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: 10475148
• 负责人: Chunyu Liu
• 金额: $ 58.3万
• 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/10475148
• 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; 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; gene network; gene regulatory network; 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.

项目摘要 能源代谢在人类疾病中起着至关重要的作用。线粒体，细胞的能量室， 拥有自己的基因组（mtDNA），每个细胞最多可拷贝。 mtDNA编码基因 能量代谢的蛋白质。我们（由刘的领导，本申请的pi）最近发现较低的mtdna副本 全血中的数量是较高水平的心血管疾病（CMD）风险因素的独立预测因素 来自多个祖先的约60,000名参与者。例如，mtDNA减少的标准偏差 拷贝数与肥胖的几率增加（OR = 1.15，p = 8E-31）和代谢综合征 （OR = 1.14，p = 1E-32），以及定义这些疾病的几种定量性状的水平增加。 尽管有这些发现，MTDNA与CMD的关联的基本基础尚不清楚，因为 核基因组（NDNA）还编码许多从事线粒体能量产生的蛋白质和 生物合成，因此，线粒体功能的维持需要广泛的MTDNA和 ndna。开发了小鼠杂交nDNA-mtDNA系统。研究人员使用此模型发现 差异NDNA甲基化，基因表达和相同NDNA杂化小鼠的细胞自适应反应， 但具有不同的mtDNA背景。此外，我们（以ARKING为首，本申请的共同I）确定了几个 与mtDNA拷贝数相关的显着DNA甲基化位点。另外，实验修改 mtDNA拷贝数通过TFAM的CRISPR-CAS9敲除，MTDNA复制的调节器， 证明mtDNA拷贝数的调节直接驱动特异性nDNA甲基化的变化 附近转录本的CpG和基因表达。基于这些先前的鼠标模型研究和我们自己的研究 研究，我们假设NDNA的甲基化和基因表达介导mtDNA对 心脏代谢性疾病特征。在此拟议的建议中，我们将利用现有资源，包括整个资源 在六个大型祖先中进行基因组测序和多摩学；我们将严格测试我们的 通过追求四个具体目标来假设。在AIM 1和AIM 2中，我们将进行关联分析以识别 MTDNA相关的NDNA甲基化位点和基因表达水平。 mtDNA功能包括 mtDNA同质和杂质突变以及mtDNA拷贝数。在AIM 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 连续心脏代谢疾病特征的异质性。在AIM 4中，我们将进行集成分析 确定mtDNA和心脏代谢性疾病特征的基因调节网络。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 该研究项目产生的知识体将加深我们对分子机制的理解 潜在的mtDNA和心脏代谢疾病，最终将有助于新的发展 诊断，预防和治疗心脏代谢疾病的方式。