NUDT15 variants confer high incidence of second malignancies in children with acute lymphoblastic leukemia

Author:

Yoshida Masanori12ORCID,Nakabayashi Kazuhiko3,Yang Wentao4,Sato-Otsubo Aiko15,Tsujimoto Shin-ichi12ORCID,Ogata-Kawata Hiroko3ORCID,Kawai Tomoko3ORCID,Ishiwata Keisuke3,Sakamoto Mika6,Okamura Kohji7ORCID,Yoshida Kaoru1,Shirai Ryota12ORCID,Osumi Tomoo18ORCID,Moriyama Takaya4,Nishii Rina4,Takahashi Hiroyuki9ORCID,Kiyotani Chikako8,Shioda Yoko8,Terashima Keita8,Ishimaru Sae10,Yuza Yuki10,Takagi Masatoshi11,Arakawa Yuki12ORCID,Kinoshita Akitoshi13,Hino Moeko14,Imamura Toshihiko15,Hasegawa Daisuke16,Nakazawa Yozo17ORCID,Okuya Mayuko18,Kakuda Harumi19,Takasugi Nao5,Inoue Akiko20ORCID,Ohki Kentaro1,Yoshioka Takako21,Ito Shuichi2ORCID,Tomizawa Daisuke8ORCID,Koh Katsuyoshi12,Matsumoto Kimikazu8ORCID,Sanada Masashi22,Kiyokawa Nobutaka1,Ohara Akira9,Ogawa Seishi23ORCID,Manabe Atsushi24,Niwa Akira25ORCID,Hata Kenichiro3ORCID,Yang Jun J.264,Kato Motohiro18ORCID

Affiliation:

1. Department of Pediatric Hematology and Oncology Research, Research Institute, National Center for Child Health and Development, Tokyo, Japan;

2. Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan;

3. Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, Japan;

4. Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, USA;

5. Department of Pediatrics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan;

6. Medical Genome Center, Research Institute, National Center for Child Health and Development, Tokyo, Japan;

7. Department of Systems BioMedicine, Research Institute, National Center for Child Health and Development, Tokyo, Japan;

8. Children’s Cancer Center, National Center for Child Health and Development, Tokyo, Japan;

9. Department of Pediatrics, Toho University, Tokyo, Japan;

10. Department of Hematology/Oncology, Tokyo Metropolitan Children’s Medical Center, Tokyo, Japan;

11. Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan;

12. Department of Hematology/Oncology, Saitama Children’s Medical Center, Saitama, Japan;

13. Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan;

14. Department of Pediatrics, Chiba University Hospital, Chiba, Japan;

15. Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan;

16. Department of Pediatrics, St. Luke’s International Hospital, Tokyo, Japan;

17. Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan;

18. Department of Pediatrics, Dokkyo Medical University School of Medicine, Shimotsuga, Japan;

19. Department of Hematology/Oncology, Chiba Children’s Hospital, Chiba, Japan;

20. Department of Pediatrics, Osaka Medical and Pharmaceutical University, Takatsuki, Japan;

21. Department of Pathology, National Center for Child Health and Development, Tokyo, Japan;

22. Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan;

23. Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan;

24. Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan;

25. Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan; and

26. Department of Oncology, St. Jude Children’s Research Hospital, Memphis, USA

Abstract

Abstract The effect of genetic variation on second malignant neoplasms (SMNs) remains unclear. First, we identified the pathogenic germline variants in cancer-predisposing genes among 15 children with SMNs after childhood leukemia/lymphoma using whole-exome sequencing. Because the prevalence was low, we focused on the association between SMNs and NUDT15 in primary acute lymphoblastic leukemia (ALL) cases. NUDT15 is one of the 6-mercaptopurine (6-MP) metabolic genes, and its variants are common in East Asian individuals. The prevalence of NUDT15 hypomorphic variants was higher in patients with SMNs (n = 14; 42.9%) than in the general population in the gnomAD database (19.7%; P = .042). In the validation study with a cohort of 438 unselected patients with ALL, the cumulative incidence of SMNs was significantly higher among those with (3.0%; 95% confidence interval [CI], 0.6% to 9.4%) than among those without NUDT15 variants (0.3%; 95% CI, 0.0% to 1.5%; P = .045). The 6-MP dose administered to patients with ALL with a NUDT15 variant was higher than that given to those without SMNs (P = .045). The 6-MP–related mutational signature was observed in SMN specimens after 6-MP exposure. In cells exposed to 6-MP, a higher level of 6-MP induced DNA damage in NUDT15-knockdown induced pluripotent stem cells. Our study indicates that NUDT15 variants may confer a risk of SMNs after treatment with 6-MP in patients with ALL.

Publisher

American Society of Hematology

Subject

Hematology

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