Establishing and Interpreting Abnormal DNA Methylation in Cancer

建立并解释癌症中的异常 DNA 甲基化

• 批准号: 10732031
• 负责人: PETER A JONES
• 金额: $ 114.65万
• 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 2030-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10732031
• 关键词: Address; Age; Binding; Biochemical; Biological; Blood Cells; Body Size; Brain; Cancer Model; Cell Differentiation process; Cell division; Cells; Chemicals; Chromatin; Chromatin Structure; Cryoelectron Microscopy; DNA; DNA Methylation; DNA Modification Methylases; DNMT3B gene; DNMT3a; Development; Embryonic Development; Enzymes; Etiology; Funding Mechanisms; Genes; Genetic; Hematopoiesis; Human; Knock-out; Malignant Neoplasms; Methylation; Mus; Mutation; Normal Cell; Nucleosomes; Prevalence; Process; Protein Isoforms; Proteins; Regulation; Role; Signal Transduction; Solid; Solid Neoplasm; Structure; Testing; Work; cancer cell; cancer initiation; carcinogenesis; cell transformation; flexibility; follow-up; insight; leukemia; methyl group; mouse model; novel; overexpression; postnatal development; transcription factor; virtual

Project Summary/Abstract The mammalian de novo DNA methyltransferase, DNMT3A is essential for postnatal development of the brain, control of body size and for the regulation of hematopoiesis. Mutations in the gene are commonly found in age- associated clonal hematopoiesis of indeterminant potential and are drivers for certain leukemias making it important that we understand how the enzyme functions in living cells. All human cancers contain DNA methylation anomalies, however mutations in DNMT3A are relatively rare in solid tumors, suggesting that altered enzyme regulation might be responsible for these changes. Although we know in exquisite detail how DNMT3A methylates naked DNA, we know virtually nothing about how this occurs in the context of nucleosomes, the fundamental building blocks of chromatin. The focus of this application is to address this issue using new insights recently developed in the lab. We will concentrate on the role of a truncated isoform, DNMT3A2, normally expressed during embryonic development but overexpressed in most solid cancers. Our novel cryo-EM structure shows how this enzyme partners with an accessory protein DNMT3B3 to bind to nucleosomes through the acidic patch – a totally unexpected discovery. We will follow up on this work using biochemical, cryo-EM, cellular and mouse studies to gain a more precise understanding of how DNA methylation works in the context of chromatin. A mouse model in which Dnmt3a2, but not the more widely studied longer isoform, Dnmt3a1, has been knocked out will be used to test for causality in the process of immortalization and carcinogenesis in genetic and chemical mouse models of cancer. This comprehensive approach will help in our understanding of how this fundamental process works in normal and transformed cells. Studies on how DNA methylation marks are interpreted in cells has long been confined to comparison between fully and completely unmethylated CpG dyad states. Because of the flexibility in the R35 funding mechanism, we serendipitously discovered that CpG hemimethylation can either stimulate or inhibit binding by CTCF depending on which duplex strand is methylated. We will investigate the prevalence of hemimethylation in cancer cells and investigate its effects on binding of other transcription factors and chromatin structure. Differential binding may play a role in asymmetric cell divisions in cancer cells. We hope to answer three critical questions: 1) Does DNMT3A2 overexpression contribute to carcinogenesis? 2) How does de novo methylation occur in a nucleosomal context? 3) What are the potential biological roles for hemimethylation?

项目总结/摘要 哺乳动物从头DNA甲基转移酶，DNMT 3A是出生后大脑发育所必需的， 控制身体大小和调节造血。基因突变通常在年龄- 相关的克隆造血的不确定的潜力，并为某些白血病的驱动程序，使其 重要的是我们要了解酶在活细胞中的功能。所有人类癌症都含有DNA 然而，DNMT 3A的突变在实体瘤中相对罕见，这表明改变的DNA甲基化异常可能导致DNA甲基化异常。 酶调节可能是造成这些变化的原因。尽管我们知道DNMT 3A是如何 甲基化裸露的DNA，我们几乎不知道这是如何发生在核小体的背景下， 染色质的基本组成部分。这个应用程序的重点是使用新的见解来解决这个问题 最近在实验室里开发的。我们将集中讨论截短的同种型DNMT 3A 2的作用，通常 在胚胎发育期间表达，但在大多数实体癌中过表达。我们的新型低温电磁结构 显示了这种酶如何与辅助蛋白DNMT 3B 3通过酸性磷酸酶结合到核小体上。 补丁-一个完全出乎意料的发现。我们将使用生物化学，冷冻EM，细胞和 小鼠研究，以更精确地了解DNA甲基化在染色质中的作用。 一种小鼠模型，其中Dnmt 3a 2，而不是更广泛研究的较长同种型Dnmt 3a 1，已被敲除， out将被用来测试在遗传和化学的永生化和致癌过程中的因果关系。 小鼠癌症模型。这种全面的方法将有助于我们理解这一基本的 这一过程在正常细胞和转化细胞中起作用。 关于DNA甲基化标记在细胞中如何解释的研究长期以来一直局限于比较 完全和完全未甲基化的CpG二联体状态。由于R35供资机制的灵活性， 我们偶然发现，CpG半甲基化可以刺激或抑制CTCF的结合， 这取决于哪个双链体链被甲基化。我们将调查癌症中半甲基化的流行情况 细胞，并研究其对其他转录因子和染色质结构的结合的影响。微分 结合可能在癌细胞的不对称细胞分裂中起作用。我们希望回答三个关键问题： 1)DNMT 3A 2过表达是否有助于癌变？2)如何从头甲基化发生在 核小体背景3)半甲基化的潜在生物学作用是什么？

项目成果

A Novel DNA Methylation Signature as an Independent Prognostic Factor in Muscle-Invasive Bladder Cancer.

• DOI: 10.3389/fonc.2021.614927
• 发表时间: 2021
• 期刊: Frontiers in oncology
• 影响因子: 4.7
• 作者: Xu Z;Gujar H;Fu G;Ahmadi H;Bhanvadia S;Weisenberger DJ;Jin B;Gill PS;Gill I;Daneshmand S;Siegmund KD;Liang G
• 通讯作者: Liang G

Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses.

• DOI: 10.1101/gr.234229.118
• 发表时间: 2018-08
• 期刊: Genome research
• 影响因子: 7
• 作者: Ohtani H;Liu M;Zhou W;Liang G;Jones PA
• 通讯作者: Jones PA

Mother-child transmission of epigenetic information by tunable polymorphic imprinting.

• DOI: 10.1073/pnas.1815005115
• 发表时间: 2018-12-18
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Carpenter BL;Zhou W;Madaj Z;DeWitt AK;Ross JP;Grønbæk K;Liang G;Clark SJ;Molloy PL;Jones PA
• 通讯作者: Jones PA

Chromosome-specific retention of cancer-associated DNA hypermethylation following pharmacological inhibition of DNMT1.

• DOI: 10.1038/s42003-022-03509-3
• 发表时间: 2022-06-02
• 期刊: Communications biology
• 影响因子: 5.9

DNA strand asymmetry generated by CpG hemimethylation has opposing effects on CTCF binding.

• DOI: 10.1093/nar/gkad293
• 发表时间: 2023-07-07
• 期刊: Nucleic acids research
• 影响因子: 14.9