The principles that govern the evolution of tumors exposed to targeted therapy are poorly understood. Here we modeled the selection and propagation of an amplification in the BRAF oncogene (BRAF^amp) in patient-derived tumor xenografts (PDXs) that were treated with a direct inhibitor of the kinase ERK, either alone or in combination with other ERK signaling inhibitors. Single-cell sequencing and multiplex fluorescence in situ hybridization analyses mapped the emergence of extra-chromosomal amplification in parallel evolutionary trajectories that arose in the same tumor shortly after treatment. The evolutionary selection of BRAF^amp was determined by the fitness threshold, the barrier that subclonal populations need to overcome to regain fitness in the presence of therapy. This differed for inhibitors of ERK signaling, suggesting that sequential monotherapy is ineffective and selects for a progressively higher BRAF copy number. Concurrent targeting of the RAF, MEK and ERK kinases, however, imposed a sufficiently high fitness threshold to prevent the propagation of subclones with high-level BRAF^amp. When administered on an intermittent schedule, this treatment inhibited tumor growth in 11/11 PDXs of lung cancer or melanoma without apparent toxicity in mice. Thus, gene amplification can be acquired and expanded through parallel evolution, enabling tumors to adapt while maintaining their intratumoral heterogeneity. Treatments that impose the highest fitness threshold will likely prevent the evolution of resistance-causing alterations and, thus, merit testing in patients.

中文翻译：

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抑制BRAFV600E突变型癌症耐药性演变的方法

人们很少了解控制接受靶向治疗的肿瘤演变的原理。在本文中，我们模拟了在患者衍生的肿瘤异种移植物（PDXs）中的BRAF癌基因（BRAF ^amp）中扩增的选择和传播，这些肿瘤异种移植物单独或与其他ERK信号抑制剂一起直接用激酶ERK的直接抑制剂处理。单细胞测序和多重荧光原位杂交分析绘制了在治疗后不久出现在同一肿瘤中的平行进化轨迹中染色体外扩增的出现。BRAF^功放的进化选择由适应度阈值确定，适应度阈值是亚克隆人群在治疗存在下要恢复适应性所需要克服的障碍。这对于ERK信号的抑制剂是不同的，表明顺序的单药治疗无效，并选择了逐渐升高的BRAF拷贝数。但是，同时靶向RAF，MEK和ERK激酶会施加足够高的适应性阈值，以防止高水平BRAF ^amp传播亚克隆。当间歇给药时，这种治疗可抑制肺癌或黑色素瘤的11/11 PDX中的肿瘤生长，而对小鼠无明显毒性。因此，可以通过平行进化来获得和扩增基因扩增，从而使肿瘤能够适应，同时保持其肿瘤内异质性。施加最高适应度阈值的治疗可能会阻止引起耐药性变化的发展，从而防止患者进行择优测试。