AMLs harboring DNMT3A-destabilizing variants show increased intratumor DNA methylation heterogeneity at bivalent chromatin domains

The mechanistic link between the complex mutational landscape of de novo methyltransferase DNMT3A and the pathology of acute myeloid leukemia (AML) has not been clearly elucidated so far. A recent discovery on the catalogue of DNMT3A-destabilizing mutations throughout the DNMT3A gene as well as the oligomerization-dependent catalytic property of DNMT3A prompted us to investigate the common effect of DNMT3A-destabilizing mutations (DNMT3A-INS) on the genomewide methylation patterns of AML cells. In this study, we describe the characteristics of DNMT3A-INS AML methylomes through the comprehensive computational analyses on three independent AML cohorts. As a result, we show that methylomes of DNMT3A-INS AMLs are considerably different from those of DNMT3A-R882 AMLs in that they exhibit both locally disordered DNA methylation states and increased across-cell DNA methylation heterogeneity in bivalent chromatin domains. This increased epigenetic heterogeneity was functionally associated with heterogeneous expression of membrane-associated factors shaping stem cell niche, implying the diversification of the modes of leukemic stem cell-niche interactions. We also present that the level of methylation disorder at bivalent domains predicts the response of AML cells to hypomethylating agents through cell line- and patient-level analyses, which supports that the survival of AML cells depends on stochastic DNA methylations at bivalent domains. Our work provides a novel mechanistic model suggesting the genomic origin of the aberrant epigenomic heterogeneity in disease conditions and underscores the clinical significance of the malignant increase of adaptive potentials of cell populations.

迄今，从头甲基转移酶DNMT3A的复杂突变谱与急性髓系白血病（AML）的病理发生之间的机制关联尚未得到明确阐释。近期有关全DNMT3A基因范围内DNMT3A不稳定突变的目录，以及DNMT3A依赖寡聚化的催化特性的研究发现，促使我们探究DNMT3A不稳定突变（DNMT3A-INS）对AML细胞全基因组甲基化模式的共性影响。本研究通过对三个独立AML队列的综合计算分析，刻画了DNMT3A-INS AML甲基化组的特征。研究结果显示，DNMT3A-INS AML的甲基化组与DNMT3A-R882 AML的甲基化组存在显著差异：前者不仅呈现局部DNA甲基化状态紊乱，还在二价染色质结构域中出现细胞间DNA甲基化异质性升高的现象。这种升高的表观遗传异质性，与调控干细胞微环境的膜相关因子的异质性表达存在功能关联，提示白血病干细胞与微环境的相互作用模式发生了多样化。此外，通过细胞系与患者水平的分析，我们证实二价结构域的甲基化紊乱程度可预测AML细胞对低甲基化药物的响应，这一结果支持AML细胞的存活依赖于二价结构域上的随机性DNA甲基化。本研究提出了一种全新的机制模型，阐释了疾病状态下异常表观基因组异质性的基因组起源，并强调了细胞群体适应性潜能恶性增强的临床意义。