Chemotherapy is a standard treatment for pediatric acute lymphoblastic leukemia (ALL), which sometimes relapses with chemoresistant features. However, whether acquired drug-resistance mutations in relapsed ALL pre-exist or are induced by treatment remains unknown. Here we provide direct evidence of a specific mechanism by which chemotherapy induces drug-resistance-associated mutations leading to relapse. Using genomic and functional analysis of relapsed ALL we show that thiopurine treatment in mismatch repair (MMR)-deficient leukemias induces hotspot TP53 R248Q mutations through a specific mutational signature (thio-dMMR). Clonal evolution analysis reveals sequential MMR inactivation followed by TP53 mutation in some patients with ALL. Acquired TP53 R248Q mutations are associated with on-treatment relapse, poor treatment response and resistance to multiple chemotherapeutic agents, which could be reversed by pharmacological p53 reactivation. Our findings indicate that TP53 R248Q in relapsed ALL originates through synergistic mutagenesis from thiopurine treatment and MMR deficiency and suggest strategies to prevent or treat TP53-mutant relapse.

化疗是小儿急性淋巴细胞白血病 (ALL) 的标准治疗方法，有时会复发并伴有化疗耐药性特征。然而，复发性 ALL 中的获得性耐药突变是预先存在还是由治疗诱导的仍然未知。在这里，我们提供了化学疗法诱导耐药相关突变导致复发的特定机制的直接证据。通过对复发性 ALL 的基因组和功能分析，我们表明在错配修复 (MMR) 缺陷型白血病中进行硫嘌呤治疗会通过特定的突变特征 (thio-dMMR)诱导热点TP53 R248Q 突变。克隆进化分析揭示了在一些 ALL 患者中连续的 MMR 失活继之以TP53突变。收购TP53R248Q 突变与治疗中复发、治疗反应差和对多种化疗药物的耐药性有关，这可以通过药理学 p53 再激活来逆转。我们的研究结果表明，复发性 ALL 中的TP53 R248Q 源于硫嘌呤治疗和 MMR 缺乏的协同诱变，并提出了预防或治疗TP53 突变体复发的策略。