation; Mitochondria; Mitochondrial DNA; Modality; Modeling; Modification; Molecular; Mouse Strains; Mus; Mutation; National Heart, Lung, and Blood Institute; Nuclear; Obesity; Participant; Pathway interactions; Play; Prevention; Production; Proteins; Regulator Genes; Reporting; Research; Research Personnel; Research Project Grants; Resources; Risk Factors; Role; Site; System; Testing; Tissues; Trans-Omics for Precision Medicine; Transcript; Translations; Whole Blood; base; cardiovascular disorder risk; cohort; disorder risk; epigenome-wide association studies; factor A; genetic epidemiology; genome sequencing; heteroplasmy; human disease; low density lipoprotein triglyceride; methylation pattern; mouse model; mtTF1 transcription factor; multiple omics; open source; peripheral blood; programs; protein protein interaction; response; trait; transcription factor; whole genome

PROJECT SUMMARY Energy metabolism plays a critical role in human disease. Mitochondria, the energy powerhouses of the cell, have their own genome (mtDNA) which is present up to thousands of copies per cell. mtDNA encodes genes for proteins of energy metabolism. We (led by Liu, PI of this application) recently discovered that lower mtDNA copy number in whole blood is an independent predictor for higher levels of cardiovascular disease (CMD) risk factors in ~60,000 participants from multiple ancestries. For example, one standard deviation of decrease in mtDNA copy number was associated with increased odds of obesity (OR=1.15, p=8e-31) and metabolic syndrome (OR=1.14, p=1e-32), as well as with increased levels of several quantitative traits defining these diseases. Despite these findings, the molecular basis underlying the association of mtDNA with CMD is unclear because the nuclear genome (nDNA) also encodes many of the proteins engaged in mitochondrial energy production and biosynthesis, and thus, maintenance of mitochondrial function requires extensive coordination of mtDNA and nDNA. A mouse hybrid nDNA-mtDNA system was developed. Using this model, the researchers found differential nDNA methylation, gene expression, and cellular adaptive response in hybrid mice of identical nDNA, but with different mtDNA background. Additionally, we (led by Arking, Co-I of this application) identified several significant DNA methylation sites associated with mtDNA copy number. In addition, experimental modification of mtDNA copy number through knockout via CRISPR-Cas9 of TFAM, a regulator of mtDNA replication, demonstrated that modulation of mtDNA copy number directly drives changes in nDNA methylation of specific CpGs and gene expression of nearby transcripts. Based on these previous studies in mouse model and our own research, we hypothesize that methylation and gene expression of nDNA mediate the effects of mtDNA on cardiometabolic disease traits. In this proposed proposal, we will leverage existing resources, including whole genome sequencing and multi-omics in six large cohorts of multiple ancestries; we will rigorously test our hypothesis by pursuing four specific aims. In Aim 1 and Aim 2, we will perform association analyses to identify mtDNA-associated nDNA methylation sites and gene expression levels, respectively. mtDNA features include mtDNA homoplasmic and heteroplasmic mutations, and mtDNA copy number. In Aim 3, we will investigate whether nDNA methylation and/or gene expression mediates the effects of mtDNA copy number and heteroplasmy on continuous cardiometabolic disease traits. In Aim 4, we will perform integrative analyses to identify gene regulation networks underlying mtDNA and cardiometabolic disease traits. We will also functionally test the impact of mtDNA on these gene networks via edited cell lines (e.g., via CRISPR-Cas9 system). The body of knowledge generated by this research project will deepen our understanding of molecular mechanisms underlying mtDNA and cardiometabolic diseases, which will ultimately facilitate the development of new modalities for the diagnosis, prevention, and treatment of cardiometabolic diseases.

项目总结 能量代谢在人类疾病中起着至关重要的作用。线粒体是细胞的能量源泉， 拥有自己的基因组(MtDNA)，每个细胞存在多达数千个拷贝。线粒体DNA编码基因 能量代谢的蛋白质。我们(由本申请的刘、派领导)最近发现，较低的mtDNA拷贝 全血中的数量是心血管疾病(CMD)风险因素水平较高的独立预测因素 来自多个祖先的约60,000名参与者。例如，线粒体DNA减少的一个标准差 拷贝数与肥胖(OR=1.15，p=8E-31)和代谢综合征的风险增加相关 (OR=1.14，p=1e-32)，以及定义这些疾病的几个数量性状水平的增加。 尽管有这些发现，线粒体DNA与CMD关联的分子基础尚不清楚，因为 核基因组(NDNA)也编码许多参与线粒体能量产生和 生物合成，因此，维持线粒体的功能需要广泛的协调线粒体DNA和 NDNA。建立了小鼠杂交nDNA-mtDNA系统。使用这个模型，研究人员发现 相同nDNA杂交小鼠的差异nDNA甲基化、基因表达和细胞适应性反应， 但有不同的线粒体DNA背景。此外，我们(由Arking牵头，本应用程序的Co-I)确定了几个 与线粒体DNA拷贝数相关的显著DNA甲基化位点。此外，试验性的修改 通过TFAM的CRISPR-Cas9敲除mtDNA拷贝数， 证实了mtDNA拷贝数的调节直接驱动了特定基因nDNA甲基化的变化 CPGS和邻近转录本的基因表达。基于这些先前对小鼠模型和我们自己的研究 研究中，我们假设nDNA的甲基化和基因表达介导了mtDNA对 心脏代谢性疾病的特征。在这项提议中，我们将利用现有资源，包括 基因组测序和多重组学在六个多祖先的大队列中；我们将严格测试我们的 通过追求四个具体目标来提出假设。在目标1和目标2中，我们将执行关联分析以确定 线粒体DNA相关的nDNA甲基化位点和基因表达水平。线粒体DNA的特征包括 线粒体DNA同质和异质突变，以及线粒体DNA拷贝数。在目标3中，我们将调查 NDNA甲基化和/或基因表达是否介导mtDNA拷贝数和 持续性心脏代谢性疾病性状的异质性。在目标4中，我们将进行综合分析，以 确定线粒体DNA和心脏代谢性疾病特征的基因调控网络。我们还将在功能上 通过编辑的细胞系(例如，通过CRISPR-CAS9系统)测试mtDNA对这些基因网络的影响。这个 这项研究项目产生的大量知识将加深我们对分子机制的理解 潜在的线粒体DNA和心脏代谢疾病，这最终将促进新的 心脏代谢性疾病的诊断、预防和治疗模式。