Deciphering Networks Controlling DNA Amplification

项目摘要 DNA扩增与病理状态如神经系统疾病、心脏病和神经系统疾病相关。 癌癌症中至少50%的扩增是瞬时染色体外DNA（ecDNA）。瞬态 行为有助于拷贝数可塑性，导致异质性癌基因表达，并改变 治疗反应尚未回答的问题仍然是是否有不同的机制控制ecDNA复制 以及它们如何影响与疾病相关的复制增益事件。我的总体目标是定义 原则调节选择性DNA拷贝增益和相关的可塑性，所以我们可以控制这些事件。 我的实验室是第一个发现染色体外瞬时位点特异性DNA复制的分子基础 人类基因组中的TSSG。具体来说，我们鉴定了第一种能够驱动位点特异性 ecDNA扩增[组蛋白3赖氨酸9和36三脱甲基酶（H3 K9/36 me 3）KDM 4A]，并证明了 表观遗传状态在控制特定DNA区域重复复制的偏好方面的基本作用， 放大我们发现了另外七种染色质酶-赖氨酸甲基转移酶（KMT）和脱甲基酶 （KDM）-其协同作用以控制非癌细胞和癌细胞中的位点特异性扩增。这些 研究确定了染色质因子及其相关状态在调节DNA中的关键作用 扩增。有了这个NIGMS R35，我的实验室将扩大我们的研究，以阐明：1） 控制DNA扩增的基本机制; 2）分子过程和特征 促进或阻止DNA扩增;和3）ecDNA生成与DNA扩增之间的关系。 相关的RNA异质性/DNA突变负荷。我们将通过利用显微镜来解决这些问题- 使用遗传和化学工具进行筛选，以确定关键放大器，并反过来生成 表观基因组图谱与这些途径相关的基因组组织图谱相结合， 解决了控制DNA扩增的特征。这些研究还将结合最先进的长期 读段测序和单细胞（DNA和RNA）测序策略， 在细胞群体和单个细胞内的信号传导可以与放大器对TSSG的作用相关。这些 研究正在具有近二倍体基因组的非转化细胞中进行， 基因组异常和突变不影响这些研究。总的来说，从这些数据中产生的数据 这些研究将增加我们对控制DNA拷贝获得的分子特征以及相关基因的了解。 异质性，这将解决新的生物标志物和治疗靶点，以控制拷贝数- 在未来几年的疾病。

PROJECT SUMMARY DNA amplification is associated with pathological states such as neurological disorders, cardiac disease and cancer. At least 50% of the amplifications in cancer are transient extrachromosomal DNA (ecDNA). The transient behavior contributes to copy number plasticity, results in heterogeneous oncogene expression and alters therapeutic response. The unanswered question remains as to whether distinct mechanisms control ecDNA copy gains within cells and how they impact copy gain events associated with disease. My overall goal is to define the principles regulating selective DNA copy gains and the associated plasticity, so we may control these events. My laboratory was the first to discover a molecular basis for extrachromosomal transient site-specific DNA copy gains (TSSGs) in the human genome. Specifically, we identified the first enzyme capable of driving site-specific ecDNA amplification [the histone 3 lysine 9 and 36 tri-demethylase (H3K9/36me3) KDM4A] and demonstrated a fundamental role for epigenetic states in controlling the predilection of specific DNA regions to rereplicate and amplify. We discovered seven more chromatin enzymes- lysine methyltransferases (KMTs) and demethylases (KDMs)- that function in concert to control site-specific amplification in both non-cancer and cancer cells. These studies established a critical role for chromatin factors and their associated states in regulating DNA amplifications. With this NIGMS R35, my laboratory will expand our studies in order to elucidate: 1) the fundamental mechanisms controlling DNA amplification; 2) the molecular processes and characteristics promoting or preventing DNA amplification; and 3) the relationship between ecDNA generation and the associated RNA heterogeneity/DNA mutation burden. We will address these points by leveraging microscopy- based screens using genetic and chemical tools in order to identify key amplifiers, and in turn, generate epigenome profiles coupled to genome organization maps associated with these pathways so that molecular features controlling DNA amplification are resolved. These studies will also be coupled to state-of-the-art long read sequencing and single cell (DNA and RNA) sequencing strategies so that the associated heterogeneity within the cell population and individual cells can be correlated with the effect of the amplifier on TSSGs. These studies are being conducted in non-transformed cells that have a nearly diploid genome so that additional genomic anomalies and mutations do not impact these studies. Collectively, the data generated from these studies will increase our knowledge about the molecular features governing DNA copy gains and the associated heterogeneity, which will resolve novel biomarkers and therapeutic targets in order to control copy number- associated diseases in the years ahead.