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4万人死亡。在这项拟议的研究中，我们将专注于乳腺癌，并确定哪些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换的想法，即参与全球基因调控的单个分子是巨大的表观遗传学变化的基础，通过与作为染色体标记的特定DNA序列的子集结合，驱动肿瘤细胞向侵袭性转移肿瘤细胞的转变。我们确认，胸腺细胞中的基因组组织者SATB1是乳腺癌转移的关键决定因素，它通过改变 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球重组建立全基因组范围的表观遗传标记变化，从而检验SATB1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SATB1与高度保守的、专门的DNA序列相互作用，称为碱基非配对区(BURS)，分布在人类基因组中。这些BURs可能作为染色体“标记”被招募到染色质修饰物，从而在侵袭性乳腺癌的整个基因组特征中导致特定的表观遗传修饰。我们将采用高通量测序的全球作图方法来定位整个人类基因组中所有假定的BURs，并识别侵袭性乳腺癌细胞中与SATB 1结合的那些细胞与激活的人类T辅助细胞中的那些细胞，T辅助细胞是一种正常表达SATB1的非癌症细胞类型。我们随后将确定表达SATB1的转移性癌症和SATB1缺陷的非转移性癌症的全基因组组蛋白修饰。 侵袭性乳腺癌细胞，以确定表观遗传标记中的侵袭性癌症相关变化是否集中在SATB1结合的BURS。从拟议的研究中，我们将通过与SATB1的相互作用来确定BURS在建立转移性乳腺癌特异性表观遗传学标记中的作用。这些实验将为疾病进展提供基本的见解，这对开发未来的治疗方法应该是有用的。

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.