Molecular basis for aberrant de novo DNA methylation in cancer

癌症中异常 DNA 从头甲基化的分子基础

• 批准号: 10565916
• 负责人: Karim Jean Armache
• 金额: $ 52.18万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-07 至 2027-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10565916
• 关键词: Ablation; Binding; Biochemistry; Cancer Biology; Cell Differentiation process; Cells; Cellular Assay; Chromatin; Complex; CpG Islands; CpG dinucleotide; Cryoelectron Microscopy; Cytosine; DNA; DNA Methylation; DNA Modification Methylases; DNMT3B gene; DNMT3a; DNMT3a mutation; Development; Enzymes; Epigenetic Process; Equilibrium; FDA approved; Family; Foundations; Frequencies; Gene Expression Regulation; Genes; Genetic; Genomics; Histones; Human; Hypermethylation; Impairment; Individual; Intercistronic Region; Length; Malignant Neoplasms; Mediating; Meta-Analysis; Methylation; Methyltransferase; Missense Mutation; Modeling; Molecular; Molecular Conformation; Monoubiquitination; Mus; Mutate; Mutation; N-terminal; Neoplastic Cell Transformation; Normal tissue morphology; Nucleosomes; Oncogenic; Organoids; PRC1 Protein; Patients; Pattern; Play; Polycomb; Post-Translational Protein Processing; Protein Isoforms; Publishing; RNA Splicing; Recurrence; Regulation; Role; Sampling; Site; Structure; Testing; Therapeutic; Therapeutic Index; Tissue Differentiation; Tissues; Toxic effect; Tumor Suppressor Genes; Variant; Work; cancer cell; cancer initiation; chromatin modification; design; epigenomics; genome-wide; histone modification; human disease; inhibitor; insight; interdisciplinary approach; member; novel; promoter; recruit; stem cells; tumor; tumorigenesis

PROJECT SUMMARY Methylation of cytosine in the context of CpG dinucleotides is an essential and highly conserved chromatin modification. It plays a critical role in gene regulation, cell differentiation and organismal development. Aberrant patterns of DNA methylation are commonly observed in human diseases including cancer. CpG islands (CGIs), regions with a high frequency of CpG sites found at the promoters of ~40% mammalian genes, are devoid of DNA methylation in normal tissues but become hypermethylated in tumors, leading to the silencing of many tumor suppressor genes. However, the molecular mechanisms underlying CGI hypermethylation in cancer remain poorly understood, and therefore therapeutic strategies that specifically target CGI hypermethylation are lacking. DNA methylation is established by the DNMT3 family of de novo DNA methyltransferases. The DNMT3 family includes two catalytically active members, DNMT3A and DNMT3B. DNMT3A has two splice variants DNMT3A1 and DNMT3A2. While DNMT3A2 and DNMT3B are expressed during early development, DNMT3A1 is the main de novo DNA methyltransferase expressed in differentiated tissues. We and others have previously demonstrated that DNMT3A1 contains regulatory domains interacting with histone post-translational modifications (PTMs) to guide its genomic targeting to regions marked by H3K36 di- and tri-methylation (H3K36me2/3). Our collaborative preliminary studies have identified an additional functional domain unique to DNMT3A1 that facilitates its interaction with histone H2AK119 mono-ubiquitination (H2AK119Ub), a PTM catalyzed by Polycomb Repressive Complex 1 (PRC1). These findings resonate with meta-analyses of patient tumor samples, which revealed a strong correlation between CGIs that gain methylation in cancers and those regulated by Polycomb complexes in normal tissues. We will pursue a hypothesis that the redistribution of DNMT3A1 from H3K36 methylation to H2AK119ub-marked CGIs drives CGI hypermethylation and neoplastic transformation. To test this hypothesis, we will employ a multidisciplinary approach that leverages the complementary expertise of Armache and Lu labs, spanning from chromatin biochemistry, structural study to cancer biology and epigenomics. These studies will reveal the molecular mechanisms of DNMT3A1 regulation by H3K36 methylation and H2AK119Ub and uncover how the balance between these PTMs mediates the recruitment, activity and function of DNMT3A1 in healthy tissues and tumors. Expected results will provide an enhanced understanding of the dynamics, cause and consequence of CGI hypermethylation – a molecular hallmark of human cancers that remains a key focus of the field. Furthermore, they will lay the foundation for developing inhibitors that target the interaction of DNMT3A1 with H2AK119Ub to specifically reverse cancer- associated CGI hypermethylation, which are expected to show less toxicity compared to current FDA-approved unspecific DNA hypomethylating agents.

项目摘要 在CpG二核苷酸的背景下，胞嘧啶的甲基化是必不可少的染色质 修改。它在基因调节，细胞分化和有机发育中起关键作用。异常 在包括癌症在内的人类疾病中通常观察到DNA甲基化的模式。 CPG岛（CGIS）， 在约40％哺乳动物基因的启动子处发现的CpG位点频率高的区域没有 正常组织中的DNA甲基化，但在肿瘤中变高甲基化，导致许多 肿瘤抑制基因。但是，癌症中CGI高甲基化的分子机制 保持不明的理解，因此，专门针对CGI高甲基化的热策略是 缺乏。 DNA甲基化由从头DNA甲基转移酶的DNMT3家族建立。 DNMT3 家庭包括两个催化活性成员DNMT3A和DNMT3B。 DNMT3A有两个剪接变体 DNMT3A1和DNMT3A2。虽然在早期开发期间表达了DNMT3A2和DNMT3B，而DNMT3A1 是在分化组织中表达的主要DNA甲基转移酶。我们和其他人以前有 证明DNMT3A1包含与组蛋白翻译后相互作用的调节域 修饰（PTM）指导其基因组靶向以H3K36二甲基和三甲基为标志的区域 （H3K36ME2/3）。我们的协作初步研究已经确定了一个独特的其他功能领域 DNMT3A1促进其与组蛋白H2AK119单素化（H2AK119UB）的相互作用，PTM 由PolyComb抑制复合物1（PRC1）催化。这些发现与患者的荟萃分析产生共鸣 肿瘤样品揭示了CGI之间存在很强的相关性，该CGI在癌症中获得甲基化 由正常组织中的聚酮复合物调节。我们将提出一个假设，即重新分配 DNMT3A1从H3K36甲基化到H2AK119UB标记的CGIS驱动CGI高甲基化和肿瘤 转型。为了检验这一假设，我们将采用一种多学科方法来利用 完全专业的Armache和Lu Labs的专业知识，从染色质生物化学，结构研究到 癌症生物学和表观基因组学。这些研究将揭示DNMT3A1调控的分子机制 由H3K36甲基化和H2AK119UB，并发现这些PTM之间的平衡如何介导 DNMT3A1在健康组织和肿瘤中的募集，活性和功能。预期结果将提供 对CGI高甲基化的动态，原因和结果的了解增强了 - 分子 人类癌的标志仍然是该领域的重点。此外，他们将为 开发针对DNMT3A1与H2AK119UB相互作用的抑制剂，以特异性逆转癌症 - 相关的CGI高甲基化，与当前FDA批准相比，预期其毒性较小 非特异性DNA低甲基化剂。