Multiagent combination chemotherapy can be curative in acute lymphoblastic leukemia (ALL). Still, patients with primary refractory disease or with relapsed leukemia have a very poor prognosis. Here we integrate an in-depth dissection of the mutational landscape across diagnostic and relapsed pediatric and adult ALL samples with genome-wide CRISPR screen analysis of gene–drug interactions across seven ALL chemotherapy drugs. By combining these analyses, we uncover diagnostic and relapse-specific mutational mechanisms as well as genetic drivers of chemoresistance. Functionally, our data identify common and drug-specific pathways modulating chemotherapy response and underscore the effect of drug combinations in restricting the selection of resistance-driving genetic lesions. In addition, by identifying actionable targets for the reversal of chemotherapy resistance, these analyses open therapeutic opportunities for the treatment of relapse and refractory disease.

多药联合化疗可治愈急性淋巴细胞白血病 (ALL)。尽管如此，患有原发性难治性疾病或复发性白血病的患者预后非常差。在这里，我们将对诊断和复发的儿科和成人 ALL 样本的突变景观的深入剖析与七种 ALL 化疗药物的基因-药物相互作用的全基因组 CRISPR 筛选分析相结合。通过结合这些分析，我们揭示了诊断和复发特异性突变机制以及化学耐药性的遗传驱动因素。在功能上，我们的数据确定了调节化疗反应的常见途径和药物特异性途径，并强调了药物组合在限制耐药性驱动基因病变选择方面的作用。此外，