Acquired thiopurine resistance and mismatch repair aberrations in paediatric B‐cell acute lymphoblastic leukaemia relapse: A real‐world data integrating mutational signatures, clones and clinical thiopurine dosing patterns

Summary Acquired thiopurine resistance and mismatch repair (MMR) deficiency are increasingly recognised drivers of relapse in paediatric B‐cell acute lymphoblastic leukaemia (B‐ALL); however, their real‐world genomic prevalence and link to maintenance dosing patterns remain poorly characterised. Paediatric B‐ALL relapse cases (2018–2024) were subjected to whole exome sequencing (WES; 200–250× depth; n = 70) and deep targeted sequencing (700–900×; n = 5). Per‐sample frequencies of resistance gene mutations, single‐base mutational signatures, tumour mutational burden‐high (≥10 mutations/Mb), microsatellite instability‐high (MSI‐H) and thiopurine S‐methyltransferase ( TPMT)/nucleoside diphosphate‐linked moiety X‐type motif 15 (NUDT15) status were determined. Clinical variables included the median weekly 6‐mercaptopurine (6‐MP) dose (mg/m 2 , time‐weighted) and duration of 6‐MP dose interruptions. A total of 18/75 (24%) relapse cases showed SBS87 (thiopurine‐related), SBS6/15 (MMR‐related) or Thio‐deficient mismatch repair (Thio‐dMMR) mutational signature. Thiopurine resistance clones in cytosolic 5'‐nucleotidase II ( NT5C2) (13), phosphoribosyl pyrophosphate synthetase 1 ( PRPS1) (2) or tumor protein p53 ( TP53) (7) were noted in 19/75 (25%) cases; germline or somatic clones in MMR genes were noted in 19/75 (25%). Correlation analysis revealed that both low median weekly 6‐MP dose (<45 mg/m 2 ) and ≥4 weeks of dose interruptions were significantly associated with higher hazard for SBS87 or Thio‐dMMR signature (hazard ratio [HR] 7.09 [95% confidence interval (CI): 1.77–28.34], p = 0.006, and HR 6.21 [95% CI: 1.66–23.32], p = 0.007 respectively). This real‐world study demonstrates that suboptimal median 6‐MP dosing and prolonged dose interruptions during maintenance are significantly associated with thiopurine resistance and MMR deficiency‐related mutational signatures at relapse. These findings underscore the importance of optimised dose intensity and minimal interruptions during maintenance therapy in paediatric B‐ALL.