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Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL

Abstract

Acute lymphoblastic leukemia (ALL) is an aggressive hematological tumor resulting from the malignant transformation of lymphoid progenitors. Despite intensive chemotherapy, 20% of pediatric patients and over 50% of adult patients with ALL do not achieve a complete remission or relapse after intensified chemotherapy, making disease relapse and resistance to therapy the most substantial challenge in the treatment of this disease1,2. Using whole-exome sequencing, we identify mutations in the cytosolic 5′-nucleotidase II gene (NT5C2), which encodes a 5′-nucleotidase enzyme that is responsible for the inactivation of nucleoside-analog chemotherapy drugs, in 20/103 (19%) relapse T cell ALLs and 1/35 (3%) relapse B-precursor ALLs. NT5C2 mutant proteins show increased nucleotidase activity in vitro and conferred resistance to chemotherapy with 6-mercaptopurine and 6-thioguanine when expressed in ALL lymphoblasts. These results support a prominent role for activating mutations in NT5C2 and increased nucleoside-analog metabolism in disease progression and chemotherapy resistance in ALL.

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Figure 1: NT5C2 mutations in relapsed pediatric ALL.
Figure 2: Structure-function analysis of the NT5C2 K359Q mutant protein.
Figure 3: Increased 5′-IMP nucleotidase activity in NT5C2 mutant proteins.
Figure 4: Expression of NT5C2 mutations in ALL cells induces resistance to chemotherapy with 6-MP and 6-TG.

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Acknowledgements

We thank A.A. Da Silva for technical support in the production of recombinant NT5C2 proteins and R. Parsons for insightful comments and advice. We also thank P.H. Wiernik as the Eastern Cooperative Oncology Group (ECOG) leukemia committee chair at the time the E2993 study was initiated. This work was supported by the St. Baldrick's Foundation (A.F.), the Partnership for Cure Foundation (R.R.), the Innovative Research Award by the Stand Up to Cancer Foundation (A.F.), the Chemotherapy Foundation (A.F.), the Leukemia and Lymphoma Society Scholar Award (A.F.), the German Federal Ministry for Education and Research in the National Genome Research Network (grant 01GS0870 to R.K.-S.), the German Foundation for Childhood Cancer (grants DKS 2003.08 and 2007.02 to R.K.-S.), the US National Institutes of Health (U24 CA114737 to E.P.) and the ECOG Leukemia Tissue Bank. A.P.-G. is a postdoctoral researcher funded by the Rally Foundation.

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G.T. and A.P.-G. performed validation and recurrence mutation analysis, enzymatic activity and cell drug-resistance assays. Z.C. performed structure function analysis and analyzed Illumina sequence data. H.K. analyzed Illumina sequence data. V.T. analyzed genomic data from diagnostic and relapse T-ALLs. M.A. performed validation analysis of Illumina sequencing results. M.P., G.B., E.P., J.R., J.H., J.M.R., M.S.T. and R.K.-S. contributed clinical samples and clinical correlative information. T.P. directed and supervised mutation analysis. R.R. directed and supervised the analysis of Illumina sequencing data. A.F. designed the study, directed and supervised research and wrote the manuscript.

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Correspondence to Teresa Palomero, Raul Rabadan or Adolfo Ferrando.

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Tzoneva, G., Perez-Garcia, A., Carpenter, Z. et al. Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL. Nat Med 19, 368–371 (2013). https://doi.org/10.1038/nm.3078

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