Purpose: Although remarkably effective in some patients, precision medicine typically induces only transient responses despite initial absence of resistance-conferring mutations. Using BRAF -mutated myeloma as a model for resistance to precision medicine we investigated if BRAF- mutated cancer cells have the ability to ensure their survival by rapidly adapting to BRAF inhibitor treatment. Experimental Design: Full-length single-cell RNA (scRNA) sequencing (scRNA-seq) was conducted on 3 patients with BRAF -mutated myeloma and 1 healthy donor. We sequenced 1,495 cells before, after 1 week, and at clinical relapse to BRAF/MEK inhibitor treatment. We developed an in vitro model of dabrafenib resistance using genetically homogeneous single-cell clones from two cell lines with established BRAF mutations (U266, DP6). Transcriptional and epigenetic adaptation in resistant cells were defined by RNA-seq and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq). Mitochondrial metabolism was characterized by metabolic flux analysis. Results: Profiling by scRNA-seq revealed rapid cellular state changes in response to BRAF/MEK inhibition in patients with myeloma and cell lines. Transcriptional adaptation preceded detectable outgrowth of genetically discernible drug-resistant clones and was associated with widespread enhancer remodeling. As a dominant vulnerability, dependency on oxidative phosphorylation (OxPhos) was induced. In treated individuals, OxPhos was activated at the time of relapse and showed inverse correlation to MAPK activation. Metabolic flux analysis confirmed OxPhos as a preferential energetic resource of drug-persistent myeloma cells. Conclusions: This study demonstrates that cancer cells have the ability to rapidly adapt to precision treatments through transcriptional state changes, epigenetic adaptation, and metabolic rewiring, thus facilitating the development of refractory disease while simultaneously exposing novel vulnerabilities.

中文翻译：

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单细胞分析揭示代谢重编程作为 BRAF 突变多发性骨髓瘤的耐药机制

目的：虽然在某些患者中非常有效，但尽管最初没有产生耐药性的突变，但精准医学通常只会引起短暂的反应。我们使用 BRAF 突变的骨髓瘤作为对精准医学产生耐药性的模型，研究了 BRAF 突变的癌细胞是否具有通过快速适应 BRAF 抑制剂治疗来确保其存活的能力。实验设计：对 3 名 BRAF 突变骨髓瘤患者和 1 名健康供体进行了全长单细胞 RNA (scRNA) 测序 (scRNA-seq)。我们在 BRAF/MEK 抑制剂治疗前、1 周后和临床复发时对 1,495 个细胞进行了测序。我们使用来自两个具有已确定 BRAF 突变（U266、DP6）的细胞系的遗传同质单细胞克隆，开发了达拉非尼耐药性的体外模型。抗性细胞的转录和表观遗传适应由 RNA-seq 和 H3K27ac 染色质免疫沉淀测序 (ChIP-seq) 定义。通过代谢通量分析表征线粒体代谢。结果：通过 scRNA-seq 进行的分析揭示了骨髓瘤和细胞系患者响应 BRAF/MEK 抑制的快速细胞状态变化。转录适应先于可检测的遗传可辨别的耐药克隆的生长，并与广泛的增强子重塑有关。作为显性弱点，诱导了对氧化磷酸化 (OxPhos) 的依赖。在接受治疗的个体中，OxPhos 在复发时被激活，并与 MAPK 激活呈负相关。代谢通量分析证实 OxPhos 是药物持久性骨髓瘤细胞的优先能量来源。