Environmental Risk Factors for Copy Number Variation in Human Chromosomes

人类染色体拷贝数变异的环境风险因素

• 批准号: 7817619
• 负责人: THOMAS W GLOVER
• 金额: $ 48.56万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-28 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7817619
• 关键词: Accounting; Address; Affect; Aphidicolin; Area; Attention; Autistic Disorder; Biological Models; Bleomycin; Cataloging; Catalogs; Categories; Cell Culture Techniques; Cell division; Cells; Chromosomal Rearrangement; Chromosome Breakage; Chromosomes; Cleft Palate; Complex; Congenital Abnormality; Congenital Heart Defects; Copy Number Polymorphism; Coupled; DNA; DNA Damage; DNA Double Strand Break; DNA Repair; DNA Sequence Rearrangement; DNA biosynthesis; Data; Data Set; Detection; Development; Disease; Dose; Environmental Exposure; Environmental Risk Factor; Epilepsy; Event; Evolution; Experimental Models; Exposure to; Floxuridine; Folate; Folic Acid Antagonists; Frequencies; Genes; Genetic; Genetic Recombination; Genetic Variation; Genome; Genomics; Goals; Hereditary Disease; Human; Human Chromosomes; Human Genome; In Vitro; Individual; Ionizing radiation; Knowledge; Lead; Lymphoid; Malignant Neoplasms; Mediating; Meiosis; Mental Retardation; Mental disorders; Methods; Microscope; Microscopic; Mitotic; Modeling; Monitor; Mutate; Mutation; Nature; Normal Cell; Paper; Parents; Partner in relationship; Pattern; Play; Population; Positioning Attribute; Prevention; Process; Publishing; Recovery; Recurrence; Recurrent disease; Research; Research Personnel; Resolution; Ribonucleotide Reductase Inhibitor; Risk; Risk Factors; Role; Schizophrenia; Staging; Stress; Structure; System; Techniques; Technology; Terminal Repeat Sequences; Testing; Time; Variant; base; cancer cell; chromosome replication; comparative; cost; developmental disease; egg; environmental agent; genetic risk factor; genome-wide; homologous recombination; human disease; hydroxyurea; in vitro Model; in vivo; insight; interest; next generation; novel; sperm cell; structural genomics; tool

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area, (08) Genomics and Specific Challenge Topic, 08-ES-106: The role of environmental exposure in copy number variation (CNV): "Microscopic deletions and replications of the genome have attracted increasing attention for their potential role in many complex human diseases. Of particular interest are spontaneous CNVs, defined as those present in an affected individual, but absent in both parents. There is limited understanding of how spontaneous CNVs arise. Studies are needed that will determine whether environmental exposures can affect risk for copy number variation and other structural variations that have been implicated in complex diseases. Given the early stage of this research area, studies should focus on changes in cells exposed in vitro". In recent years, copy number variants (CNVs) have been found to be widely distributed throughout the human genome where they represent an important component of genetic variation and play an integral role in phenotypic diversity, complex disease and evolution. Over 1300 CNVs with frequencies of >1% have been described in healthy individuals that exist as deletions or duplications ranging in size from a few Kb to over a Mb, and this number will surely increase as more data become available. Similar spontaneous CNVs are now well known to be a major cause of genetic and developmental disorders, including mental retardation, autism, schizophrenia, epilepsy, cleft palate and many others. Studies of idiopathic mental retardation and developmental disorders have found de novo CNVs in 5-17% of affected individuals, suggesting a high mutation rate. Similar copy number alterations are also found at high frequency in many cancers where a role in initiation or progression is likely. CNVs are thus a key factor in normal genetic variation and evolution and are a very important class of mutation in genetic and developmental disorders and cancer. There is very limited understanding of how CNVs arise, the cellular mechanisms and risk factors that are involved, and the effects of environmental agents on their formation. As with all mutation classes, it is almost certain that environmental insults can induce or increase the risk for new and deleterious CNVs, however we have little knowledge of the mechanisms and frequency of such events. Meiotic unequal recombination [or non-allelic homologous recombination (NAHR)] mediated by flanking repeated sequences or segmental duplications leads to many recurrent, disease-related CNVs. However, there is growing evidence that many or most normal and sporadic, nonrecurrent CNVs, which account for the majority of disease-associated CNVs in humans and those in cancers arise via mechanisms coupled to aberrant DNA replication and/or non-homologous repair of DNA damage. This suggests an unexpected mitotic, rather than meiotic, cell origin for many CNVs and has a number of important implications for the role of environmental exposures in their formation and the development of in vitro model systems for their study. The Challenge, and our goal, is to determine the role of environmental factors in the formation of CNVs and to gain novel insight into the mechanisms by which these frequent mutations are generated. We have assembled a strong team of investigators and have developed a normal human cell culture model system coupled with leading edge genome analysis technologies, placing us in a unique position to address this timely Challenge. Using this system we have found that aphidicolin-induced replication stress leads to a remarkably high frequency of de novo CNVs. These findings lead us to hypothesize that environmentally-induced replication stress and/or DNA double strand breaks are two major factors leading to CNVs during mitotic cell divisions in the human germline and in cancer cells. To test this hypothesis, we will characterize environmental agent-induced CNVs at the genome-wide scale and directly compare the strength of these two non-exclusive models for CNV formation, thus providing for the first time a high resolution catalog of genomic manifestations of two different categories of environmental agents most likely to be associated with CNV formation. These are (1) agents that lead to replication stress, which might lead to CNVs through secondary breakage or replicative template switching, and (2) agents that directly induce DNA double-strand breaks (DNA DSBs), which might lead to CNVs through inappropriate joining of broken ends. Specifically, we will examine hydroxyurea and folate stress, which inhibit replication through different mechanisms than aphidicolin, and on ionizing radiation and bleomycin, which lead directly to DNA DSBs. Our "shovel ready" in vitro model system coupled with high resolution genomic microarrays and next-generation sequencing will allow us to determine the effects of these agents on the frequency, spectrum, distribution and structure of CNVs and other submicroscopic structural variations. The combined results will address a major gap in our knowledge about a very important class of mutations and allow predictions of the environmental agents that confer the greatest risk for ongoing structural alteration of the human genome.

描述（由申请人提供）： 该申请涉及广泛的挑战领域，（08）基因组学和特定挑战主题，08-es-106：环境暴露在拷贝数变化中的作用（CNV）：“微观缺失和基因组的复制引起了人们的越来越多的关注，因为他们在许多复杂的人类疾病中的潜在作用越来越有效。在许多复杂的人类疾病中，这些人都在限制的cnv中，在某种情况下，在某种程度上存在着一种限制，但在某种程度上，在某种情况下，在某种程度上存在着一种限制，但在某种程度上，在某种程度上存在着一种限制，但在某种程度上，在某种情况下，在某种情况下，在某种程度上存在着限制性的理解。出现自发的CNV。近年来，发现拷贝数变体（CNV）广泛分布在整个人类基因组中，它们代表了遗传变异的重要组成部分，并且在表型多样性，复杂疾病和进化中起着不可或缺的作用。在健康个体中，已经描述了超过1300个频率> 1％的CNV，这些频率是从几个KB到MB超过MB的删除或重复的存在，并且随着更多数据可用，该数字肯定会增加。现在众所周知，类似的自发CNV是遗传和发育障碍的主要原因，包括智力低下，自闭症，精神分裂症，癫痫，癫痫，left裂等。对特发性智力低下和发育障碍的研究发现，在5-17％的受影响个体中，从头cnvs表明很高的突变率。在许多癌症中可能在开始或进展中作用的许多癌症中，在高频中也发现了类似的拷贝数变化。因此，CNV是正常遗传变异和进化的关键因素，并且是遗传和发育障碍和癌症中非常重要的突变类别。对CNV的出现，所涉及的细胞机制和危险因素以及环境药物对其形成的影响的了解非常有限。与所有突变类别一样，几乎可以肯定的是，环境损害可以诱导或增加新的和有害的CNV的风险，但是我们对此类事件的机制和频率知之甚少。通过侧翼重复序列或分段重复介导的减数分裂不平等重组[或非平行性同源重组（NAHR）]导致许多复发性，疾病相关的CNV。然而，越来越多的证据表明，许多或最正常和零星的非急流CNV是人类中大多数与疾病相关的CNV，而癌症中的大多数CNV则是通过与异常的DNA复制和/或非同胞修复DNA损害的机制产生的。这表明许多CNV的出乎意料的有丝分裂，而不是减数分裂的细胞来源，并且对环境暴露在其形成中的作用以及其研究体外模型系统的发展具有许多重要的含义。挑战和我们的目标是确定环境因素在CNV形成中的作用，并对产生这些频繁突变的机制进行新颖的见解。我们已经组建了一个强大的研究人员团队，并开发了正常的人类细胞培养模型系统，再加上领先的基因组分析技术，使我们处于独特的位置，以应对及时的挑战。使用该系统，我们发现蚜虫蛋白诱导的复制应力导致从头cnvs的频率很高。这些发现导致我们假设，环境诱导的复制应力和/或DNA双链断裂是导致人类生殖和癌细胞中有丝分裂细胞分裂期间CNV的两个主要因素。为了检验这一假设，我们将在全基因组量表上表征环境剂诱导的CNV，并直接比较了CNV形成的这两个非排斥模型的强度，因此首次提供了两种不同类别环境药物的基因组表现目录，最可能与CNV形成相关。这些是（1）导致复制应力的药物，这可能会通过次级断裂或复制模板切换导致CNV，以及（2）直接诱导DNA双链断裂（DNA DSB）的代理，这可能会导致CNV通过不当折断的末端连接而导致CNV。具体而言，我们将检查羟基脲和叶酸应激，这些应激通过与蚜虫蛋白不同的机制抑制复制，以及直接导致DNA DSB的电离辐射和博来霉素。我们的“铲子就绪”体外模型系统以及高分辨率基因组微阵列和下一代测序将使我们能够确定这些药物对CNVS和其他下检查率结构变化的频率，光谱，分布和结构的影响。结合结果将解决我们关于非常重要的突变类别的知识差距，并允许对赋予人类基因组持续结构性改变最大风险的环境药物进行预测。