Association of Genetic Variants in NUDT15 With Thiopurine-Induced Myelosuppression in Patients With Inflammatory Bowel Disease

Abstract

Importance: Use of thiopurines may be limited by myelosuppression. TPMT pharmacogenetic testing identifies only 25% of at-risk patients of European ancestry. Among patients of East Asian ancestry, NUDT15 variants are associated with thiopurine-induced myelosuppression (TIM).

Objective: To identify genetic variants associated with TIM among patients of European ancestry with inflammatory bowel disease (IBD).

Design, setting, and participants: Case-control study of 491 patients affected by TIM and 679 thiopurine-tolerant unaffected patients who were recruited from 89 international sites between March 2012 and November 2015. Genome-wide association studies (GWAS) and exome-wide association studies (EWAS) were conducted in patients of European ancestry. The replication cohort comprised 73 patients affected by TIM and 840 thiopurine-tolerant unaffected patients.

Exposures: Genetic variants associated with TIM.

Main outcomes and measures: Thiopurine-induced myelosuppression, defined as a decline in absolute white blood cell count to 2.5 × 109/L or less or a decline in absolute neutrophil cell count to 1.0 × 109/L or less leading to a dose reduction or drug withdrawal.

Results: Among 1077 patients (398 affected and 679 unaffected; median age at IBD diagnosis, 31.0 years [interquartile range, 21.2 to 44.1 years]; 540 [50%] women; 602 [56%] diagnosed as having Crohn disease), 919 (311 affected and 608 unaffected) were included in the GWAS analysis and 961 (328 affected and 633 unaffected) in the EWAS analysis. The GWAS analysis confirmed association of TPMT (chromosome 6, rs11969064) with TIM (30.5% [95/311] affected vs 16.4% [100/608] unaffected patients; odds ratio [OR], 2.3 [95% CI, 1.7 to 3.1], P = 5.2 × 10-9). The EWAS analysis demonstrated an association with an in-frame deletion in NUDT15 (chromosome 13, rs746071566) and TIM (5.8% [19/328] affected vs 0.2% [1/633] unaffected patients; OR, 38.2 [95% CI, 5.1 to 286.1], P = 1.3 × 10-8), which was replicated in a different cohort (2.7% [2/73] affected vs 0.2% [2/840] unaffected patients; OR, 11.8 [95% CI, 1.6 to 85.0], P = .03). Carriage of any of 3 coding NUDT15 variants was associated with an increased risk (OR, 27.3 [95% CI, 9.3 to 116.7], P = 1.1 × 10-7) of TIM, independent of TPMT genotype and thiopurine dose.

Conclusions and relevance: Among patients of European ancestry with IBD, variants in NUDT15 were associated with increased risk of TIM. These findings suggest that NUDT15 genotyping may be considered prior to initiation of thiopurine therapy; however, further study including additional validation in independent cohorts is required.

Figure 1.. Flow Diagram and Study Overview of Case and Control Cohorts

^aIndicates non-Finnish European ancestry based on principal component analysis. ^bIndicates patients too closely related to each other. ^cIndicates a discrepancy between genetically determined sex and phenotype data.

Figure 2.. Manhattan Plot for the Discovery Exome-Wide Association Studies Analysis Among 328 Individuals Affected by Thiopurine-Induced Myelosuppression and 633 Thiopurine-Tolerant Unaffected Individuals

Each colored dot represents a single variant within each respective chromosome. The negative log₁₀ P value represents a Fisher exact test analysis between affected and unaffected patients. The orange dotted horizontal line indicates genome-wide significance at Fisher exact P = 5.0 × 10⁻⁸. Gene names correspond to the gene in closest proximity to the variant with the lowest P value at each locus if within 50 kilobase pairs.

Figure 3.. Box Plot for Time to Thiopurine-Induced Myelosuppression Among Affected Individuals Defined by NUDT15 and TPMT Genotype

Data points are each represented by a dot. The lower and upper boundaries of the box correspond to the first and third quartiles. The line within the box represents the median. The upper whisker extends from the upper boundary of the box to the largest value no further than 1.5 × the interquartile range (IQR). The lower whisker extends from the lower boundary of the box to the lowest value, at most no further than 1.5 × the IQR. The time to thiopurine-induced myelosuppression (TIM) was calculated using the following formula: (time to TIM in weeks) = date meeting entry criteria for TIM minus start date of highest dose prior to TIM). The median values and IQRs are provided to facilitate interpretation of time to TIM. One TIM case carried 2 NUDT15 variants (rs746071566 [p.Gly17_Val18dup] and rs116855232 [p.Arg139Cys]); however, it was unknown if this represented a compound heterozygote or a heterozygote (*2 NUDT15 haplotype). For the purpose of the analysis, this patient was grouped with NUDT15 heterozygotes and annotated as NUDT15^var/*. One TIM case was TPMT^var/var and NUDT15^var/ref; for the purpose of the analysis, this patient was grouped with 5 others who carried single NUDT15 and TPMT variants (TPMT^var/ref and NUDT15^var/ref). Compared with the leftmost group, the Mann-Whitney P values for the differences in time to onset of TIM were .14, .009, .002, and <.001, respectively. Ref indicates reference genotype or haplotype; var, variant.