The origins of chromosome rearrangement in the cancer genome

癌症基因组中染色体重排的起源

基本信息

批准号：
9352813
负责人：
JOHN MACIEJOWSKI
金额：
$ 11.98万
依托单位：
ROCKEFELLER UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-09-14 至 2017-11-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9352813
关键词：
Algorithms Alpha Cell Aneuploidy Bioinformatics Biological Assay Biology Cancer Etiology Cancer Patient Cell Cycle Checkpoint Cell Death Cell Line Cell division Chemicals Chromosome Segregation Chromosomes Chronic Lymphocytic Leukemia Cicatrix Clinical Clinical Research Clonal Evolution Complex Cytidine Deaminase DNA Repair Pathway DNA Sequence Alteration DNA sequencing Data Defect Development Diagnosis Dicentric chromosome Disease Disease Progression Ensure Environment Enzymes Event Evolution Failure Foundations Frequencies Functional disorder Genes Genetic Genetic Variation Genome Genomic Instability Genomic approach Genomics Goals Growth Human In Vitro Incidence Institution Interdisciplinary Study Karyotype Laboratories Link Malignant Neoplasms Mathematics Mentors Methods Mitosis Mitotic Chromosome Modeling Molecular Mutation Outcome Pathology Patients Phase Phenotype Play Positioning Attribute Process Proteins Protocols documentation Research Research Personnel Research Project Summaries Resources Role Sampling Scientist Solid Solid Neoplasm Structure System TP53 gene TREX1 gene Technology Tetraploidy Training Universities Variant Work base cancer genome cancer genomics career career development chromothripsis clinical practice computerized tools experimental study genetic variant genome sequencing human tissue improved insight malignant breast neoplasm mouse model novel nuclease outcome forecast overexpression prognostic value screening telomere tenure track tissue culture tool tumor tumor progression tumorigenesis whole genome

项目摘要

Project Summary Research Advances in DNA sequencing have revealed that cancer genomes harbor chromosome rearrangements of unexpected frequency and staggering complexity. Despite the recognition that these variations can enable cancer development by inducing pro-growth genetic change and facilitating clonal evolution, the instigating factors and mechanisms behind rearrangement are often unknown. This proposal aims to identify the underlying causes of cancer-associated chromosome rearrangements by focusing on errors during mitosis, especially in the context of dicentric chromosome formation. Telomere fusions, which occur during human tumorigenesis when critically short telomeres become dysfunctional, generate dicentric chromosomes. This stage of telomere fusion, genomic instability, and frequent cell death is known as telomere crisis (TC). Dr. John Maciejowski's previous work has shown that the dicentric chromosomes formed during TC are resolved after attack by the cytoplasmic nuclease, TREX1, yielding chromothripsis (chromosome shattering) and kataegis (clustered hypermutation). Here, Dr. Maciejowski will use his established, genetically tractable model of TC to determine if enzymatic attack is directly responsible for observed genomic variants (Aim 1). This approach will utilize whole genome sequencing to assess rearrangement and mutation phenotypes associated with loss of a specific gene. In addition, he will develop novel assays to detect prior TC in cancer genomes (Aim 2) with the overall goal of defining the role of TC in cancer etiology (Aim 3). Finally, he will use his previously developed karyotype-based rearrangement screening and whole genome sequencing pipeline to identify additional causes of genome rearrangement by defining the genomic changes associated with dysfunction of the spindle assembly checkpoint, a cell cycle checkpoint that ensures high fidelity chromosome segregation during mitosis and is often dysregulated in cancer (Aim 4). Collectively, this proposal combines the versatility of mammalian tissue culture genetics and the power of whole genome sequencing with the aim to provide deep insights into a key aspect of tumorigenesis: the genome rearrangements that spur cancer progression and tumor evolution. Candidate Dr. Maciejowski's long-term goal is to understand the impact of errors in chromosome segregation on chromosome rearrangement, aneuploidy, and cancer development. He plans to use whole genome sequencing to assess genomic instability after the introduction of chemical or genetic perturbations in chromosome segregation or DNA repair pathways. His background in Mathematics and extensive training in chromosomal biology, the mechanisms of mitotic chromosome segregation, and human tissue culture systems provide him a solid foundation to achieve this goal. During the K99/Mentored Phase, Dr. Maciejowski will be trained in bioinformatic methods with applications in whole genome sequencing analysis. This will be critical for his future research and help launch his career as an independent investigator. Environment During the K99/Mentored Phase, Dr. Maciejowski will be supported by an outstanding group of scientists: Dr. Titia de Lange is an expert in the consequences of telomere dysfunction and will serve as primary mentor. Dr. Marcin Imielinski is a computational biologist with expertise in developing algorithms to probe cancer genome structure. Collaborators will include Dr. Peter J. Campbell, a leader in cancer genomics, and Dr. Achim Jungbluth, an expert in pathology. Together, this group comprises a strong multidisciplinary research team that will successfully execute the proposed experiments and advance a training plan that will help Dr. Maciejowski transition to an independent academic position. Dr. Maciejowski will be trained in advanced sequencing approaches including: paired end sequencing, inferring copy number from read depth, and identifying rearrangements and mutations. Career development will also be emphasized. Research will primarily be performed at The Rockefeller University, which offers unsurpassed resources, established mechanisms for career development, and a collegial academic environment. Given the strong support of his mentoring team and the excellent environment at RU, Dr. Maciejowski expects to identify and transition to an independent tenure track position at an institution supportive of his R00/Independent Phase research goals. !

项目概要研究 DNA 测序的进展揭示了癌症基因组中存在染色体重排意想不到的频率和惊人的复杂性。尽管认识到这些变化可以使通过诱导促生长基因变化和促进克隆进化来控制癌症的发展，重排背后的因素和机制通常是未知的。该提案旨在确定通过关注有丝分裂期间的错误来研究与癌症相关的染色体重排的根本原因，特别是在双着丝粒染色体形成的背景下。端粒融合，发生在人类当极其短的端粒变得功能失调时，肿瘤发生就会产生双着丝粒染色体。这端粒融合、基因组不稳定和频繁细胞死亡的阶段被称为端粒危机（TC）。约翰博士 Maciejowski 之前的工作表明，TC 期间形成的双着丝粒染色体在 TC 后被解析。受到细胞质核酸酶 TREX1 的攻击，产生染色体碎裂（染色体破碎）和 kataegis （成簇超突变）。在这里，Maciejowski 博士将使用他建立的、遗传上易于处理的 TC 模型来确定酶攻击是否直接导致观察到的基因组变异（目标 1）。这种方法将利用全基因组测序来评估与缺失相关的重排和突变表型特定基因。此外，他将开发新的检测方法来检测癌症基因组中的先前 TC（目标 2）确定 TC 在癌症病因学中的作用的总体目标（目标 3）。最后，他将使用他之前开发的基于核型的重排筛选和全基因组测序流程，以确定额外的通过定义与纺锤体功能障碍相关的基因组变化来确定基因组重排的原因装配检查点，一种细胞周期检查点，可确保有丝分裂期间染色体的高保真度分离并且在癌症中经常失调（目标 4）。总的来说，该提案结合了哺乳动物的多功能性组织培养遗传学和全基因组测序的力量，旨在提供深入的见解肿瘤发生的关键方面：刺激癌症进展和肿瘤进化的基因组重排。候选人 Maciejowski 博士的长期目标是了解染色体分离错误对染色体重排、非整倍性和癌症发展。他计划利用全基因组测序以评估在引入化学或遗传扰动后基因组的不稳定性染色体分离或 DNA 修复途径。他的数学背景和广泛的训练染色体生物学、有丝分裂染色体分离机制和人体组织培养系统为他实现这一目标奠定了坚实的基础。在 K99/指导阶段，Maciejowski 博士将接受过生物信息方法培训，并在全基因组测序分析中应用。这对于他未来的研究并帮助开启他作为独立调查员的职业生涯。环境在 K99/指导阶段，Maciejowski 博士将得到一群杰出科学家的支持：蒂蒂亚·德·兰格 (Titia de Lange) 是研究端粒功能障碍后果的专家，并将担任主要导师。博士。 Marcin Imielinski 是一位计算生物学家，擅长开发探测癌症基因组的算法结构。合作者将包括癌症基因组学领域的领导者 Peter J. Campbell 博士和 Achim 博士 Jungbluth，病理学专家。该小组共同组成了一支强大的多学科研究团队，将成功执行拟议的实验并推进培训计划，这将有助于 Maciejowski 博士过渡到独立的学术职位。 Maciejowski 博士将接受高级测序培训方法包括：配对末端测序、从读取深度推断拷贝数以及识别重排和突变。职业发展也将受到重视。研究将主要是在洛克菲勒大学进行，该大学提供无与伦比的资源，并建立了机制职业发展和学院学术环境。得到了导师团队的大力支持以及 RU 的优良环境，Maciejowski 博士希望找到并过渡到独立在支持他的 R00/独立阶段研究目标的机构中获得终身教职。！