Extreme genomic instability at large transcribed genes: mechanisms and consequences for the cancer genome

大转录基因的极端基因组不稳定性：癌症基因组的机制和后果

基本信息

批准号：
9756149
负责人：
THOMAS W GLOVER
金额：
$ 47.07万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
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：
2016-09-01 至 2021-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9756149
关键词：
Address Aphidicolin Behavior Bioinformatics Bromouridine sequencing Cancer Etiology Cell Cycle Cell Line Chromosomal Rearrangement Chromosome Fragile Sites Chromosome Structures Colon Carcinoma Conflict (Psychology)Copy Number Polymorphism Cultured Cells DNA Sequence Alteration Data Data Set Development Dose Epithelium Failure Floods Functional disorder Genes Genetic Transcription Genomic Instability Genomics Health Hereditary Disease Human Ionizing radiation Knowledge Lead Lesion Link Malignant Neoplasms Measurement Measures Modeling Modification Monitor Mutagenesis Mutate Mutation Nature Nonhomologous DNA End Joining Normal Cell Oncogene Activation Oncogenes Pathogenicity Peptide Nucleic Acids Ploidies Process Recurrence Replication Error Replication Origin Replicon Reporting Role S Phase Shapes Site Somatic Cell Source Structure Testing The Cancer Genome Atlas Tissues Variant cancer genome cancer type cell type design genome sequencing genome-wide genomic RNA genomic data hydroxyurea in vivo interstitial mouse model novel strategies overexpression replication stress tissue culture transcriptome sequencing tumor

项目摘要

PROJECT SUMMARY/ABSTRACT Chromosomal rearrangements are a fundamental form of mutagenesis with a profound impact on human health. Poorly understood processes of structural mutagenesis are active in somatic cells where they ultimately lead to cancer. A flood of genomic data from The Cancer Genome Atlas (TCGA) and other projects is revealing that intrachromosomal rearrangements are especially common and that certain genomic loci are highly prone to their occurrence. The nature and mechanisms of unstable loci are thus of central importance to cancer etiology. We are exploring these questions using models of acquired genomic copy number variants (CNVs), a term encompassing interstitial deletions and duplications and representing the same mechanisms as copy- number-neutral inversions and translocations. In these models, exogenous replication stress in the form of low- dose aphidicolin or hydroxyurea is a potent inducer of new CNVs in cultured somatic cells. CNVs are characterized by microhomologous junctions typical of pathogenic rearrangements that likely arise as replication errors. Hotspots of induced CNV formation are the same loci as common fragile sites, and it is the active transcription of large genes that leads to their extreme cell-type-specific instability. This project explores the hypothesis that the same instability mechanism(s) observed in these models of exogenous somatic CNV induction lead to recurrent genomic alterations in cancer as a result of endogenous replication stress. This idea is tested in three aims that examine the mechanisms leading to the extreme locus instability at large transcribed genes and the consequences of these mechanisms for the cancer genome. Aims 1 and 2 address non-exclusive hypotheses for how transcription interacts with replication stress to confer locus instability. Aim 1 argues that large genes create a dynamic conflict in which transcription into S-phase removes late-firing replication origins and creates large replicons highly sensitive to replication inhibition. Novel approaches will test this hypothesis by determining the cell-cycle timing of replication, transcription, and origin presence and firing. Aim 2 argues that transcription leads to persistent R-loops that cause fork stalling and thus precursor lesions for CNV formation. Monitoring and manipulating R-loop formation in cell lines that variably express specific large genes will test this hypothesis. Aim 3 addresses the consequences of these mechanisms on the cancer genome first through bioinformatic explorations of TCGA cancer data sets to correlate deletion hotspots with tumor- and cancer-type-specific transcription. Tissue-culture models of forced oncogene activation and mouse models of colon cancer will relate de novo CNV formation with the endogenous replication stress inherent to cancer.

项目概要/摘要染色体重排是诱变的一种基本形式，对人类产生深远的影响健康。人们对结构突变的过程知之甚少，它在体细胞中活跃，最终在体细胞中发挥作用。导致癌症。来自癌症基因组图谱 (TCGA) 和其他项目的大量基因组数据揭示了这一点染色体内重排特别常见，并且某些基因组位点很容易发生到它们的发生。因此，不稳定位点的性质和机制对于癌症至关重要病因学。我们正在使用获得性基因组拷贝数变异（CNV）模型来探索这些问题，这是一种该术语涵盖间质性删除和重复，并代表与复制相同的机制数中性倒位和易位。在这些模型中，外源复制应激以低阿菲迪霉素或羟基脲是培养体细胞中新 CNV 的有效诱导剂。 CNV 是以微同源连接为特征，典型的致病重排可能出现复制错误。诱导CNV形成的热点与常见的脆弱位点是相同的位点，这是大基因的活跃转录导致其极端的细胞类型特异性不稳定。该项目探索假设在这些外源体细胞 CNV 模型中观察到相同的不稳定机制由于内源性复制应激，诱导导致癌症中反复出现的基因组改变。这个想法在三个目标中进行了测试，检查导致整体基因座极端不稳定的机制转录基因以及这些机制对癌症基因组的影响。目标 1 和 2 的地址关于转录如何与复制应激相互作用以赋予基因座不稳定性的非排他性假设。目标1 认为大基因会产生动态冲突，其中转录到 S 期会消除延迟放电复制起始并产生对复制抑制高度敏感的大复制子。新颖的方法将通过确定复制、转录和起源存在的细胞周期时间来检验这一假设射击。目标 2 认为转录会导致持久的 R 环，从而导致分叉停滞，从而导致前体 CNV 形成的病变。监测和操纵不同表达的细胞系中 R 环的形成特定的大基因将检验这一假设。目标 3 解决了这些机制对癌症基因组首先通过 TCGA 癌症数据集的生物信息学探索来关联删除热点具有肿瘤和癌症类型特异性转录。强迫癌基因激活的组织培养模型结肠癌小鼠模型将把 CNV 的从头形成与内源性复制应激联系起来癌症固有的。