Molecular basis for aberrant de novo DNA methylation in cancer

项目总结 胞嘧啶在CpG二核苷酸背景下的甲基化是一种基本的高度保守的染色质 修改。它在基因调控、细胞分化和生物发育中起着至关重要的作用。反常的 DNA甲基化模式在包括癌症在内的人类疾病中常见。CPG岛(CGI)， 在~40%的哺乳动物基因启动子上发现CpG位点频率较高的区域，缺乏 DNA在正常组织中甲基化，但在肿瘤中变得高度甲基化，导致许多 肿瘤抑制基因。然而，癌症中CGI高甲基化的分子机制 仍然知之甚少，因此针对CGI高甲基化的治疗策略是 缺乏。DNA甲基化是由从头DNA甲基转移酶DNMT3家族建立的。DNMT3 该家族包括两个催化活性成员，DNMT3A和DNMT3B。DNMT3A有两种剪接变体 DNMT3A1和DNMT3A2。虽然DNMT3A2和DNMT3B在早期发育过程中表达，但DNMT3A1 是在分化组织中表达的主要从头DNA甲基转移酶。我们和其他人之前 证明DNMT3A1含有与组蛋白翻译后相互作用的调控结构域 修饰(PTM)以引导其基因组靶向H3K36二甲基化和三甲基化标记的区域 (H3K36me2/3)。我们的合作初步研究已经确定了另一个独特的功能域 促进其与组蛋白H_2AK119单泛素化(H_2AK119Ub)相互作用的DNMT3A1 由多梳抑制络合物1(PRC1)催化。这些发现与对患者的荟萃分析相一致 肿瘤样本，这表明在癌症中获得甲基化的CGI和那些 在正常组织中受多梳复合体的调节。我们将追寻一种假设，即 从H3K36甲基化到H2 AK119 ub标记的CGI的DNMT3A1驱动CGI超甲基化和肿瘤 转型。为了检验这一假设，我们将采用一种多学科的方法，利用 Armache和Lu实验室的互补专业知识，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 通过H3K36甲基化和H2AK119Ub，揭示这些PTM之间的平衡是如何介导 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 加深对CGI超甲基化的动力学、原因和后果的理解 人类癌症的特征仍然是该领域的一个关键焦点。此外，它们将为以下方面奠定基础 开发靶向DNMT3A1与H2AK119Ub相互作用的抑制剂，以特异性逆转癌症- 相关的CGI超甲基化，与目前FDA批准的相比，预计毒性较小 非特异性DNA低甲基化试剂。

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.