Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection. 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. Overall design: 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。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。我们构建了一套实验模型系统，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，用以评估AML群体动力学特征及化疗耐药性形成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，可预防化疗难治性复发的发生。机制层面，DNMTi可抑制一组具有干细胞特性的预设化疗耐药AML克隆的增殖，转而促进更为罕见且适应性较差的化疗敏感克隆的扩增。重要的是，我们在异种移植模型与原代AML患者样本中均验证了DNMTi联合疗法可抑制干细胞依赖性化疗耐药性形成的能力。综上，这些结果表明DNMTi联合治疗有望规避化疗难治性AML复发的发生。
整体实验设计：我们对3组未处理的HEL细胞系（AML细胞系）重复样本、3组经阿霉素处理的HEL重复样本、3组经阿霉素+阿糖胞苷处理的HEL重复样本、4组经阿霉素+阿糖胞苷+地西他滨处理的HEL样本进行了RNA测序（RNA-Seq）分析。