Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

A common missense variant in NUDT15 confers susceptibility to thiopurine-induced leukopenia

Nature Genetics volume 46, pages 1017–1020 (2014)Cite this article

Subjects

Abstract

Thiopurine therapy, commonly used in autoimmune conditions, can be complicated by life-threatening leukopenia. This leukopenia is associated with genetic variation in TPMT (encoding thiopurine S-methyltransferase). Despite a lower frequency of TPMT mutations in Asians, the incidence of thiopurine-induced leukopenia is higher in Asians than in individuals of European descent. Here we performed an Immunochip-based 2-stage association study in 978 Korean subjects with Crohn's disease treated with thiopurines. We identified a nonsynonymous SNP in NUDT15 (encoding p.Arg139Cys) that was strongly associated with thiopurine-induced early leukopenia (odds ratio (OR) = 35.6; Pcombined = 4.88 × 10−94). In Koreans, this variant demonstrated sensitivity and specificity of 89.4% and 93.2%, respectively, for thiopurine-induced early leukopenia (in comparison to 12.1% and 97.6% for TPMT variants). Although rare, this SNP was also strongly associated with thiopurine-induced leukopenia in subjects with inflammatory bowel disease of European descent (OR = 9.50; P = 4.64 × 10−4). Thus, NUDT15 is a pharmacogenetic determinant for thiopurine-induced leukopenia in diverse populations.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Regional association plot of the SUCLA2-NUDT15-MED4 locus at 13q14.

Similar content being viewed by others

References

  1. Timmer, A., McDonald, J.W., Tsoulis, D.J. & Macdonald, J.K. Azathioprine and 6-mercaptopurine for maintenance of remission in ulcerative colitis. Cochrane Database Syst. Rev. 9, CD000478 (2012).

    Google Scholar 

  2. Prefontaine, E., Sutherland, L.R., Macdonald, J.K. & Cepoiu, M. Azathioprine or 6-mercaptopurine for maintenance of remission in Crohn's disease. Cochrane Database Syst. Rev. 1, CD000067 (2009).

    Google Scholar 

  3. Present, D.H., Meltzer, S.J., Krumholz, M.P., Wolke, A. & Korelitz, B.I. 6-Mercaptopurine in the management of inflammatory bowel disease: short- and long-term toxicity. Ann. Intern. Med. 111, 641–649 (1989).

    Article  CAS  Google Scholar 

  4. Connell, W.R., Kamm, M.A., Ritchie, J.K. & Lennard-Jones, J.E. Bone marrow toxicity caused by azathioprine in inflammatory bowel disease: 27 years of experience. Gut 34, 1081–1085 (1993).

    Article  CAS  Google Scholar 

  5. Fraser, A.G., Orchard, T.R. & Jewell, D.P. The efficacy of azathioprine for the treatment of inflammatory bowel disease: a 30 year review. Gut 50, 485–489 (2002).

    Article  CAS  Google Scholar 

  6. Colombel, J.F. et al. Genotypic analysis of thiopurine S-methyltransferase in patients with Crohn's disease and severe myelosuppression during azathioprine therapy. Gastroenterology 118, 1025–1030 (2000).

    Article  CAS  Google Scholar 

  7. Dewit, O. et al. Limitations of extensive TPMT genotyping in the management of azathioprine-induced myelosuppression in IBD patients. Clin. Biochem. 44, 1062–1066 (2011).

    Article  CAS  Google Scholar 

  8. Booth, R.A. et al. Assessment of thiopurine S-methyltransferase activity in patients prescribed thiopurines: a systematic review. Ann. Intern. Med. 154, 814–823 (2011).

    Article  Google Scholar 

  9. Kumagai, K. et al. Allelotype frequency of the thiopurine methyltransferase (TPMT) gene in Japanese. Pharmacogenetics 11, 275–278 (2001).

    Article  CAS  Google Scholar 

  10. Cao, Q., Zhu, Q., Shang, Y., Gao, M. & Si, J. Thiopurine methyltransferase gene polymorphisms in Chinese patients with inflammatory bowel disease. Digestion 79, 58–63 (2009).

    Article  CAS  Google Scholar 

  11. Kim, J.H. et al. Influences of thiopurine methyltransferase genotype and activity on thiopurine-induced leukopenia in Korean patients with inflammatory bowel disease: a retrospective cohort study. J. Clin. Gastroenterol. 44, e242–e248 (2010).

    Article  CAS  Google Scholar 

  12. Takatsu, N. et al. Adverse reactions to azathioprine cannot be predicted by thiopurine S-methyltransferase genotype in Japanese patients with inflammatory bowel disease. J. Gastroenterol. Hepatol. 24, 1258–1264 (2009).

    Article  CAS  Google Scholar 

  13. Collie-Duguid, E.S. et al. The frequency and distribution of thiopurine methyltransferase alleles in Caucasian and Asian populations. Pharmacogenetics 9, 37–42 (1999).

    Article  CAS  Google Scholar 

  14. Lee, H.J. et al. The safety and efficacy of azathioprine and 6-mercaptopurine in the treatment of Korean patients with Crohn's disease. Intest. Res. 7, 22–31 (2009).

    Google Scholar 

  15. Lewis, J.D. et al. Timing of myelosuppression during thiopurine therapy for inflammatory bowel disease: implications for monitoring recommendations. Clin. Gastroenterol. Hepatol. 7, 1195–1201 (2009).

    Article  CAS  Google Scholar 

  16. Fangbin, Z. et al. Should thiopurine methyltransferase genotypes and phenotypes be measured before thiopurine therapy in patients with inflammatory bowel disease? Ther. Drug Monit. 34, 695–701 (2012).

    Article  CAS  Google Scholar 

  17. Takagi, Y. et al. Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine and deoxyguanosine diphosphates: comparison with MTH1 and MTH2. J. Biol. Chem. 287, 21541–21549 (2012).

    Article  CAS  Google Scholar 

  18. Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).

    Article  CAS  Google Scholar 

  19. Howie, B.N., Donnelly, P. & Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529 (2009).

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank all participants who provided the DNA and clinical information necessary for this study. J.L. and W.Z. are supported by the Biomedical Research Council, the Agency for Science, Technology and Research (A*STAR; BMRC SPF2014/001), Singapore. D.P.B.M., T.H. and M.D. are supported by the US National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (P01DK046763, U01DK062413, U01AI067068, R01HS021747), the European Union (IBD-BIOM 305479), the Leona M. and Harry B. Helmsley Charitable Trust (2011PG-MED004, 2014PG-IBD014) and internal funding from the F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute. This work was supported by a Mid-Career Researcher Program grant through NRF (National Research Foundation of Korea) to K.S. (2010-0015648, 2014R1A2A1A09005824) funded by the Ministry of Science, Information and Communication Technology (ICT) and Future Planning and by a Korean Health Technology R&D Project grant to S.-K.Y. (A120176) from the Ministry of Health and Welfare, the Republic of Korea.

Author information

Authors and Affiliations

  1. Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea

    Suk-Kyun Yang, Byong Duk Ye, Kyung-Jo Kim, Sang Hyoung Park, Soo-Kyung Park & Dong-Hoon Yang

  2. Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea

    Myunghee Hong, Jiwon Baek, Hyunchul Choi, Yusun Jung & Kyuyoung Song

  3. Human Genetics Group, Genome Institute of Singapore, Singapore

    Wanting Zhao & Jianjun Liu

  4. The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA

    Talin Haritunians & Dermot P B McGovern

  5. Pediatric Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California, USA

    Marla Dubinsky

  6. Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea

    Inchul Lee

Authors
  1. Suk-Kyun Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Myunghee Hong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jiwon Baek
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hyunchul Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wanting Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yusun Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Talin Haritunians
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Byong Duk Ye
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Kyung-Jo Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Sang Hyoung Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Soo-Kyung Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Dong-Hoon Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Marla Dubinsky
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Inchul Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Dermot P B McGovern
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Jianjun Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Kyuyoung Song
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

K.S. and S.-K.Y. obtained financial support and conceived and designed the study. K.S. supervised genotyping, data analysis and interpretation, and S.-K.Y. supervised all the sample collection, data analysis and interpretation. J.L. supervised data analysis and interpretation. S.-K.Y., B.D.Y., K.-J.K., S.H.P., S.-K.P., D.-H.Y. and I.L. recruited subjects and participated in diagnostic evaluation. S.-K.Y., S.H.P. and S.-K.P. assessed clinical features. T.H., M.D. and D.P.B.M. supervised the Immunochip genotyping and provided their data. M.H., W.Z., Y.J. and H.C. performed data analyses. M.H., J.B. and H.C. prepared DNA samples and performed genotyping. J.B. performed in vitro transfection experiments and data analysis. K.S. and S.-K.Y. drafted the manuscript. K.S., S.-K.Y., D.P.B.M. and J.L. revised the manuscript.

Corresponding author

Correspondence to Kyuyoung Song.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Study design.

Leukopenia was classified as 'early' when it occurred within the first 8 weeks of thiopurine therapy and as 'late' when it occurred more than 8 weeks after the start of therapy. The discovery and replication analyses were initially focused on early leukopenia. The SNPs identified from the initial analyses were confirmed in patients with late leukopenia.

Supplementary Figure 2 Quantile-quantile plot for the Immunochip association P values of SNPs in 33 cases and 307 controls.

–log10 P values are plotted against the expected null distribution. Black data points and red data points represent the results of 95,405 genotyped SNPs and 531,416 genotyped + imputed SNPs in the Immunochip set, respectively.

Supplementary Figure 3 Manhattan plot for the discovery Immunochip association analysis in 33 cases and 307 controls.

Data represent the trend test result of 531,416 genotyped + imputed SNPs. –log10 P values are shown according to chromosomal location. SNPs within the SUCLA2-NUDT15-MED4 locus at 13q14 achieve genome-wide significance. The red horizontal line indicates SNPs at a genome-wide significance level (here P = 9.41 × 10–8). The blue horizontal line indicates SNPs with P < 1.0 × 10–5.

Supplementary Figure 4 Regional association plots after conditional analysis of the SUCLA2-NUDT15-MED4 locus at 13q14.

(a,b) Regional association plots after conditional analysis was performed to control for the association at rs116855232 (a) and rs7320366 (b).

Supplementary Figure 5 Receiver operating characteristic curve for an additive prediction model of early leukopenia using NUDT15 SNP rs116855232.

The area under the curve with 95% CI = 0.88–0.97 is 0.92. Overall sensitivity is 89.4%, whereas specificity is 93.2%.

Supplementary Figure 6 Sensitivity of Jurkat cells to 7.5 μM 6-MP following transfection with wild-type or mutant NUDT15.

(a) NUDT15 mRNA levels in Jurkat cells transfected with wild-type or mutant NUDT15, as determined by RT-PCR analysis. (b) The number of viable mutant NUDT15-transfected cells decreases compared to wild type–transfected control cells. (c) Cytotoxicity assay with annexin V and propidium iodide staining showing that cells are more sensitive to 6-MP when they have been transfected with mutant NUDT15, compared to cells transfected with wild-type NUDT15. Data are presented as mean ± s.d. of three independent experiments.

Supplementary Figure 7 Principal-component analysis (PCA).

(a) PCA of 340 samples and 194 reference DNA samples from HapMap. (b) Plots of first eight principal components from the principal-component analysis using 340 samples (33 cases, 307 controls).

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Tables 1–7 and Supplementary Note. (PDF 3352 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yang, SK., Hong, M., Baek, J. et al. A common missense variant in NUDT15 confers susceptibility to thiopurine-induced leukopenia. Nat Genet 46, 1017–1020 (2014). https://doi.org/10.1038/ng.3060

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3060

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing