Project 2: Normal Cell Evolution

项目2：正常细胞进化

• 批准号: 10392868
• 负责人: Darryl K Shibata
• 金额: $ 50.72万
• 依托单位: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-04-12 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10392868
• 关键词: ATAC-seq; Adenocarcinoma; Age; Animals; Apoptosis; Arizona; Biological Assay; Biology; Cancer Etiology; Candidate Disease Gene; Cell Count; Cell Line; Cells; Cessation of life; Clonal Evolution; Colon; Colorectal Cancer; DNA; DNA Damage; Data; Elephants; Epigenetic Process; Evolution; Fibroblasts; Future; Gatekeeping; Genes; Genetic Engineering; Genome; Genotype; Human; In Vitro; Incidence; Individual; Intervention; Intestines; Knowledge; Large Intestine; Lead; Malignant Neoplasms; Mammalian Cell; Measurement; Measures; Methodology; Methods; Methylation; Modeling; Mus; Mutation; Normal Cell; Normal tissue morphology; Pathway interactions; Patient Care; Phenotype; Population Sizes; Process; Publishing; Replicon; Resistance; Resources; Sampling; Small Intestines; Somatic Cell; Somatic Mutation; Systems Biology; Testing; Tissues; Translating; Variant; Work; aged; base; biological adaptation to stress; cancer prevention; cancer risk; cost effective; de novo mutation; deep sequencing; driver mutation; epigenome; experimental study; genome sequencing; in vivo; indexing; intestinal crypt; life history; malignant small intestine tumor; nano-string; neoantigens; predictive test; prevent; response; side effect; simulation; stem cells; trait; tumor; whole genome

Abstract: Somatic Cell Evolution in Small Human Replicative Units This Project studies fundamental parameters of evolution (mutation, drift, and selection "MDS") in normal human and animal cells. Although MDS underlies somatic cell evolution, very little is understood about these parameters because they are difficult to study in humans. We will translate methods from evolutionary biology into systems biology. We will study MDS in distinct, small replicative units (intestinal crypts). The compartmentalization of cells into small replicative units can modify evolution because selection and drift (random cell turnover) is limited to immediately adjacent cells. The advantages of analyzing small replicative units are that experimentally they large enough to measure with conventional methods yet small enough to simulate in detail. Characterizing somatic cell evolution in replicative units can lead to better understanding of tumor evolution because selection or drift occurs between neighboring cells. We will better characterize MDS in crypts based on our existing published (Shibata, Graham) human crypt simulations. These simulations have already inferred stem cell numbers and dynamics based on smaller amounts of data. The new sequencing data are a richer resource because more MDS parameters are encoded by mutations (mutation rates and mechanisms, dN/dS, passenger versus driver, neoantigen accumulation). The sequencing data is augmented by crypt epigenetic and expression data to more fully characterize normal somatic cell evolution. We will sample 8 colon and small intestinal crypts from 40 different aged individuals. For each crypt, we will measure mutations (whole genome sequencing), epigenetic alterations (ATAC-seq), and expression (NanoString). We will also measure APC+/- crypts to determine whether somatic cell evolution changes after a gatekeeper mutation. We will also measure crypt somatic cell evolution in mouse and elephant crypts to determine if their evolution differs. We will also determine the DNA damage and stress response in fibroblasts from 57 different mammalian species. We will determine de novo mutation rates across the same 57 mammalian cell lines through expansion of single fibroblast cells followed by deep sequencing. We will correlate mutation rates with cancer rates in the same mammalian species as determined in Project 1. Finally, using prioritized candidate gene lists generated in Project 1, we will perform gene editing experiments on the top 5 genes from different species most likely to contribute to their evolution of cancer resistance. The significance of these studies is a better characterization of basic MDS evolution parameters. The species studies will provide perspective on whether MDS parameters are "fixed" or can vary with age or species, identifying which parameters are more amenable for intervention. A complete systems biology solution of normal human crypts will facilitate further efforts with much larger groups of somatic cells. This Project will lay the groundwork for future work to impact patient care through evolutionary-based solutions to cancer.

翻译后摘要：体细胞进化在小人类复制单位 本项目研究正常人中进化的基本参数（突变、漂移和选择“MDS”）。 人类和动物细胞。虽然MDS是体细胞进化的基础，但对这些方面的了解很少。 因为它们很难在人类中进行研究。我们将把进化生物学的方法 系统生物学。我们将在不同的小复制单位（肠隐窝）中研究MDS。的 将细胞分隔成小的复制单位可以改变进化，因为选择和漂移 （随机细胞更替）限于紧邻的细胞。分析小型复制品的优势 实验上，它们大到足以用传统方法测量，但小到足以 详细模拟。表征复制单位中的体细胞进化可以更好地理解 肿瘤进化是因为相邻细胞之间发生选择或漂移。 我们将根据我们现有的已发表的（柴田，格雷厄姆）人类 地穴模拟这些模拟已经推断出干细胞的数量和动态， 数据量较小。新的测序数据是更丰富的资源，因为更多的MDS参数 由突变编码（突变率和机制，dN/dS，乘客与司机，新抗原 积累）。测序数据通过隐窝表观遗传和表达数据来增强，以更充分地 表征正常体细胞进化。我们将从40个不同的结肠和小肠隐窝中抽取8个样本 老年人。对于每个隐窝，我们将测量突变（全基因组测序），表观遗传改变 （ATAC-seq）和表达（NanoString）。我们还将测量APC+/-隐窝，以确定是否 体细胞进化在看门突变后发生变化。我们还将测量隐窝体细胞 在老鼠和大象的隐窝中进行进化，以确定它们的进化是否不同。 我们还将确定57种不同哺乳动物成纤维细胞的DNA损伤和应激反应 物种我们将通过扩增来确定相同的57个哺乳动物细胞系的从头突变率。 单个成纤维细胞，然后进行深度测序。我们将把突变率与癌症发病率联系起来， 与项目1中确定的哺乳动物物种相同。最后，使用优先化的候选基因列表， 项目1，我们将对来自不同物种的前5个基因进行基因编辑实验， 有助于它们的癌症抵抗力的进化。 这些研究的意义是更好地表征基本MDS演化参数。的 物种研究将提供MDS参数是“固定”还是随年龄变化的观点， 物种，确定哪些参数更适合干预。完整的系统生物学解决方案 正常人类隐窝的细胞分裂将有助于进一步研究更大的体细胞群。该项目将奠定 为未来的工作奠定基础，通过基于进化的癌症解决方案来影响患者护理。