Determinants for genome-wide epigenomics in metastatic breast cancer

转移性乳腺癌全基因组表观基因组学的决定因素

• 批准号: 7726410
• 负责人: Terumi Kohwi-Shigematsu
• 金额: $ 45.98万
• 依托单位: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-21 至 2014-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7726410
• 关键词: Adopted; Binding; Breast Cancer Cell; CD4 Positive T Lymphocytes; Cancerous; Cessation of life; Characteristics; Chromatin; Chromosomes; DNA; DNA Packaging; DNA Sequence; Disease Progression; Disseminated Malignant Neoplasm; Epigenetic Process; Future; Gene Expression Regulation; Gene Mutation; Genes; Genome; Helper-Inducer T-Lymphocyte; Higher Order Chromatin Structure; Human; Human Genome; Individual; Malignant Neoplasms; Maps; Modification; Neoplasm Metastasis; Proteins; Recruitment Activity; Research; Role; Testing; United States; Woman; base; cell type; chromatin modification; epigenomics; genome-wide; histone modification; insight; malignant breast neoplasm; neoplastic cell; outcome forecast; public health relevance; research study; single molecule; thymocyte

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.

描述（由申请人提供）：乳腺癌是美国女性最常见的癌症，每年导致约 40,000 人死亡。在拟议的研究中，我们将重点关注乳腺癌，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形成的。染色质的表观遗传修饰与单个基因的表达状态相关。在这里，我们提出了一个范式转变的想法，即参与全局基因调控的单个分子是大规模表观遗传变化的基础，这些变化通过与充当染色体标记的专门 DNA 序列子集结合，驱动肿瘤细胞转变为侵袭性转移性肿瘤细胞。我们通过改变约 1000 个基因（包括许多与不良预后相关的基因）的表达，确定了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。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 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 与分布在整个人类基因组中的高度保守、专门的 DNA 序列（称为碱基不配对区域 (BUR)）的相互作用。这些 BUR 可能充当染色体“标记”，染色质修饰剂被招募到其中，从而导致侵袭性乳腺癌的整个基因组特征发生特定的表观遗传修饰。我们将采用高通量测序的全局作图方法来绘制人类基因组中所有假定的 BUR，并识别侵袭性乳腺癌细胞中与 SATB1 结合的 BUR 和激活的人类 T 辅助细胞（SATB1 通常表达 SATB1 的非癌细胞类型）中的 BUR。随后，我们将确定表达 SATB1 的转移性癌症和 SATB1 缺陷的非侵袭性乳腺癌细胞中的全基因组组蛋白修饰，以确定与侵袭性癌症相关的表观遗传标记变化是否集中在 SATB1 结合的 BUR 上。根据拟议的研究，我们将通过与 SATB1 相互作用来定义 BUR 在建立转移性乳腺癌特异性表观遗传标记中的作用。这些实验将为疾病进展提供基本见解，这对于开发未来的疗法很有用。公共健康相关性：越来越多的证据表明，癌症不一定是基因突变累积的结果，还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，转移性乳腺癌和非转移性乳腺癌之间的这些修饰是不同的。我们将确定转移性乳腺癌背后的表观基因组变化以及这些变化产生的机制。