Prevalence of TPMT and NUDT15 diplotypes in Mexican children with B-cell acute lymphoblastic leukemia

Abstract

Abstract Introduction: B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer worldwide and the leading cause of cancer-related death among Mexican children. Although advances in treatment have significantly improved survival rates in pediatric B-ALL, treatment-related mortality remains a concern. Some of these adverse effects are attributed to interindividual variability in thiopurine metabolism, influenced by genetic variants in the NUDT15 and TPMT genes. These variants can result in prolonged myelotoxicity and hepatotoxicity, often requiring dose reductions, treatment interruptions, or discontinuation of chemotherapy, potentially compromising treatment efficacy. In this study, we characterize the allelic and diplotype variability of the TPMT and NUDT15 genes in a cohort of pediatric B-ALL patients from the central-southern region of Mexico Methods A total of 275 pediatric B-ALL patients, born in nine different states across Mexico, were enrolled in the study. The mean age at diagnosis was 7.9 ± 4.8 years (range: 0–17 years). DNA was extracted from bone marrow aspirates. TPMT and NUDT15 genotyping was performed using a customized NGS-based panel synthesized by ArcherDX. Libraries were sequenced on the Illumina NextSeq 2000 platform. Alleles and diplotypes were classified according to the Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. Diplotype distribution was compared across Mexican states and global populations. To assess the structural and functional impact of TPMT variants not assigned to established star alleles, in silico analyses were conducted. Results The wild-type (WT) 1 allele, associated with normal enzymatic activity, was predominant in both genes: TPMT (94.15%) and NUDT15 (90.45%). Greater allelic diversity was observed in TPMT compared to previous studies in Mexican populations. Alleles conferring absent or indeterminate enzymatic activity in TPMT were distributed across six diplotypes, affecting 11.62% of patients. The *1/*3A diplotype was the most frequent (9.45%) and corresponds to an intermediate metabolizer phenotype. In two patients, the p.(G126A) and p.(D137Y) variants, both located in exon 5, were identified. These variants are not currently assigned to any CPIC-defined TPMT star allele and are predicted to alter enzyme function. Notably, both have been previously reported in healthy Mexican individuals based on exome sequencing data from the Mexico City Prospective Study. For NUDT15, three non-WT alleles (*2, *3, and *4) were identified, with *2 being the most prevalent (6.74%). The *1/*2 diplotype was the most common altered genotype (13.48%). In our cohort, 71.91% of patients were classified as normal metabolizers for both genes, 25.09% were heterozygous for a variant with reduced or absent enzymatic activity in either NUDT15 or TPMT, and 3% carried functionally altered alleles in both genes. Conclusion This study demonstrates that approximately 28% of Mexican pediatric B-ALL patients are predicted to have reduced enzymatic activity in TPMT, NUDT15, or both, placing them at increased risk for mercaptopurine-induced myelotoxicity. Pre-emptive genotyping of TPMT and NUDT15 in Mexican B-ALL patients is essential for minimizing treatment-related toxicity, improving clinical outcomes, and advancing precision medicine strategies.