Abstract
Relapse is the leading cause of mortality in children with acute lymphoblastic leukemia (ALL). Among chemotherapeutics, thiopurines are key drugs in ALL combination therapy. Using whole-exome sequencing, we identified relapse-specific mutations in the phosphoribosyl pyrophosphate synthetase 1 gene (PRPS1), which encodes a rate-limiting purine biosynthesis enzyme, in 24/358 (6.7%) relapsed childhood B cell ALL (B-ALL) cases. All individuals who harbored PRPS1 mutations relapsed early during treatment, and mutated ALL clones expanded exponentially before clinical relapse. Our functional analyses of PRPS1 mutants uncovered a new chemotherapy-resistance mechanism involving reduced feedback inhibition of de novo purine biosynthesis and competitive inhibition of thiopurine activation. Notably, the de novo purine synthesis inhibitor lometrexol effectively abrogated PRPS1 mutant–driven drug resistance. These results highlight the importance of constitutive activation of the de novo purine synthesis pathway in thiopurine resistance, and they offer therapeutic strategies for the treatment of relapsed and thiopurine-resistant ALL.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Accession codes
References
Pui, C.H., Carroll, W.L., Meshinchi, S. & Arceci, R.J. Biology, risk stratification, and therapy of pediatric acute leukemias: an update. J. Clin. Oncol. 29, 551–565 (2011).
Pui, C.H. Recent advances in the biology and treatment of childhood acute lymphoblastic leukemia. Curr. Opin. Hematol. 5, 292–301 (1998).
Aarbakke, J., Janka-Schaub, G. & Elion, G.B. Thiopurine biology and pharmacology. Trends Pharmacol. Sci. 18, 3–7 (1997).
Wyngaarden, J.B. Regulation of purine biosynthesis and turnover. Adv. Enzyme Regul. 14, 25–42 (1976).
Becker, M.A. & Kim, M. Regulation of purine synthesis de novo in human fibroblasts by purine nucleotides and phosphoribosylpyrophosphate. J. Biol. Chem. 262, 14531–14537 (1987).
Nosal, J.M., Switzer, R.L. & Becker, M.A. Overexpression, purification, and characterization of recombinant human 5-phosphoribosyl-1-pyrophosphate synthetase isozymes I and II. J. Biol. Chem. 268, 10168–10175 (1993).
Meyer, J.A. et al. Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia. Nat. Genet. 45, 290–294 (2013).
Tzoneva, G. et al. Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL. Nat. Med. 19, 368–371 (2013).
Mullighan, C.G. et al. Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science 322, 1377–1380 (2008).
Gu, L.J. et al. Clinical outcome of children with newly diagnosed acute lymphoblastic leukemia treated in a single center in Shanghai, China. Leuk. Lymphoma 49, 488–494 (2008).
Tang, J.Y. et al. [Evaluation on protocol SCMS-ALL-2005 for childhood B lineage acute lymphoblastic leukemia]. J. Chin. Med. Assoc. 92, 546–550 (2012).
Conter, V. et al. Molecular response to treatment redefines all prognostic factors in children and adolescents with B-cell precursor acute lymphoblastic leukemia: results in 3184 patients of the AIEOP-BFM ALL 2000 study. Blood 115, 3206–3214 (2010).
Escherich, G., Zimmermann, M. & Janka-Schaub, G. Doxorubicin or daunorubicin given upfront in a therapeutic window are equally effective in children with newly diagnosed acute lymphoblastic leukemia. A randomized comparison in trial CoALL 07–03. Pediatr. Blood Cancer 60, 254–257 (2013).
Henze, G., v Stackelberg, A. & Eckert, C. ALL-REZ BFM–the consecutive trials for children with relapsed acute lymphoblastic leukemia. Klin. Padiatr. 225 (Suppl. 1), S73–S78 (2013).
Becker, M.A., Smith, P.R., Taylor, W., Mustafi, R. & Switzer, R.L. The genetic and functional basis of purine nucleotide feedback-resistant phosphoribosylpyrophosphate synthetase superactivity. J. Clin. Invest. 96, 2133–2141 (1995).
Hof, J., Szymansky, A., Stackelberg, A., Eckert, C. & Kirschner-Schwabe, R. Clinical significance of NT5C2 mutations in children with first relapse of B-cell precursor acute lymphoblastic leukemia. Abstract 3789. In 56th American Society of Hematology Annual Meeting and Exposition (San Francisco, California, USA, December 6–9, 2014) (American Society of Hematology, 2014).
Tang, W. et al. Expression, purification, crystallization and preliminary X-ray diffraction analysis of human phosphoribosyl pyrophosphate synthetase 1 (PRS1). Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 62, 432–434 (2006).
Li, S., Lu, Y., Peng, B. & Ding, J. Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site. Biochem. J. 401, 39–47 (2007).
Fox, I.H. & Kelley, W.N. Human phosphoribosylpyrophosphate synthetase. Distribution, purification, and properties. J. Biol. Chem. 246, 5739–5748 (1971).
de Brouwer, A.P. et al. PRPS1 mutations: four distinct syndromes and potential treatment. Am. J. Hum. Genet. 86, 506–518 (2010).
Moran, R. et al. Phosphoribosylpyrophosphate synthetase superactivity and recurrent infections is caused by a p.Val142Leu mutation in PRS-I. Am. J. Med. Genet. A. 158A, 455–460 (2012).
Karran, P. & Attard, N. Thiopurines in current medical practice: molecular mechanisms and contributions to therapy-related cancer. Nat. Rev. Cancer 8, 24–36 (2008).
Zoref, E., De Vries, A. & Sperling, O. Mutant feedback-resistant phosphoribosylpyrophosphate synthetase associated with purine overproduction and gout. Phosphoribosylpyrophosphate and purine metabolism in cultured fibroblasts. J. Clin. Invest. 56, 1093–1099 (1975).
Gerhart, J. From feedback inhibition to allostery: the enduring example of aspartate transcarbamoylase. FEBS J. 281, 612–620 (2014).
Breton, A. et al. Lethal accumulation of guanylic nucleotides in Saccharomyces cerevisiae HPT1-deregulated mutants. Genetics 178, 815–824 (2008).
Christopherson, R.I., Lyons, S.D. & Wilson, P.K. Inhibitors of de novo nucleotide biosynthesis as drugs. Acc. Chem. Res. 35, 961–971 (2002).
Adams, J. & Elliott, P.J. New agents in cancer clinical trials. Oncogene 19, 6687–6692 (2000).
Tallen, G. et al. Long-term outcome in children with relapsed acute lymphoblastic leukemia after time-point and site-of-relapse stratification and intensified short-course multidrug chemotherapy: results of trial ALL-REZ BFM 90. J. Clin. Oncol. 28, 2339–2347 (2010).
Tong, X., Zhao, F. & Thompson, C.B. The molecular determinants of de novo nucleotide biosynthesis in cancer cells. Curr. Opin. Genet. Dev. 19, 32–37 (2009).
Bester, A.C. et al. Nucleotide deficiency promotes genomic instability in early stages of cancer development. Cell 145, 435–446 (2011).
Aird, K.M. et al. Suppression of nucleotide metabolism underlies the establishment and maintenance of oncogene-induced senescence. Cell Reports 3, 1252–1265 (2013).
Zhou, B.B. & Elledge, S.J. The DNA damage response: putting checkpoints in perspective. Nature 408, 433–439 (2000).
Kozhevnikova, E.N. et al. Metabolic enzyme IMPDH is also a transcription factor regulated by cellular state. Mol. Cell 47, 133–139 (2012).
Reddy, B.A. et al. Nucleotide biosynthetic enzyme GMP synthase is a TRIM21-controlled relay of p53 stabilization. Mol. Cell 53, 458–470 (2014).
Wintzerith, M., Ciesielski-Treska, J., Dierich, A. & Mandel, P. Comparative investigation of free nucleotides in two neuroblastoma clonal cell lines. J. Neurochem. 26, 205–207 (1976).
Cunningham, J.T., Moreno, M.V., Lodi, A., Ronen, S.M. & Ruggero, D. Protein and nucleotide biosynthesis are coupled by a single rate-limiting enzyme, PRPS2, to drive cancer. Cell 157, 1088–1103 (2014).
Zhang, J. et al. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature 481, 329–334 (2012).
Zhang, J. et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481, 157–163 (2012).
Alderwick, L.J. et al. Biochemical characterization of the Mycobacterium tuberculosis phosphoribosyl-1-pyrophosphate synthetase. Glycobiology 21, 410–425 (2011).
Eriksen, T.A., Kadziola, A., Bentsen, A.K., Harlow, K.W. & Larsen, S. Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase. Nat. Struct. Biol. 7, 303–308 (2000).
Dervieux, T. et al. HPLC determination of thiopurine nucleosides and nucleotides in vivo in lymphoblasts following mercaptopurine therapy. Clin. Chem. 48, 61–68 (2002).
Acknowledgements
We thank the BioBank staff at Shanghai Children's Medical Center for the clinical sample collection, W.L. Carroll (New York University) for providing the NT5C2 R238 plasmid, Y. Zhang and Z. Tang for making reagents, Z. Carpenter for suggesting PRPS1 superactivity references, and G. Wu and X. Chen for assisting in genomics data analysis. We are grateful to W.E. Evans, C.H. Pui, X.M. Tong, and G.L. Waldrop for critical comments and constructive suggestions on the manuscript. This work is supported by grants from the National Basic Research Program of China (973 program 2015CB553904 to B.-B.S.Z.), the National Natural Science Foundation of China (81372349 to B.-B.S.Z., 81470313 to J.C.), the Science and Technology Commission of Shanghai Municipality (13431900502 to B.-B.S.Z.; 14411950600 to J.C.; 10411965100 to B.S.L.; 11JC1408100 to J.Y.T.; 13431902000, 13DZ2291800 and 11DZ2292600 to S.Y.W.), the Science and Technology Commission of Pudong New Area Foundation (PKJ2014-Y02 to B.S.L.), the Project HOPE–Hospital Foundation Supporting Children with Cancer Program (to B.S.L.), the Programs of Shanghai Municipal Education Commission (12ZZ111 to B.S.L.), US National Institutes of Health grants CA21765 and ALSAC (American Lebanese Syria Associated Charities; to C. H. Pui), the German Foundation for Childhood Cancer (DKS 2003.08, 2007.02 to A.v.S. and 2011.14 to R.K.-S.), the Charité-Universitätsmedizin Berlin (Rahel Hirsch Fellowship to R.K.-S.), the Innovative Research Award by the Alex's Lemonade Stand Foundation and the Quest for Cures grant by the Leukemia and Lymphoma Society (both to A.F.), the China Postdoctoral Science Foundation (2014M561484 to H.L.), and a Howard Hughes Medical Institute International Student Research Fellowship (to G.T.).
Author information
Authors and Affiliations
Contributions
B.L., B.-B.S.Z., H. Li, S.W., Y.B., A.F., R.K.-S., J.T., J.Z., J.J.Y. and J.D. designed the research strategy and wrote the manuscript. B.L., S.W. and J.T. designed the genomic study. B.-B.S.Z. and H. Li designed the functional study, analyzed the functional data, and coordinated and managed the overall project. H. Liang, L.D., X.H., L.J., H.K. and S.C. performed the Chinese cohort sample collection, DNA preparation, exome capture and exome sequencing. J.Z., Y.B., G.L., S.W., X.M. and M.Y. analyzed the exome sequencing data. A.F. and G.T. performed the German cohort DNA sequencing and analyzed the data. L.G., J.T., B.L., S.S. and J.C. analyzed the Chinese cohort clinical data. R.K.-S. and A.v.S. analyzed the German cohort clinical data and prepared the DNA samples. H. Li and Y.C. performed cell biology experiments. W.L. and J.D. analyzed the PRPS1 structure. H. Lu and H. Li performed enzyme experiments. T.W. and Y.C. performed the DNA damage response assay and western blots. H. Li, Y.C., H. Lu, A.D. and H.C. performed metabolite flux and thiopurine conversion experiments.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–26 and Supplementary Tables 1–11 (PDF 4167 kb)
Rights and permissions
About this article
Cite this article
Li, B., Li, H., Bai, Y. et al. Negative feedback–defective PRPS1 mutants drive thiopurine resistance in relapsed childhood ALL. Nat Med 21, 563–571 (2015). https://doi.org/10.1038/nm.3840
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nm.3840
This article is cited by
-
Direct stimulation of de novo nucleotide synthesis by O-GlcNAcylation
Nature Chemical Biology (2024)
-
Targeting DNA polymerase β elicits synthetic lethality with mismatch repair deficiency in acute lymphoblastic leukemia
Leukemia (2023)
-
Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia
Nature Communications (2023)
-
Hypoxanthine phosphoribosyl transferase 1 metabolizes temozolomide to activate AMPK for driving chemoresistance of glioblastomas
Nature Communications (2023)
-
Targeting nucleotide metabolism: a promising approach to enhance cancer immunotherapy
Journal of Hematology & Oncology (2022)