The origins of chromosome rearrangement in the cancer genome

项目摘要 研究 DNA测序的进展揭示了癌症基因组中存在着染色体重排 出乎意料的频率和惊人的复杂性。尽管人们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而发生癌症 重排背后的因素和机制通常是未知的。这项提案旨在确定 通过关注有丝分裂过程中的错误来研究癌症相关染色体重排的潜在原因， 特别是在双着丝粒染色体形成的背景下。端粒融合，这发生在人类 肿瘤发生当极短的端粒功能失调时，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的细胞死亡阶段称为端粒危机(TC)。约翰博士 Maciejowski之前的工作表明，在TC过程中形成的双着丝粒染色体在 受到细胞质核酸酶TREX1的攻击，产生嗜铬(染色体碎裂)和卡塔吉斯 (簇状超突变)。在这里，Maciejowski博士将使用他建立的、遗传上易驯化的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)。这一方法将 利用全基因组测序评估与A基因缺失相关的重排和突变表型 特定的基因。此外，他还将开发新的分析方法来检测癌症基因组中先前的TC(目标2)。 明确TC在癌症病因学中的作用的总体目标(目标3)。最后，他将用他以前开发的 基于核型的重排筛查和全基因组测序流水线以识别额外的 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，细胞周期检查点，确保有丝分裂期间高保真的染色体分离 并经常在癌症中失控(目标4)。总的来说，这一建议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，目的是为 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。 侯选人 Maciejowski博士的长期目标是了解染色体分离错误对 染色体重排、非整倍体与癌症的发展。他计划使用全基因组 在引入化学或遗传扰动后用于评估基因组不稳定性的测序 染色体分离或DNA修复途径。他在数学方面的背景和在 染色体生物学、有丝分裂染色体分离机制和人类组织培养系统 为他实现这一目标提供了坚实的基础。在K99/指导阶段，Maciejowski博士将 接受生物信息学方法培训，并将其应用于全基因组测序分析。这将是至关重要的 他未来的研究并帮助他开始了作为一名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的科学家的支持：Dr。 蒂蒂娅·德兰格是端粒功能障碍后果方面的专家，将担任主要导师。Dr。 Marin Imielinski是一位计算生物学家，在开发探测癌症基因组的算法方面拥有专业知识 结构。合作者将包括癌症基因组学领域的领导者彼得·J·坎贝尔博士和阿希姆博士 容格布鲁斯，病理学专家。这个团队共同组成了一个强大的多学科研究团队， 将成功地执行拟议的实验并推进一项培训计划，这将帮助Maciejowski博士 过渡到独立的学术立场。Maciejowski博士将接受高级测序方面的培训 方法包括：配对末端测序，根据阅读深度推断拷贝数，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 在洛克菲勒大学执行，该大学提供无与伦比的资源，建立了 职业发展，以及大学的学术环境。考虑到他的指导团队的大力支持 和RU的良好环境，Maciejowski博士希望找到并过渡到独立的 在一家机构担任终身教职，支持他的R00/独立阶段研究目标。 好了！

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. !