Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection

Chemotherapy-resistant cancer recurrence is a major cause of mortality. In acute myeloid leukemia (AML), chemorefractory relapses result from the complex interplay between altered genetic, epigenetic and transcriptional states in leukemic cells. We developed an experimental model system using in vitro lineage tracing coupled with exome, transcriptome and in vivo functional readouts to assess the AML population dynamics and associated molecular determinants underpinning chemoresistance development. We found that combining standard chemotherapeutic regimens with low doses of DNA methyltransferase inhibitors (DNMTi, hypomethylating drugs) prevents chemoresistant relapses. Mechanistically, DNMTi suppressed the outgrowth of a pre-determined set of chemoresistant AML clones with stemness properties, instead favoring the expansion of rarer and unfit chemosensitive clones. Importantly, we confirmed the capacity of DNMTi combination to suppress stemness-dependent chemoresistance development in both xenotransplantation models and primary AML patient samples. Together, these results support the potential of DNMTi combination treatment to circumvent the development of chemorefractory AML relapses. We preformed RNA-Seq analysis of 3 untreated HEL (AML cell line) replicates; 3 Doxorubicin treated HEL replicates; 3 Doxorubicn + Cytarabine treated HEL replicates; 4 Doxorubicin + Cytarabine + Decitabine

化疗耐药性癌症复发是导致患者死亡的主要诱因之一。在急性髓系白血病（acute myeloid leukemia, AML）中，化疗难治性复发源于白血病细胞内发生改变的遗传、表观遗传与转录状态之间的复杂相互作用。本研究建立了一套实验模型体系，结合体外谱系追踪、外显子组测序、转录组分析与体内功能检测，以评估AML的群体动力学特征及介导化疗耐药发生的相关分子决定因素。研究发现，将标准化疗方案与低剂量DNA甲基转移酶抑制剂（DNA methyltransferase inhibitors, DNMTi，低甲基化药物）联合使用，可阻断化疗耐药性复发的进程。从机制层面分析，DNMTi可抑制一组预先存在的具有干细胞特性的化疗耐药性AML克隆的增殖，转而促进更为罕见且增殖能力较弱的化疗敏感克隆的扩增。尤为重要的是，本研究在异种移植模型与原代AML患者样本中均证实，DNMTi联合疗法可抑制依赖于干细胞特性的化疗耐药的产生。综上，上述研究结果支持DNMTi联合疗法在规避AML化疗难治性复发方面的应用潜力。本研究对如下样本开展了RNA测序（RNA-Seq）分析：3份未处理的HEL（AML细胞系）生物学重复样本；3份经阿霉素处理的HEL生物学重复样本；3份经阿霉素+阿糖胞苷处理的HEL生物学重复样本；4份经阿霉素+阿糖胞苷+地西他滨处理的HEL生物学重复样本。