Cytosolic DNA, Telomeres/Subtelomeres, and Epigenetics: A Longitudinal Twin Study to Assess the Role of Genetics and Environment on their Frequency and Inter-relationships

细胞质 DNA、端粒/亚端粒和表观遗传学：评估遗传和环境对其频率和相互关系的作用的纵向双胞胎研究

• 批准号: 10722866
• 负责人: COLLEEN K JACKSON-COOK
• 金额: $ 82.05万
• 依托单位: VIRGINIA COMMONWEALTH UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-15 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10722866
• 关键词: Age; Aging; Algorithms; Atomic Force Microscopy; Basic Science; Biological; Biological Assay; Biological Markers; Blood; CRISPR/Cas technology; Cell physiology; Cells; Chromatin; Chromosomes; Chronic; Circular DNA; DNA; DNA Methylation; Data; Development; Dizygotic Twins; Early Diagnosis; Early treatment; Environment; Environmental Risk Factor; Epigenetic Process; Fluorescent in Situ Hybridization; Frequencies; Functional disorder; Future; Gene Expression Profile; Genes; Genetic; Genetic Predisposition to Disease; Genome; Health; Health Sciences; Homeostasis; Human; Human Chromosomes; Immunologic Surveillance; Individual; Individual Differences; Inflammation; Interferons; Knowledge; Length; Longitudinal Studies; Measures; Mediating; Mediator; Methods; Methylation; Mitochondria; Modeling; Monozygotic twins; Mutation; Oral mucous membrane structure; Outcome; Pathway interactions; Pattern; Persons; Pharmacogenomics; Play; Ploidies; Predisposition; Protocols documentation; Quantitative Genetics; Resolution; Role; Site; Somatic Cell; Source; Specimen; Spectral Karyotyping; Statistical Models; Stimulator of Interferon Genes; Technology; Telomere Maintenance; Testing; Time; Tissues; Twin Multiple Birth; Twin Studies; Variant; age related; beta-Galactosidase; bioinformatics tool; cohort; cytokine; design; efficacy testing; genetic makeup; genome-wide; innate immune pathways; methylation pattern; micronucleus; neuronal cell body; new therapeutic target; novel; predictive tools; reduce symptoms; response; screening; senescence; targeted treatment; telomere; tool; trait; transcriptome; transcriptomics

Cystolic DNA (cyDNA), which is acquired in somatic cells, is emerging as an instigator/integrator of cellular functions associated with aging, yet the causes/consequences of cyDNA are poorly understood. Do individuals have a genetic predisposition to develop cyDNA or is its frequency most heavily influenced by environmental factors? Is cyDNA an early trigger for the acquisition of other age-related biomarker hallmarks, or does it arise in response to perturbations involving a subset of these hallmarks? To answer these primary questions, we will complete a longitudinal study (10 to 15 years timeframe) of 100 twin pairs [70 identical (MZ) and 30 fraternal (DZ) twin pairs; 200 individuals] who are discordant (35 MZ; 15 DZ) or concordant (35 MZ; 15 DZ) for cyDNA frequencies. The twin pairs will vary in age (currently 22 to at least 80 y.o) to allow us to chronicle associations between aging hallmarks and the acquisition of cyDNA. For each time point we will determine: (a) cyDNA levels, (b) chromosome specific-telomere/subtelomere lengths, (c) senescence markers, and (d) DNA methylation patterns in cells from two different tissues (blood and buccal mucosa cells [to assess potential soma-related differences]). Two measures of cyDNA will be quantified: (1) micronuclei (MN) frequency; and (2) extrachromosomal circular DNA (eccDNA) frequency. The MN frequencies will be identified for each of the 24 human chromosomes using a novel assay we developed that combines spectral karyotyping and fluorescence in situ hybridization technologies. The genetic contents of the eccDNA will be determined using our rolling circle amplification and sequencing protocol. Chromosome-specific telomere and subtelomere lengths will be determined using our Q-FISH method and our newly developed nanomapping method that exploits atomic force microscopy, CRISPR-Cas9, and our novel genome sequence algorithm to provide unprecedented resolution of telomere/subtelomere measures. We will also use “state of the art” tools we developed/optimized, to quantify telomere dysfunction; senescence (SADS, classical, and transcriptome studies), and genome-wide DNA methylation patterns. Using a method of robust variance component estimation (implemented in the FISHER quantitative genetics package), this study will provide the first measure of the extent to which individual differences in cyDNA and subtelomere lengths (which are associated with TERRA) are determined by additive genetic, common environmental, and specific environmental effects. We will also use “state of the art” statistical modeling and bioinformatic tools that we developed/optimized to analyze biomarker patterns within individuals, between co-twins, and among twin pairs to determine the stability of patterns with aging, and to identify temporal, as well as driver/mediator, relationships among cyDNA and other aging hallmarks (telomeres/subtelomeres, DNA methylation, senescence). The information gained from this study could also lead to the development of a health screening test(s) and/or identify new therapeutic targets that could transform our approach for developing treatments to alleviate symptoms of age-related health conditions.

在体细胞中获取的阳离子DNA（CyDNA）正在成为细胞的刺激器/积分器 与衰老相关的功能，但是cydna的原因/后果知之甚少。个人吗？ 具有开发cydna的遗传易感性，或者是其频率受环境影响最大的频率 因素？ cydna是获得其他与年龄相关的生物标志的早期触发因素，还是出现 响应涉及这些标志的子集的扰动？要回答这些主要问题，我们将 完成100对的纵向研究（10到15年）[70（MZ）和30个兄弟 （DZ）双对； 200个个人（35 mz; 15 dz）或一致的人（35 mz; 15 dz） 频率。双胞胎对年龄将有所不同（目前22至少80 y.o），使我们能够慢性关联 在老化的标志和cydna的获取之间。对于每个时间点，我们将确定：（a）cydna 水平，（b）染色体特异性 - 凝集粒/亚端粒长度，（c）感应标记和（d）DNA 来自两个不同组织的细胞中的甲基化模式（血液和颊粘膜细胞[评估潜力 与SOM相关的差异]）。将量化两种cydna的度量：（1）微核（Mn）频率； （2） 外圆形DNA（ECCDNA）频率。将确定24个中的每个频率 我们开发了使用新颖的测定法结合光谱核分型和荧光的人类染色体 原位杂交技术。 ECCDNA的遗传含量将使用我们的滚动确定 圆圈放大和测序协议。染色体特异性的端粒和亚电位长度将是 使用我们的Q-fish方法和我们新开发的纳米化方法来确定原子 力显微镜，CRISPR-CAS9和我们的新型基因组序列算法以提供前所未有的 端粒/亚电位测量的分辨率。我们还将使用我们开发/优化的“最先进”工具， 量化端粒功能障碍；感应（SADS，经典和转录组研究）和全基因组 DNA甲基化模式。使用强大的方差组件估计方法（在 Fisher定量遗传学包），这项研究将提供首先测量的程度 确定cydna和亚电位长度的个体差异（与Terra相关） 通过添加遗传，常见环境和特定的环境影响。我们还将使用“ 我们开发/优化以分析生物标志物模式的统计建模和生物信息学工具 在个体内部，联合双胞胎之间以及双对之间，以确定衰老的模式的稳定性，以及 为了确定CyDNA和其他老化标志之间的临时性以及驾驶员/调解人 （端粒/亚端子，DNA甲基化，感应）。从这项研究中获得的信息也可能 导致开发健康筛查测试和/或确定可能的新治疗靶标 改变我们开发治疗方法以减轻与年龄相关的健康状况的症状的方法。