Integrative, age-related changes in genome and epigenome in human lung in relation to smoking

与吸烟相关的人肺基因组和表观基因组的综合、年龄相关变化

• 批准号: 10320918
• 负责人: SIMON D SPIVACK
• 金额: $ 66.36万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10320918
• 关键词: Affect; Age; Aging; Airway Disease; Aneuploidy; Cell Aging; Cell Nucleus; Cell division; Cells; Chromosome abnormality; Chronic Obstructive Pulmonary Disease; Complex; Copy Number Polymorphism; Cytosine; DNA; DNA Damage; DNA Methylation; DNA Repair; DNA Sequence Alteration; DNA Structure; DNA biosynthesis; Data; Depurination; Detection; Development; Disease; Early Diagnosis; Environmental Risk Factor; Epigenetic Process; Future; Gene Expression; Genetic; Genetic Code; Genetic Transcription; Genome; Genomic Instability; Genomics; Human; Individual; Lead; Link; Lung; Lung diseases; Malignant Neoplasms; Maps; Methods; Methylation; Molecular; Mutation; Noise; Normal tissue morphology; Organ; Pattern; Prevention; Pulmonary Fibrosis; Retrotransposition; Risk; Risk Factors; Sampling; Smoker; Smoking; Source; Stress; Testing; Therapeutic; Time; Tobacco smoke; Variant; age related; base; bronchial epithelium; cigarette smoking; crosslink; environmental tobacco smoke exposure; epigenome; epigenomics; functional loss; human tissue; methylation pattern; methylome; methylomics; non-smoker; normal aging; repaired; response; single cell analysis; single-cell RNA sequencing; tobacco exposure; tobacco smoke exposure; transcriptome; transcriptomics

ABSTRACT Aging is the main risk factor for many age-related lung diseases, including COPD and pulmonary fibrosis. It has been speculated that this aging-disease relationship is due to the complex interaction of multiple genetic, epigenetic and transcriptomic alterations that occur in normal human lung over time. In turn, these age-related changes are impacted by environmental factors, such as cigarette smoking. Unfortunately, little is known about age-related molecular alterations in human lung. To some extent this is due to the lack of methods to analyze human tissues for changes occurring stochastically, i.e., affecting individual cells or groups of cells in different ways. The best example is genome instability, one of the hallmarks of aging. Genome instability can be defined as changes in the genetic code, varying from large chromosomal aberrations, to smaller deletions, insertions and copy number variation, and base substitution mutations. The underlying causes of genome instability are errors during cell division, DNA replication or DNA repair of DNA damage. Such changes are irreversible and are in striking contrast to DNA damage, which can be repaired. DNA damage involves physical alterations in DNA structure, e.g., breaks, depurination, depyrimidination, crosslinks, modified bases. Unfortunately, mutations in normal tissues are different from cell to cell and very difficult to study, except using single cell approaches as we will do in the proposed project. However, DNA damage induced in the lung during aging also evokes a DNA damage response, which can lead to multiple epigenetic alterations that are consistent from cell to cell and can be detected in bulk DNA. In addition, a stochastic pattern of age-related changes is likely to occur during aging, the detection of which requires a single cell approach. Here we propose to comprehensively analyze human lung bronchial epithelium for both stochastic and adaptive changes in the genome, epigenome and transcriptome. This project will integrate these comprehensive spectra of genomic and epigenomic change of normal human bronchial epithelium in relation to age and tobacco smoke exposure. This will provide reference data for future comparisons of lung disease states, enhance our understanding of age-and smoking-related mechanisms of lung disease, and thereby facilitate the development of early detection, prevention and therapeutic strategies.

摘要 衰老是许多与年龄相关的肺部疾病的主要危险因素，包括COPD和肺纤维化。它 据推测，这种衰老与疾病的关系是由于多种遗传因素的复杂相互作用， 表观遗传学和转录组学改变随时间发生在正常人肺中。反过来，这些与年龄有关的 这些变化受到环境因素的影响，例如吸烟。不幸的是， 与年龄相关的人类肺部分子改变在某种程度上这是由于缺乏分析方法造成的 人体组织中随机发生的变化，即，影响不同细胞中的单个细胞或细胞群 的方式最好的例子是基因组的不稳定性，这是衰老的标志之一。基因组不稳定性可以定义为 遗传密码的变化，从大的染色体畸变，到较小的缺失，插入， 拷贝数变异和碱基替换突变。基因组不稳定的根本原因是 细胞分裂、DNA复制或DNA损伤修复过程中的错误。这种变化是不可逆转的， 与可以修复的DNA损伤形成鲜明对比。DNA损伤包括身体的改变， DNA结构，例如，断裂、脱嘌呤、脱嘧啶、交联、修饰碱基。不幸的是， 正常组织中的突变在细胞与细胞之间是不同的，除了使用单细胞外， 就像我们在项目中所做的那样。然而，在衰老过程中， 也引起DNA损伤反应，这可能导致多种表观遗传改变， 从细胞到细胞，并且可以在大量DNA中检测到。此外，与年龄有关的变化的随机模式是 可能发生在老化过程中，其检测需要单细胞方法。在此，我们建议 全面分析人肺支气管上皮细胞的随机和适应性变化， 基因组、表观基因组和转录组。该项目将整合这些全面的基因组谱， 正常人支气管上皮细胞表观基因组变化与年龄和烟草烟雾暴露的关系。 这将为今后肺部疾病状态的比较提供参考数据， 年龄和吸烟相关的肺部疾病的机制，从而促进早期发展， 检测、预防和治疗策略。

项目成果

FOXO3a acts to suppress DNA double-strand break-induced mutations.

• DOI: 10.1111/acel.13184
• 发表时间: 2020-09
• 期刊: Aging cell
• 影响因子: 7.8
• 作者: White RR;Maslov AY;Lee M;Wilner SE;Levy M;Vijg J
• 通讯作者: Vijg J

Genetics of extreme human longevity to guide drug discovery for healthy ageing.

• DOI: 10.1038/s42255-020-0247-0
• 发表时间: 2020-08
• 期刊: Nature metabolism
• 影响因子: 20.8
• 作者: Zhang ZD;Milman S;Lin JR;Wierbowski S;Yu H;Barzilai N;Gorbunova V;Ladiges WC;Niedernhofer LJ;Suh Y;Robbins PD;Vijg J
• 通讯作者: Vijg J

Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing.

• DOI: 10.1126/sciadv.abm3259
• 发表时间: 2022-04-08
• 期刊: Science advances
• 影响因子: 13.6
• 作者: Maslov AY;Makhortov S;Sun S;Heid J;Dong X;Lee M;Vijg J
• 通讯作者: Vijg J