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.

摘要：小型人类复制单元中的体细胞演变 该项目研究了正常的进化（突变，漂移和选择“ MDS”）的基本参数 人类和动物细胞。尽管MD是躯体细胞进化的基础，但对此几乎没有理解 参数是因为它们在人类中很难学习。我们将从进化生物学中翻译方法 进入系统生物学。我们将以不同的小复制单元（肠道隐窝）研究MD。这 细胞将细胞分为小复制单元可以改变进化，因为选择和漂移 （随机细胞更新）仅限于紧接相邻的细胞。分析小复制的优点 单位是实验性的，它们足够大，可以用常规方法进行测量，但足够小以至于 详细模拟。在复制单元中表征体细胞演变可以使人们更好地理解 肿瘤的演化是因为选择或漂移发生在相邻细胞之间。 我们将根据我们现有出版的人（shibata，graham）人类更好地描述MD的MD 地穴模拟。这些模拟已经根据基于干细胞的数量和动力学推断 较少的数据。新的测序数据是一个更丰富的资源，因为更多的MDS参数 由突变（突变率和机制，DN/DS，乘客与驱动器，新抗原）编码 积累）。通过隐窝表观遗传学和表达数据增强了测序数据，以更全面 表征正常的体细胞演化。我们将从40种不同 老年人。对于每个地下世界，我们将测量突变（整个基因组测序），表观遗传改变 （atac-seq）和表达（纳米弦）。我们还将测量APC +/-隐窝以确定是否是否 守门人突变后体细胞的演化发生了变化。我们还将测量隐窝体细胞 小鼠和大象隐窝的进化，以确定其进化是否有所不同。 我们还将确定来自57种不同哺乳动物的成纤维细胞中的DNA损伤和应力反应 物种。我们将通过膨胀来确定从相同57个哺乳动物细胞系上的从头突变率 单个成纤维细胞，然后进行深度测序。我们将将突变率与癌症率相关联 最后，使用项目1中确定的哺乳动物物种。最后，使用优先的候选基因列表 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 有助于他们对癌症抗性的演变。 这些研究的重要性是更好地表征基本的MDS进化参数。这 物种研究将提供有关MDS参数是“固定”或可能随着年龄或年龄而变化的观点 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 正常的人隐窝将有助于大量较大的体细胞群体进一步努力。这个项目将奠定 通过基于进化的癌症解决方案来影响患者护理的未来工作的基础。