Development of resistance to targeted therapies has tempered initial optimism that precision oncology would improve poor outcomes for cancer patients. Resistance mechanisms, however, can also confer new resistance-specific vulnerabilities, termed collateral sensitivities. Here we investigated anaplastic lymphoma kinase (ALK) inhibitor resistance in neuroblastoma, a childhood cancer frequently affected by activating ALK alterations. Genome-wide forward genetic CRISPR-Cas9 based screens were performed to identify genes associated with ALK inhibitor resistance in neuroblastoma cell lines. Furthermore, the neuroblastoma cell line NBLW-R was rendered resistant by continuous exposure to ALK inhibitors. Genes identified to be associated with ALK inhibitor resistance were further investigated by generating suitable cell line models. In addition, tumor and liquid biopsy samples of four patients with ALK-mutated neuroblastomas before ALK inhibitor treatment and during tumor progression under treatment were genomically profiled. Both genome-wide CRISPR-Cas9-based screens and preclinical spontaneous ALKi resistance models identified NF1 loss and activating NRASQ61K mutations to confer resistance to chemically diverse ALKi. Moreover, human neuroblastomas recurrently developed de novo loss of NF1 and activating RAS mutations after ALKi treatment, leading to therapy resistance. Pathway-specific perturbations confirmed that NF1 loss and activating RAS mutations lead to RAS-MAPK signaling even in the presence of ALKi. Intriguingly, NF1 loss rendered neuroblastoma cells hypersensitive to MEK inhibition. Our results provide a clinically relevant mechanistic model of ALKi resistance in neuroblastoma and highlight new clinically actionable collateral sensitivities in resistant cells.

中文翻译：

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ALK 信号通路突变对 ALK 抑制剂治疗产生耐药性，导致神经母细胞瘤细胞的附带脆弱性


靶向治疗耐药性的发展削弱了最初的乐观情绪，即精准肿瘤学将改善癌症患者的不良预后。然而，抵抗机制也可能带来新的抵抗特定的脆弱性，称为附带敏感性。在这里，我们研究了神经母细胞瘤对间变性淋巴瘤激酶 (ALK) 抑制剂的耐药性，神经母细胞瘤是一种经常受激活 ALK 改变影响的儿童癌症。进行基于全基因组正向遗传 CRISPR-Cas9 的筛选，以确定与神经母细胞瘤细胞系中 ALK 抑制剂耐药性相关的基因。此外，神经母细胞瘤细胞系 NBLW-R 通过持续暴露于 ALK 抑制剂而产生耐药性。通过生成合适的细胞系模型，进一步研究了与 ALK 抑制剂耐药性相关的基因。此外，对 ALK 抑制剂治疗前和治疗期间肿瘤进展期间的 4 名 ALK 突变神经母细胞瘤患者的肿瘤和液体活检样本进行了基因组分析。基于全基因组 CRISPR-Cas9 的筛选和临床前自发 ALKi 抗性模型均鉴定出 NF1 缺失和激活 NRASQ61K 突变，从而赋予对化学多样性 ALKi 的抗性。此外，人类神经母细胞瘤在 ALKi 治疗后反复出现 NF1 重新缺失和激活 RAS 突变，导致治疗耐药。通路特异性扰动证实，即使在 ALKi 存在的情况下，NF1 丢失和激活 RAS 突变也会导致 RAS-MAPK 信号传导。有趣的是，NF1 缺失使得神经母细胞瘤细胞对 MEK 抑制过度敏感。我们的结果提供了神经母细胞瘤中 ALKi 耐药的临床相关机制模型，并强调了耐药细胞中新的临床可行的附带敏感性。