Computational evaluation of the causal role of somatic mutations in human aging

体细胞突变在人类衰老中因果作用的计算评估

• 批准号: 10380149
• 负责人: Xiao Dong
• 金额: $ 24.9万
• 依托单位: UNIVERSITY OF MINNESOTA
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-15 至 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10380149
• 关键词: 3' Untranslated Regions; 5' Untranslated Regions; Affect; Age; Aging; B-Cell Activation; B-Lymphocytes; Binding Sites; Blood Cells; CRISPR/Cas technology; Cancer Etiology; Cell physiology; Cells; Centenarian; Code; Collecting Cell; Copy Number Polymorphism; DNA; DNA Damage; DNA Repair; DNA Replication Damage; DNA Sequence Alteration; DNA Transposable Elements; DNA amplification; Data; Defect; Deoxyribonuclease I; Disease; Elderly; Enhancers; Evaluation; Exons; Frequencies; Functional disorder; Genes; Genome; Genomic Instability; Genomic Segment; Goals; Human; Hypersensitivity; Immunization; Individual; Knowledge; Laboratories; Lead; Learning; Location; Locus Control Region; Machine Learning; Mentors; Methods; Mutation; Mutation Analysis; Mutation Spectra; Nucleic Acid Regulatory Sequences; Organism; Pathway Analysis; Process; Proteins; Protocols documentation; RNA; RNA amplification; Regulator Genes; Research; Retrotransposition; Role; Single Nucleotide Polymorphism; Site; Software Tools; Somatic Cell; Somatic Mutation; Source; Stimulus; Study models; Testing; Time; Tissues; Variant; age related; base; cell type; crosslink; dietary restriction; gene regulatory network; genome sequencing; genome-wide; improved; insertion/deletion mutation; nonsynonymous mutation; promoter; repair enzyme; repaired; response; single cell sequencing; single cell technology; theories; transcription factor; whole genome

Project Abstract Although genome instability has long been considered as one of the major causal factors of aging, little is known about the actual number of genome alterations per cell and their effects on aging organisms, most notably humans. In the research proposed here I will take a single cell approach to identify the most common types of somatic mutations, i.e., base substitutions, small INDELS, copy number variation, genome structural variation and retrotranspositions, in human B lymphocytes as a function of age. The overarching goal is then to estimate functional effects of these DNA mutations accumulated during human aging in this particular cell type, which will also serve as a model for studying somatic mutations and their consequences in other cell types. This could never be tested before, because it was never possible to analyze random somatic mutations in a tissue by sequencing bulk DNA from that tissue (mutations are low- abundant), I will achieve this goal by utilizing a new, single-cell, whole genome sequencing (SCWGS) protocol that we developed. In this project I will focus on human B lymphocytes from individuals varying in age from about 30 to over 100 years and determine the genome-wide frequency and location of the different types of mutations in multiple cells from each individual (Aim 1). Preliminary results already show a significant increase of both base substitution mutations and CNVs with age, with a substantial number of these mutations in B cell genomic regions that are potentially functional. Hence, in Aim 2 I will predict the actual functional effects of these potentially functional, age-related mutations using machine learning approaches and integrative network analysis. Finally, in Aim 3 I will empirically test these predictions as to whether the mutation loads observed affect B cell's ability of response to stimulus. Hence, to test the long-standing hypothesis of genome instability as a causal factor in aging ,I will determine age-related mutations in single cells at four levels: (1) number of mutations, mutation spectra and genome distribution in individual cells; (2) potential functional effects of individual mutations, i.e., non-synonymous mutations in exons and mutations in gene regulatory regions; (3) mutations collectively affecting the gene regulatory network; and (4) relationship between mutation load and B cell activation status. In summary, the results of the proposed project will, for the first time uncover possible direct functional effects of somatic mutations on cellular function.

项目摘要 尽管基因组不稳定长期以来一直被认为是衰老的主要因素之一，但很少有人对此进行研究。 了解每个细胞基因组改变的实际数量及其对衰老生物体的影响，大多数 尤其是人类。在这里提出的研究中，我将采用单细胞方法来识别最常见的 体细胞突变的类型，即碱基替换、小 INDELS、拷贝数变异、基因组结构 人类 B 淋巴细胞中随年龄变化的变异和逆转录转座。那么总体目标是 评估人类衰老过程中积累的这些 DNA 突变的功能影响 特定的细胞类型，这也将作为研究体细胞突变及其 对其他细胞类型的影响。这以前从未被测试过，因为永远不可能 通过对组织中的大量 DNA 进行测序来分析组织中的随机体细胞突变（突变是低水平的） 丰富），我将通过利用新的单细胞全基因组测序（SCWGS）协议来实现这一目标 我们开发的。在这个项目中，我将重点关注不同年龄个体的人类 B 淋巴细胞 大约 30 到 100 多年，并确定不同类型的基因组频率和位置 每个个体的多个细胞发生突变（目标 1）。初步结果已经显示显着增加 随着年龄的增长，碱基替换突变和 CNV 都会发生变化，其中大量突变发生在 B 细胞中 具有潜在功能的基因组区域。因此，在目标 2 中我将预测实际的功能效果 使用机器学习方法和综合网络研究这些潜在的功能性、与年龄相关的突变 分析。最后，在目标 3 中，我将根据经验测试这些预测是否观察到突变负载 影响B细胞对刺激的反应能力。因此，为了检验基因组不稳定性的长期假设 作为衰老的致病因素，我将在四个层面上确定单细胞中与年龄相关的突变：（1） 单个细胞中的突变、突变谱和基因组分布； (2) 潜在的功能效应 个体突变，即外显子的非同义突变和基因调控区的突变； (3) 突变共同影响基因调控网络； (4)突变负荷与B的关系 细胞激活状态。总之，拟议项目的结果将首次揭示可能的 体细胞突变对细胞功能的直接功能影响。