Hierarchical Lineage Tracing Reveals Diverse Pathways of AML Treatment Resistance [scRNA-seq]. Hierarchical Lineage Tracing Reveals Diverse Pathways of AML Treatment Resistance [scRNA-seq]

Cancer cells adapt to treatment, leading to the emergence of clones that are more aggressive and resistant to anti-cancer therapies. We have a limited understanding of the evolution of treatment resistance as we have lacked technologies to map the evolution of cancer under the selective pressures. To address this, we developed a hierarchical, dynamic lineage tracing method called FLARE (Following Lineage Adaptation and Resistance Evolution). We use this technique to track the progression of acute myeloid leukemia (AML) cell lines through exposure to Cytarabine (AraC), a front-line treatment in AML, in vitro and in vivo. We map distinct cellular lineages in murine and human AML cell lines that are predisposed to AraC persistence and/or resistance via upregulation of cell adhesion and motility pathways. Additionally, we highlight heritable increased expression of immunoproteasome 11S regulatory cap subunits as a potential mechanism aiding AML cell survival, proliferation, and immune escape in vivo. Finally, we validate the clinical relevance of these signatures in the TARGET-AML cohort, with a bisected response in blood and bone marrow. Our findings reveal a broad spectrum of resistance signatures attributed to significant cell transcriptional changes, and we expect this high-resolution profiling of treatment response to be a useful tool to dissect the evolution of treatment response in a wide range of tumor types. Overall design: Sequencing of cultured AML cell transcriptomes and FLARE lineage tags and recorders to follow the emergence of AraC resistance in vitro and in vivo.

癌细胞可适应治疗压力，进而产生侵袭性更强、对抗癌疗法产生耐药性的克隆亚群。此前因缺乏可在选择压力下解析癌症演化过程的技术手段，我们对治疗耐药性的演化机制认知仍十分有限。为此，我们开发了一种层级化动态谱系追踪技术，命名为FLARE（Following Lineage Adaptation and Resistance Evolution）。我们利用该技术，在体外与体内环境中追踪急性髓系白血病（acute myeloid leukemia, AML）细胞系在暴露于阿糖胞苷（Cytarabine, AraC，AML一线治疗药物）时的演化进程。我们绘制了小鼠与人类AML细胞系中的特异性细胞谱系图谱，这些谱系通过上调细胞黏附与运动通路，易出现阿糖胞苷耐受和/或耐药表型。此外，我们还发现免疫蛋白酶体11S调节帽亚基的可遗传表达上调，这可能是体内AML细胞存活、增殖与免疫逃逸的潜在驱动机制。最后，我们在TARGET-AML队列中验证了上述特征的临床相关性，其在血液与骨髓样本中均呈现出二分应答模式。本研究揭示了由显著细胞转录重编程所介导的多样化耐药特征谱，我们预期这种高分辨率的治疗应答表征方法，可作为解析多种肿瘤类型治疗应答演化过程的有效工具。整体实验设计：对体外培养的AML细胞转录组、FLARE谱系标签与记录元件进行测序，以追踪体外与体内阿糖胞苷耐药克隆的出现过程。