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

基本信息

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
项目类别：
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

项目摘要

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) 在个体之间表现出显着差异，并且会随着年龄的增长而改变。基于生物年龄的估计（DNAmAge；又名“表观遗传时钟”）是一种稳健且广泛使用的生物标志物衰老，但其根本机制仍然未知。表观遗传时钟的滴答速度，通常称为表观遗传年龄加速（EAA 或 DNAmAge-acc），是衡量年龄增长速度的指标。我们发现，生物衰老可以预测健康和预期寿命，并且可以通过饮食来改变。 EAA 在属于 BXD 家族的小鼠品系之间存在显着差异，并且是一种高度遗传性状，引人注目的是，我们在 BXD、重叠位点和中发现了 EAA 的 QTL。也与人类 EAA 相关的候选基因包括 Stxbp4、Nkx2-3 等基因。在目标 1a 中，我们将对这些候选基因中的一些进行基于 CRISPR/Cas9 的基因删除。我们将使用来自 BXD 的两个亲本品系（C57BL/6J 和 DBA/2J）如果发现基因缺失或敲低对表观遗传时钟有影响，我们将跟进。对转录组进行深度测序（目标 1b），以更深入地了解相关基因在目标 2 中，我们将应用积分系统遗传学来定义表达变化和潜在机制。通过执行甲基化 QTL 导致较大甲基化组变异的遗传变异 (meQTL) 分析将在更大的 BXD 重组近交和高级面板中进行。为我们的 QTL 检测提供足够能力的杂交菌株将利用现有资源。通过初步工作，我们发现一些高度可变的 CpG。肝脏区域与体重以及预期寿命的菌株差异显着相关。我们将绘制顺式和反式作用遗传变异的网络，这些变异以高度的方式配置甲基化组。代谢组织（即肝脏），并检查这些顺式和反式 meQTL 是否也与复杂性状相关例如体重和寿命的自然变化此外，这些肝脏样本已经具有多种特征。组学数据集（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，该层将促进多标量综合分析，这两个目标将揭示调节基因的基因。表观遗传时钟，以及有助于塑造更大甲基化组的遗传变异。能够研究这些表观遗传特征如何与下游分子特征相关，并可能介导下游分子特征例如基因表达，以及体重、新陈代谢和寿命等高阶特征。