Targeting DNA Methylation and the Cancer Epigenome

靶向 DNA 甲基化和癌症表观基因组

• 批准号: 10320866
• 负责人: PETER A JONES
• 金额: $ 109.5万
• 依托单位: VAN ANDEL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10320866
• 关键词: Address; Affect; Ascorbic Acid; Cancer Patient; Cell Differentiation process; Chromatin; Chromatin Remodeling Factor; Chromatin Structure; Clinical; Complex; Cryoelectron Microscopy; DNA Methylation; Data; Double-Stranded RNA; Drug Combinations; Effectiveness; Endogenous Retroviruses; Enhancers; Enzymes; Epigenetic Process; FDA approved; Future; Gene Expression; Gene-Modified; Genes; Grant; High-Throughput Nucleotide Sequencing; Histones; Human; Laboratories; Link; Malignant Neoplasms; Modification; Mutation; Nucleosomes; Outcome; Oxides; Pharmaceutical Preparations; Positioning Attribute; Promoter Regions; Proteins; Role; SETDB1 gene; Structure; Supplementation; Technology; Testis; The Cancer Genome Atlas; Work; cancer cell; cancer genome; cancer therapy; chromatin remodeling; cofactor; demethylation; design; epigenetic drug; epigenome; histone modification; improved; inhibitor; knock-down; novel strategies; novel therapeutics; patient response; response; success; translational impact

Project Summary Our laboratory discovered in 1980 that methylation of DNA (epigenetic modification) affected gene expression and cell differentiation. High-throughput sequencing and the unexpected outcomes from The Cancer Genome Atlas and other projects show that many mutations in cancer are in genes that modify the epigenome. This has validated our long-term hypothesis that abnormal epigenetic processes are major contributors to human cancer and offer novel therapeutic opportunities. Understanding how the epigenome is changed in cancer requires an integrated approach, which we have developed over the last five years. We wish to determine the mechanisms by which key features such as DNA methylation, nucleosome positioning, and histone modifications influence each other. We then will determine how DNA methylation inhibitors (DNMTi’s) work. This grant is designed to use our powerful new NOMe-seq technology to understand the relationship between DNA methylation and nucleosomal positioning; to use knock-down and other approaches to examine the effects of altering both chromatin-remodeling and histone-modifying enzymes on the epigenome as a whole; and to understand how the epigenome controls endogenous retroviruses (ERVs). We will study how the epigenome is altered in human cancer, characterizing changes not only in gene promoter regions but also in enhancer and insulator regions and in genes themselves. Major questions to be addressed include 1) Why are there so many mutations in chromatin modifiers, and what are the effects of these mutations on the structure of the epigenome? 2) What are the functional consequences of activating the expression of cancer/testis genes by 5-azanucleoside? 3) What double-stranded RNAs are activated by 5-azanucleosides and how do these relate to cellular responses? 4) Can we design combinations of epigenetic drugs which might increase the effectiveness of 5-azanucleoside treatment? and 5) Can cryo-EM help to visualize complexes relevant to chromatin structure and functions? We will also study the roles of TET enzymes, which oxidize 5- methylcytosine to 5-hydroxymethylcytosine and require vitamin C as a cofactor, and the enzymes G9A and SETDB1, which methylate histone protein H3K9. Combinations that increase the expression of ERVs will be prioritized, because recent data strongly suggests that ERV expression may be linked to cellular changes, and quite possibly to clinical outcomes in cancer. Cancer patients are often deficient in vitamin C, implying that supplementation may markedly increase TET activity and patient response. Our approach is designed not only to understand the epigenome holistically but also to devise strategies which will increase patients' responses to drugs, perhaps by defining future rational drug combinations, in particular making use of DNMTi’s. Success of this project should have rapid mechanistic and translational impact, as DNMTi’s are FDA-approved or are currently in trials for cancer treatment.

项目摘要 我们的实验室在1980年发现DNA的甲基化（表观遗传修饰）影响了基因表达 和细胞分化。高通量测序和癌症基因组的意外结果 阿特拉斯（Atlas）和其他项目表明，癌症中的许多突变都在改变表观基因组的基因中。这 已经验证了我们的长期假设，即异常的表观遗传过程是人类的主要因素 癌症并提供新颖的治疗机会。了解癌症中的表观基因组如何改变 需要一种综合方法，我们在过去五年中已经开发了这种方法。我们希望确定 关键具有DNA甲基化，核小体定位和组蛋白等关键特征的机制 修改相互影响。然后，我们将确定DNA甲基化抑制剂（DNMTI）如何起作用。 该赠款旨在利用我们强大的新Nome-Seq技术来了解 DNA甲基化和核小体定位；使用敲门和其他方法来检查 整个表观基因组上改变染色质复制和组蛋白修饰酶的影响； 并了解表观组如何控制内源性逆转录病毒（ERV）。我们将研究如何 人类癌症的表观基因组发生了变化，不仅在基因启动子区域中的变化，而且表征 增强子和绝缘体区域以及基因本身。要解决的主要问题包括1）为什么 染色质修饰剂中的突变太多，这些突变对结构有什么影响 表观基因组？ 2）激活癌症/睾丸基因表达的功能后果是什么 通过5-氮杂剂？ 3）哪些双链RNA被5-氮杂剂激活，这些如何 与细胞反应有关吗？ 4）我们可以设计表观遗传药物的组合，这可能会增加 5-氮杂剂治疗的有效性？ 5）可以使Cryo-Em有助于可视化与 染色质结构和功能？我们还将研究TET酶的作用，氧化物5-- 甲基胞嘧啶至5-羟基环霉素，需要维生素C作为辅因子，以及酶G9A和 setDB1，甲基化组蛋白蛋白H3K9。增加ERV表达的组合将是 优先级，因为最近的数据强烈表明ERV表达可能与细胞变化有关，并且 癌症的临床结果很可能。癌症患者通常缺乏维生素C，这意味着 补充可能明显增加TET活性和患者反应。我们的方法不仅设计 从整体上理解表观基因组，也可以制定策略，以增加患者对 药物，也许是通过定义未来的理性药物组合，特别是使用DNMTI。成功 该项目应该具有快速的机械和翻译影响，因为DNMTI是FDA批准的，或者是 目前正在接受癌症治疗的试验。