NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity

Abstract

Widely used as anti-cancer and immunosuppressive agents, thiopurines have narrow therapeutic indices due to frequent toxicities, partly explained by TPMT genetic polymorphisms. Recent studies identified germline NUDT15 variation as another critical determinant of thiopurine intolerance, but the underlying molecular mechanisms and its clinical implications remain unknown. In 270 children enrolled in clinical trials for acute lymphoblastic leukemia in Guatemala, Singapore, and Japan, we identified 4 NUDT15 coding variants (p.Arg139Cys, p.Arg139His, p.Val18Ile, p.Val18_Val19insGlyVal) that resulted in 74.4%–100% loss of nucleotide diphosphatase activity. Loss-of-function NUDT15 diplotypes were consistently associated with thiopurine intolerance across three cohorts (P=0.021, 2.1×10−5, and 0.0054, respectively; meta-analysis P=4.45×10−8, allelic effect size=−11.5). Mechanistically, NUDT15 inactivated thiopurine metabolites and decreased its cytotoxicity in vitro, and patients with defective NUDT15 alleles showed excessive thiopurine active metabolites and toxicity. Taken together, our results indicate that a comprehensive pharmacogenetic model integrating NUDT15 variants may inform personalized thiopurine therapy.

Impact of NUDT15 polymorphisms on thiopurines-induced myelotoxicity and thiopurines tolerance dose

“…Multiple strong transcription factors and H3K27Ac binding signal can be detected around this rs554405994-located region according to the epigenomic information from public resource (i.e., Epigenome Browser [38], Figure 6C), indicating variant allele of rs554405994 may be associated with NUDT15 expression through altering the binding affinity of transcription factors with gene promoter. Interestingly, rs554405994 also induces a GlyVal insertion between position 18 and 19 of NUDT15, and causes a slight reduction in NUDT15 activity according to the previous report [24]. Therefore, rs554405994 can impact thiopurine metabolism through both down-regulating gene expression and reducing enzyme activity, thus may be considered as a new causal variant for thiopurines-induced myelotoxicity.…”

“…As down-regulation of NUDT15 in cell lines can also sensitize leukemia cells to thiopurines [24], we thus conducted an eQTLs analyses for NUDT15 to search additional potential pharmacogenetic markers in this gene. Expression level and SNP genotypes of LCLs were retrieved from the public resource (see Methods), and submitted for association analyses.…”

“…Recently, two independent studies have identified a variant in NUDT15 gene (i.e., rs116855232, inducing p.Arg139Cys) to be associated with intolerance to thiopurines or thiopurines-induced ADR in patients with ALL and IBD, respectively [2, 12]. Such association has been replicated by multiple independent studies [14, 21–28], and expanded to several other NUDT15 SNPs, including rs147390019 (inducing p.Arg139His) [24]. Large genetic population studies (e.g., ExAC project) demonstrate that variant allele of rs116855232 of NUDT15 is most common in East Asians (10.4%) and Hispanics (7.1%), rare in Europeans (0.46%), but barely detected in Africans, while rs147390019 is mostly in Hispanic (1.75%) [29], contributing to ancestry-related differences in thiopurine drugs tolerance [12, 19, 30].…”

Pharmacogenetic Predictors of Treatment-Related Toxicity Among Children With Acute Lymphoblastic Leukemia

“…Among East Asian and Hispanic populations, four coding variants (p.Arg139Cys, p.Arg139His, p.Val18Ile, and p.Val18_Val19insGlyVal) result in over 75% loss of nucleotide diphosphatase activity. In a recent study, this information was used to classify patients as normal, intermediate, or low NUDT15 activity and their dose of 6-MP was prospectively modified during maintenance [73]. Guidelines from the Clinical Pharmacogenetics Implementation Consortium (CPIC) are currently being updated to include dosing recommendations for patients with NUDT15 variants [74].…”

Future cancer research priorities in the USA: a Lancet Oncology Commission

“…For instance, investigators in an international collaboration identified genetic polymorphisms associated with thiopurine toxicity has a major implication for care of subgroups of children in all settings. 175 The explosion of data arising from tumour genome sequencing comes almost exclusively from high-income countries; sequencing of samples from LMICs might yield important implications for therapy for children in both LMICs and high-income countries. Innovative programmes such as medical telecommunication could improve access to quality cancer care for children in LMICs and have application to underserved populations in high-income countries.…”