Functional genetic analysis of epigenetic age acceleration and the regulatory landscape of the methylome

表观遗传年龄加速的功能遗传分析和甲基化组的调控景观

• 批准号: 10674263
• 负责人: Khyobeni Mozhui
• 金额: $ 31.54万
• 依托单位: UNIVERSITY OF TENNESSEE HEALTH SCI CTR
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10674263
• 关键词: Acceleration; Adult; Affect; Age; Aging; Alleles; Biological; Biological Aging; Biological Assay; Biological Markers; Body Weight; CRISPR/Cas technology; Caloric Restriction; Candidate Disease Gene; Cell Culture Techniques; Cells; Chromosome 19; Chromosome Mapping; Chronology; Cis-Acting Sequence; Complement; Complex; DNA; DNA Methylation; Data Set; Detection; Development; Diet; Dwarfism; Epigenetic Process; Exhibits; Family; Fibroblasts; Freezing; Funding; Gene Deletion; Gene Expression; Genes; Genetic; Genetic Transcription; Genetic study; Genotype; Goals; Health; Heritability; High Fat Diet; Human; Human Genome; In Vitro; Inbreeding; Individual; Intervention; Life Expectancy; Light; Link; Liver; Longevity; Measures; Mediating; Mediator of activation protein; Metabolic; Metabolism; Methylation; Molecular; Mouse Strains; Mus; Obesity; Parents; Pattern; Phenotype; Population; Proteomics; Quantitative Trait Loci; RNA Interference; Recombinants; Resources; Sampling; Shapes; Sirolimus; Site; Specimen; System; Testing; Ticks; Tissues; Validation; Variant; Work; base; biobank; cohort; deep sequencing; epigenome; epigenomics; follow-up; functional genomics; genetic analysis; genetic architecture; genetic manipulation; genetic variant; genome wide association study; genome-wide; insight; knock-down; metabolomics; methylome; mouse genetics; multiple omics; next generation sequencing; trait; transcriptome sequencing; transcriptomics

DNA methylation (DNAm) shows significant variation between individuals and is altered by aging. The DNAm- based estimate of biological age (DNAmAge; aka, “epigenetic clock”) is a robust and widely used biomarker of aging, but its underlying mechanisms remain mostly unknown. The rate at which the epigenetic clock ticks, commonly referred to as epigenetic age acceleration (EAA or DNAmAge-acc), is a measure of the rate of biological aging and is predictive of health and life expectancy, and modifiable by diet. We have found that EAA varies significantly between mouse strains belonging to the BXD family, and is a highly heritable trait that is linked to strong QTLs. Strikingly, the QTLs we have uncovered for EAA in the BXDs, overlap loci and candidate genes that are also associated with EAA in humans. These include genes such as Stxbp4, Nkx2–3, and Cutc. In Aim 1a, we will perform CRISPR/Cas9 based gene deletion of few of these candidate genes in mouse fibroblast cells. We will use cells derived from the two parent strains of the BXDs (C57BL/6J, and DBA/2J). If gene deletion or knockdown is found to have an impact on the epigenetic clock, we will follow-up with deep sequencing of the transcriptome (Aim 1b) to gain deeper insights into the associated gene expression changes and potential mechanisms. In Aim 2, we will apply integrative systems genetics to define the genetic variants that contribute to variability in the larger methylome by performing methylation QTL (meQTL) analyses. This will be carried out in a larger panel of the BXD recombinant inbred and advanced intercross strains that will give us sufficient power for QTL detection. Aim 2 will leverage an existing resource of biobanked liver specimens. From preliminary work, we have found that some of the highly variable CpG regions in the liver are significantly correlated with body weight, and with strain differences in life expectancy. We will chart the networks of cis- and trans-acting genetic variants that configure the methylome in a highly metabolic tissue (i.e., liver), and examine whether these cis and trans-meQTLs also relate to complex traits such as body weight, and natural variation in lifespan. Furthermore, these liver samples already have multi- omics datasets (transcriptomics, proteomics, and metabolomics), and this will add an epigenomic layer that will facilitate multi-scalar integrative analyses. Together, the two aims will shed light on the genes that regulate the epigenetic clock, and the genetic variants that contribute to shaping the larger methylome. Additionally, we will be able to study how these epigenetic traits associate with, and possibly mediate, downstream molecular traits such as gene expression, and higher order traits such as body weight, metabolism, and longevity.

DNA甲基化（DNAM）显示了个体之间的显着差异，并通过衰老改变。 dnam- 基于生物年龄的估计值（damage; aka，“表观遗传钟”）是一种强大而广泛使用的生物标志物 衰老，但其基本机制仍然主要未知。表观遗传时钟的速度， 通常称为表观遗传年龄加速度（EAA或Damage-ACC），是对率的量度 生物衰老，可以预测健康和预期寿命，并且可以通过饮食进行修改。我们发现 EAA品种在属于BXD家族的老鼠菌株之间显着，并且是一个高度可遗传的特征 与强QTL有关。令人惊讶的是，我们在BXD，重叠基因座和 候选基因也与人类中的EAA相关。这些包括诸如stxbp4，nkx2-3的基因， 和CUTC。在AIM 1A中，我们将对这些候选基因中的几个基因缺失进行基于CRISPR/CAS9的基因缺失 小鼠成纤维细胞。我们将使用源自BXDS的两个母体菌株（C57BL/6J和）的单元格 DBA/2J）。如果发现基因缺失或敲除对表观遗传时钟有影响，我们将跟进 通过对转录组的深度测序（AIM 1B），以获得对相关基因的更深入的见解 表达变化和潜在机制。在AIM 2中，我们将应用集成系统遗传学来定义 通过执行甲基化QTL来导致较大甲基机变异性的遗传变异 （MEQTL）分析。这将在较大的BXD重组和高级面板中进行 间折叠菌株将为我们提供足够的QTL检测功率。 AIM 2将利用现有资源 生物群的肝样品。从初步工作中，我们发现一些高度可变的CpG 肝脏中的区域与体重显着相关，并且预期寿命差异。 我们将绘制顺式和反式作用遗传变异的网络，这些网络在高度配置甲基 代谢组织（即肝脏），并检查这些顺式和反式 - 米克特人是否也与复杂性状有关 例如体重和寿命的自然变化。此外，这些肝脏样品已经具有多种多样 OMICS数据集（转录组学，蛋白质组学和代谢组学），这将添加一个表观基因组层 促进多量表综合分析。这两个目标在一起将阐明调节的基因 表观遗传时钟以及有助于塑造较大甲基团的遗传变异。此外，我们会的 能够研究这些表观遗传特征如何与下游分子性状相关联和可能的介导 例如基因表达以及高阶性状，例如体重，代谢和寿命。