Nudix hydrolase 15 (NUDT15) loss-of-function variants in an Australian inflammatory bowel disease population

Abstract

Background: Thiopurine-related adverse events such as leukopenia, liver dysfunction and pancreatitis are associated with variants in the NUDT15 gene. Loss-of-function (low or no enzyme activity) alleles are more common in Asian and Hispanic populations. The prevalence of these variants in the Australian inflammatory bowel disease (IBD) population has not yet been reported.

Aim: To evaluate the presence of NUDT15 loss-of-function alleles *2,*3,*9 in the Australian IBD population.

Methods: The NUDT15 screening cohort included 423 IBD patients from Brisbane, Australia. Study patients were recruited by: (i) retrospective review of clinical charts for thiopurine-related severe adverse events; (ii) pathology data (white blood cell (WBC) and neutrophil counts). NUDT15 genotyping was performed using polymerase chain reaction (PCR)-high-resolution melt (HRM), TaqMan genotyping and Sanger sequencing.

Results: NUDT15 mutation R139C (allele *3) was identified in 8 of 423 (1.9%) IBD patients. Seven of eight patients were R139C heterozygous (C/T) and one patient was R139C homozygous (T/T). One of the C/T group and the T/T patient developed thiopurine-induced myelosuppression (TIM) within 60 days of dosing. One patient in the C/T group developed TIM after 60 days of thiopurine dosing. The remaining five patients in the C/T group did not show TIM; however, other thiopurine-related events could not be ruled out and therefore careful monitoring over a long period is recommended.

Conclusions: This is the first study to report the frequency of NUDT15 haplotypes *2,*3,*9 in an Australian IBD population. The most common variant detected was the R139C mutation. PCR and Sanger sequencing are efficient and cost-effective approaches for NUDT15 genotyping.

Keywords: Crohn disease; NUDT15; inflammatory bowel disease; myelosuppression; thiopurine; ulcerative colitis.

Figure 1

The role of NUDT15 in thiopurine metabolism pathway. The drugs and metabolites are depicted using brown squares. The enzymes involved in the pathways are depicted using yellow ovals. SLC28A3 and SLC29A2 are cell membrane transporters. This schematic representation was created using images from https://smart.servier.com. 6‐MeM‐8‐OHP, 6‐methylmercapto‐8‐hydroxypurine; 6‐MMP, 6‐methylmercaptopurine; 6‐MP, mercaptopurine; 6‐TdGMP, 6‐thio‐deoxyguanine monophosphate; 6‐TdGTP, 6‐thiodoxyguanine triphosphate; 6‐TGMP, 6‐thioguanine monophosphate; 6‐TGMP, 6‐TdGMP, 6‐TGTP and 6‐TdGTP together form the 6‐TGN; 6‐TGN, thioguanine nucleotides; 6‐TGTP, 6‐thioguanine triphosphate; 6‐TIMP, 6‐thioinosine monophosphate; 6‐TU, 6‐thiouracil; 6‐TXMP, 6‐thioxanthosine monophosphate; AOX, aldehyde oxidase; AZA, azathioprine; GMPS, guanosine monophosphate synthetase; GST, glutathione‐S‐transferase; HGPRT, hypoxanthine‐guanine phosphoribosyl transferase; IMPDH, inosine monophosphate dehydrogenase; MTG, methylthioguanine; NUDT15, nudix hydrolase 15; TG, thioguanine; TPMT, thiopurine S‐methyltransferase; XO, xanthine oxidase.

Figure 2

Kaplan–Meier survival plot for myelosuppression in thiopurine‐exposed inflammatory bowel disease patients. A myelosuppression event was defined as having an absolute white blood cell count ≤2.5 ×10⁹/L or absolute neutrophil count ≤1.0 ×10⁹/L within 60 days post 6‐thiopurine testing.