The Dynamics of Mitochondrial Mutations

线粒体突变的动力学

• 批准号: 8945838
• 负责人: KATERYNA MAKOVA
• 金额: $ 52.34万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2019-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8945838
• 关键词: ATP Synthesis Pathway; Accounting; Address; Affect; Age; Aging-Related Process; Alleles; Area; Biochemical Process; Blood; Blood Cells; Categories; Cell Count; Cell Lineage; Cell division; Cells; Child; Communities; Computer software; DNA Sequence; DNA Sequence Alteration; Data; Development; Disease; Embryo; Environment; Evolution; Family Planning; Female; Fertilization; Frequencies; Gene Frequency; Generations; Genetic Drift; Genetic Models; Genetic Population Study; Genome; Germ Lines; Germ-Line Mutation; Goals; Hereditary Disease; Human; Human Genetics; Human body; Individual; Life; Malignant Neoplasms; Methodology; Methods; Mitochondria; Mitochondrial DNA; Mitotic; Modeling; Mothers; Mutation; Oocytes; Oogenesis; Oogonia; Organism; Pennsylvania; Population; Population Genetics; Process; Recommendation; Relative (related person); Reproduction; Resources; Risk Factors; Sampling; Sequence Analysis; Severities; Shapes; Site; Societies; Somatic Mutation; Testing; Tissues; Trees; Uncertainty; Vertical Disease Transmission; Woman; age effect; age related; base; disease-causing mutation; embryo cell; genetic makeup; improved; innovation; mitochondrial DNA mutation; mutant; next generation sequencing; novel; public health relevance; segregation; tool; transmission process; tumor

 DESCRIPTION (provided by applicant): Mutations in mtDNA cause >200 genetic diseases. One in eight unrelated females is a carrier of an mtDNA disease. Most of mtDNA diseases are heteroplasmic - for them, the disease‐associated alleles are present alongside the wild‐type alleles. The severity of the mtDNA diseases depends on the frequency of the disease associated alleles in a tissue. Therefore, it is critical to study how mtDNA allele frequencies change between generations and within a human body. Such changes are governed by mutation, genetic drift, and selection. Yet the basic parameters and relative contribution of these evolutionary processes to shaping the mtDNA genetic makeup have neither been modeled nor characterized in detail. The goal of this proposal is to investigate evolutionary processes governing mtDNA allele frequency changes between generations and among tissues of an individual. To achieve this goal, we have created a unique resource - collected samples from buccal and blood cells of mother and two child (mother‐2child) trios from a human population (from Central Pennsylvania). We will sequence and analyze their mtDNA with newly developed computational and statistical tools packaged in a reproducible software pipeline that will be shared with the scientific community. In Aim 1 we will develop a novel population genetics framework for mtDNA mutation and drift, and will apply it to mtDNA sequences from 200 mother‐2 child trios. We will estimate germ‐line, embryonic, and somatic mutation rates and bottleneck sizes. The germ‐line bottleneck size estimate is needed to predict heteroplasmy levels in children, and the embryonic one to parse the distribution of heteroplasmies among tissues. The germ‐line mutation rate estimate will be useful for human evolutionary studies, and the somatic mutation rate estimate will inform us about mutation accumulation in mtDNA diseases. Aim 2 will test a potential effect of age on accumulation of mtDNA mutations in the female germ line. In addition to mother‐2 child trios, here we will examine female germ line directly - by sequencing mtDNA from unfertilized oocytes from 100 women of different ages. mtDNA germ‐line mutation rates might increase because of oocyte aging processes which create a mutagenic environment. An age‐related increase in mtDNA mutation rate, if found, will be important for formulating family planning recommendations in modern Western societies in which reproduction is frequently delayed. In Aim 3 we will develop novel likelihood‐based methods for detecting selection at mtDNA. Applying these methods to the mtDNA sequencing data from mother‐2child trios and unfertilized oocytes, we will contrast the strength of germ‐line vs. somatic mtDNA selection, and evaluate whether mitochondrial selection operates predominantly at the level of individual mitochondria in a cell (or cells within a tissue), or amon individuals in a population. This will significantly contribute to an ongoing debate about where in an organism mtDNA selection operates. Thus, using innovative methodology, we will address pivotal questions about mtDNA evolution and disease.

 描述（由申请人提供）：mtDNA 突变会导致超过 200 种遗传疾病。八分之一的无关女性是线粒体 DNA 疾病的携带者。大多数 mtDNA 疾病都是异质性的——对它们来说，与疾病相关的等位基因与野生型等位基因一起存在。 mtDNA 疾病的严重程度取决于组织中疾病相关等位基因的频率。因此，研究 mtDNA 等位基因频率在代际之间和人体内如何变化至关重要。这些变化是由突变、遗传漂变和选择控制的。然而这些的基本参数和相对贡献 塑造 mtDNA 基因组成的进化过程尚未被详细建模或表征。该提案的目标是研究控制个体各代之间和组织之间 mtDNA 等位基因频率变化的进化过程。为了实现这一目标，我们创建了一种独特的资源——从人群（来自宾夕法尼亚州中部）的母亲和两个孩子（mother-2child）三人组的口腔和血细胞中收集样本。我们将使用新开发的计算和统计工具对他们的 mtDNA 进行测序和分析，这些工具封装在可复制的软件管道中，并将与科学界共享。在目标 1 中，我们将开发一种新的 mtDNA 突变和漂移群体遗传学框架，并将其应用于 200 个母子三人组的 mtDNA 序列。我们将估计种系、胚胎和体细胞突变率以及瓶颈大小。需要生殖系瓶颈大小估计来预测儿童的异质性水平，并需要胚胎瓶颈大小来解析组织间异质性的分布。种系突变率估计将对人类进化研究有用，体细胞突变率估计将告诉我们 mtDNA 疾病中突变积累的信息。目标 2 将测试年龄对女性种系 mtDNA 突变积累的潜在影响。除了母二子三重奏之外，我们还将直接检查女性生殖系 - 通过对来自 100 名不同年龄女性的未受精卵母细胞的 mtDNA 进行测序。由于卵母细胞老化过程创造了诱变环境，mtDNA 种系突变率可能会增加。如果发现与年龄相关的 mtDNA 突变率增加，对于在生殖经常延迟的现代西方社会制定计划生育建议非常重要。在目标 3 中，我们将开发新的基于可能性的方法来检测 mtDNA 的选择。将这些方法应用于母二子三重奏和未受精卵母细胞的 mtDNA 测序数据，我们将对比种系 mtDNA 选择与体细胞 mtDNA 选择的强度，并评估线粒体选择是否主要在细胞（或组织内的细胞）中的单个线粒体或群体中的个体水平上进行。这将极大地促进关于在哪里的持续争论 生物体线粒体DNA选择起作用。因此，我们将利用创新的方法来解决有关线粒体DNA进化和疾病的关键问题。