Determinants for genome-wide epigenomics in metastatic breast cancer

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变的想法，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，作为染色体标记的功能。我们通过改变胸腺细胞中的基因组组织者SATB 1，将其鉴定为乳腺癌转移的关键决定因素。 约1000个基因表达，包括许多与预后不良相关的基因。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相互作用的高度保守的，专门的DNA序列称为碱基不配对区（布尔斯），分布在整个人类基因组。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。我们随后将确定表达SATB 1的转移性癌症和SATB 1缺陷、非转移性癌症中的全基因组蛋白修饰。 侵袭性乳腺癌细胞，以确定表观遗传标记中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。

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 metastastic 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.