Determinants for genome-wide epigenomics in metastatic breast cancer

描述（由申请人提供）：乳腺癌是美国女性最常见的癌症，每年造成约40，000人死亡。在拟议的研究中，我们将专注于乳腺癌，并确定是什么表观基因组变化导致乳腺癌获得转移活性以及这些变化是如何建立的。染色质的表观遗传修饰与单个基因的表达状态有关。在这里，我们提出了一个范式转移的想法，一个单一的分子参与全球基因调控的基础上，大规模的表观遗传变化，驱动肿瘤细胞转化为侵略性转移性肿瘤细胞通过结合到一个子集的专门的DNA序列，作为染色体标记。我们确定SATB 1是胸腺细胞中的基因组组织者，通过改变约1000个基因的表达，包括许多与预后不良相关的基因，成为乳腺癌转移的关键决定因素。我们将通过高阶染色质结构的全局重组建立表观遗传标记的全基因组变化来检验SATB 1导致非侵袭性乳腺癌进展为转移性癌症的假设。我们进一步假设，这种重组涉及SATB 1与分布在整个人类基因组中的高度保守的、被称为碱基不配对区（布尔斯）的特异性DNA序列的相互作用。这些布尔斯可以作为染色体“标记”，染色质修饰剂被募集到这些标记上，从而导致侵袭性乳腺癌特征性的整个基因组的特异性表观遗传修饰。我们将采用高通量测序的全球定位方法，在人类基因组中定位所有推定的布尔斯，并确定那些在侵袭性乳腺癌细胞中与SATB 1结合的BURs，以及那些在活化的人类T辅助细胞中与SATB 1结合的BURs，这是一种非癌细胞类型，SATB 1通常表达。随后，我们将确定表达SATB 1的转移性癌症和SATB 1缺陷的非侵袭性乳腺癌细胞中的全基因组蛋白修饰，以确定表观遗传标记的侵袭性癌症相关变化是否集中在SATB 1结合的布尔斯。从拟议的研究中，我们将确定布尔斯的作用，在建立转移性乳腺癌特异性表观遗传标记，通过与SATB 1的相互作用。这些实验将提供对疾病进展的基本见解，这对开发未来的治疗方法是有用的。公共卫生相关性：越来越多的证据表明，癌症不一定是累积的基因突变的结果，但也可能涉及表观基因组的改变，DNA或包装DNA的蛋白质的修饰。事实上，最近的证据表明，这些修饰在转移性和非转移性乳腺癌之间是不同的。我们将确定转移性乳腺癌的表观基因组变化以及这些变化的机制。

DESCRIPTION (provided by applicant): Breast cancer is the most common cancer in women in the United States, causing ~40,000 deaths each year. In the proposed study, we will focus on breast cancer and determine what epigenomic changes cause breast cancer to acquire metastatic activity and how the changes are established. Epigenetic modifications of chromatin are associated with the expression status of individual genes. Here we propose a paradigm-shifting idea that a single molecule involved in global gene regulation underlies the massive epigenetic changes that drive the transformation of a tumor cell to aggressive metastatic tumor cells through binding to a subset of specialized DNA sequence that functions as chromosomal marks. We identified SATB1, a genome organizer in thymocytes, to be a key determinant in breast cancer metastasis by altering expression of ~1000 genes, including many associated with poor prognosis. We will test a hypothesis that SATB1 causes progression of non-aggressive breast cancer to metastatic cancer by establishing genome-wide changes in epigenetic marks through global re- organization of higher-order chromatin structure. We further hypothesize that such re- organization involves SATB1 interaction with highly conserved, specialized DNA sequences called base unpairing regions (BURs), distributed throughout the human genome. These BURs may function as chromosome "marks" to which chromatin modifiers are recruited, thus resulting in specific epigenetic modifications throughout the genome characteristic of aggressive breast cancer. We will adopt a global mapping approach by high-throughput sequencing to map all putative BURs across the human genome and identify those that are bound by SATB1in aggressive breast cancer cells versus those in activated human T helper cells, a non cancerous cell-type where SATB1 is normally expressed. We will subsequently determine genome-wide histone modifications in SATB1-expressing metastatic cancer and SATB1-deficient, non- aggressive breast cancer cells to determine whether aggressive cancer-associated changes in epigenetic marks are centered at SATB1-bound BURs. From the proposed research, we will define the role of BURs in establishing metastatic breast cancer-specific epigenetic marks through interaction with SATB1. These experiments will provide fundamental insight into disease progression that should be useful for developing future therapies. Public Health Relevance: Mounting evidence suggest that cancer is not necessarily a result of accumulated genetic mutations, but may also involve alterations in the epigenome, the modifications on the DNA or the proteins that package the DNA. In fact, recent evidence suggests that these modifications are different between metastatic and non-metastatic breast cancer. We will determine what epigenomic changes underlie metastatic breast cancer and the mechanisms by which these changes are established.