Loss of DKM6A confers drug resistance in acute myeloid leukemia (ChIP-seq of AML cell lines MM-1 and MM-6). Loss of DKM6A confers drug resistance in acute myeloid leukemia (ChIP-seq of AML cell lines MM-1 and MM-6)

Acute myeloid leukemia (AML) is an aggressive hematologic neoplasm resulting from the malignant transformation of myeloid progenitors. Despite intensive chemotherapy leading to initial treatment responses, relapse caused by intrinsic or acquired drug resistance represents a major challenge. Here, we report that histone 3 lysine 27 demethylase KDM6A (UTX) is targeted by inactivating mutations and mutation-independent regulation in relapsed AML. Analyses of matched diagnosis and relapse specimens from individuals with KDM6A mutations showed an outgrowth of the KDM6A mutated tumor population at relapse. KDM6A-null myeloid leukemia cells were more resistant to treatment with the chemotherapeutic agents cytarabine (AraC) and daunorubicin. Inducible re-expression of KDM6A in KDM6A-null cell lines suppressed proliferation and sensitized cells again to AraC treatment. RNA expression analysis and functional studies revealed that resistance to AraC was conferred by downregulation of the nucleoside membrane transporter ENT1 (SLC29A1). Our results show that loss of KDM6A provides cells with a selective advantage during chemotherapy, which ultimately leads to the observed outgrowth of clones with KDM6A mutations or reduced KDM6A expression at relapse. Overall design: H3K27ac and H3K27me3 ChIP-seq of AML cell lines MM-1 and MM-6

急性髓系白血病（Acute myeloid leukemia, AML）是一类由髓系祖细胞恶性转化引发的侵袭性血液系统肿瘤。尽管强化化疗可使患者获得初始治疗应答，但由内在耐药或获得性耐药引发的复发仍是当前临床面临的主要难题。本研究发现，组蛋白3赖氨酸27去甲基化酶KDM6A（UTX）在复发型急性髓系白血病中，可通过失活突变及不依赖突变的调控机制成为靶向靶点。对携带KDM6A突变患者的配对诊断样本与复发样本进行分析后发现，复发阶段携带KDM6A突变的肿瘤克隆发生了扩增。缺失KDM6A的髓系白血病细胞对化疗药物阿糖胞苷（cytarabine, AraC）及柔红霉素（daunorubicin）的耐药性显著增强。在缺失KDM6A的细胞系中诱导重表达KDM6A，可抑制细胞增殖并使细胞重新对阿糖胞苷治疗产生敏感性。RNA表达分析与功能实验结果显示，核苷膜转运蛋白ENT1（SLC29A1）的下调是介导阿糖胞苷耐药的关键机制。本研究结果表明，KDM6A的缺失可使肿瘤细胞在化疗过程中获得选择优势，最终导致复发阶段携带KDM6A突变或KDM6A表达下调的克隆出现扩增。整体实验设计：针对AML细胞系MM-1与MM-6开展H3K27乙酰化（H3K27ac）及H3K27三甲基化（H3K27me3）染色质免疫共沉淀测序（ChIP-seq）。