Progressive DNA Hypomethylation as a Measure of Mitotic History and Potential Contributor to Replicative Senescence.

进行性 DNA 低甲基化作为有丝分裂历史的衡量标准和复制衰老的潜在贡献者。

基本信息

批准号：
10672187
负责人：
PETER W LAIRD
金额：
$ 59.7万
依托单位：
VAN ANDEL RESEARCH INSTITUTE
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-30 至 2025-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10672187
关键词：
Acceleration Aging Anatomy Attention Attenuated Automobile Driving Behavior Biological Clocks Biology Calibration Cell Aging Cell Culture Techniques Cell Cycle Cell Cycle Inhibition Cell Line Cell Lineage Cell division Cells Chromatin Chromosome Mapping Chronology Circadian Rhythms Complex Contact Inhibition CpG Islands CpG dinucleotide Cues Cytosine DNA DNA Maintenance DNA Methylation DNA Modification Methylases DNA methyltransferase inhibition DNMT3B gene DNMT3a Data Degenerative Disorder Dependence Development Disease Elasticity Epigenetic Process Fibroblasts Gene Expression Genome Genomics Health Histones Human Individual Intervention Link Longevity Maintenance Malignant Neoplasms Measures Metabolic Methylation Mitosis Mitotic Modeling Molecular Outcome Phenotype Physiological Process Recording of previous events Reporting Research Resistance Role Serum Techniques Telomerase Testing Time Tissues cell type deprivation design genomic locus human disease human tissue inhibitor malignant phenotype molecular clock overexpression premalignant premature prevent senescence tool ubiquitin-protein ligase

项目摘要

PROJECT SUMMARY / ABSTRACT Cellular and molecular alterations that accumulate during cell division are considered to be contributors to aging phenotypes. Changes in epigenetic marks, including DNA methylation, have been widely documented in aging. This has spurred the development of epigenetic molecular clocks, which rely primarily on replication- independent gain of methylation at CpG islands. As molecular clocks tuned to chronological time across different tissue types with varying mitotic rates and histories, these clocks are not directly linked to mitotic cell division. In contrast, we have found that loss of DNA methylation at lamina-attached, late-replicating regions of the genome is closely tied to apparent mitotic history. We propose to use primary human cell culture to experimentally validate that mitosis is a driver of hypomethylation, and to explore the underlying mechanisms and consequences of this hypomethylation, to define genomic and chromatin features driving hypomethylation, and use this data to construct a mitotic molecular clock. In Specific Aim 1 we propose to use primary human cell culture to provide experimental evidence for the contribution of mitosis to PMD hypomethylation, and to disentangle the time-dependency and mitosis- dependency of the phenomenon using cell cycle inhibition. We will also investigate whether enhancing maintenance methylation machinery is able to counteract the progressive loss of DNA methylation. In Specific Aim 2 we propose to investigate whether DNA hypomethylation contributes to replicative senescence or associated phenotypes in primary human cell culture. We will investigate whether inhibition of maintenance methylation accelerates senescence, and whether progressive hypomethylation is extended in telomerase- immortalized primary human fibroblasts, contributing to premalignant phenotypes associated with such immortalization. We will also investigate whether accelerated senescence by progerin expression or supra- physiologic O2 leads to accelerated DNA hypomethylation. In Specific Aim 3 we will characterize the genomic and chromatin features that influence individual CpG hypomethylation rates. We will measure the rates of DNA hypomethylation of individual CpGs in six different primary human cell types and use this information to identify cell-type-specific, as well as universal genomic and chromatin drivers of hypomethylation. Finally, we will use elastic net regression on the assembled data to construct cell-type-specific and universal epigenetic mitotic clocks in Specific Aim 4. The preliminary studies strongly support the concept and feasibility of a DNA hypomethylation-based mitotic clock. The outcome of this proposed research could have important impacts on our understanding of the contribution of widespread hypomethylation to aging phenotypes, with potential implications for aging interventions. The availability of accurate molecular clocks specifically designed to measure mitotic history would provide a valuable molecular tool to characterize cells and tissues in human health and disease.

项目概要/摘要细胞分裂过程中积累的细胞和分子改变被认为是促成衰老表型。表观遗传标记的变化，包括 DNA 甲基化，已被广泛记录在老化。这刺激了表观遗传分子钟的发展，它主要依赖于复制- CpG 岛甲基化的独立增益。随着分子钟调整到按时间顺序排列的时间不同的组织类型具有不同的有丝分裂率和历史，这些时钟与有丝分裂细胞没有直接联系分配。相比之下，我们发现，DNA 甲基化的缺失位于核纤层附着的晚期复制区域。基因组与明显的有丝分裂历史密切相关。我们建议使用原代人类细胞培养物通过实验验证有丝分裂是低甲基化的驱动因素，并探索其潜在机制以及这种低甲基化的后果，以确定驱动低甲基化的基因组和染色质特征，并使用这些数据构建有丝分裂分子钟。在具体目标 1 中，我们建议使用原代人类细胞培养物来提供实验证据有丝分裂对 PMD 低甲基化的贡献，并解开时间依赖性和有丝分裂- 使用细胞周期抑制现象的依赖性。我们还将调查是否加强维持甲基化机制能够抵消 DNA 甲基化的逐渐丧失。具体来说目标 2 我们建议研究 DNA 低甲基化是否会导致复制衰老或原代人类细胞培养中的相关表型。我们将调查是否抑制维护甲基化加速衰老，以及端粒酶中进行性低甲基化是否延长永生化的原代人成纤维细胞，导致与此类相关的癌前表型永生化。我们还将研究早老蛋白表达或超表达是否会加速衰老。生理性 O2 会加速 DNA 低甲基化。在具体目标 3 中，我们将表征基因组以及影响个体 CpG 低甲基化率的染色质特征。我们将测量 DNA 的比率六种不同的原代人类细胞类型中单个 CpG 的低甲基化，并使用此信息来识别细胞类型特异性以及低甲基化的通用基因组和染色质驱动因素。最后，我们将使用对组装数据进行弹性网络回归，以构建细胞类型特异性和通用的表观遗传有丝分裂具体目标 4 中的时钟。初步研究强烈支持 DNA 的概念和可行性基于低甲基化的有丝分裂时钟。这项拟议研究的结果可能会产生重要影响我们对广泛的低甲基化对衰老表型的贡献的理解，具有潜在的意义对老龄化干预措施的影响。专门设计的精确分子钟的可用性测量有丝分裂历史将为表征人类细胞和组织提供有价值的分子工具健康和疾病。