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Negative feedback–defective PRPS1 mutants drive thiopurine resistance in relapsed childhood ALL

Nature Medicine volume 21, pages 563–571 (2015)Cite this article

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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.

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Figure 1: Identification and characterization of relapse-specific somatic mutations.
Figure 2: Relapse-specific PRPS1 mutations confer thiopurine resistance.
Figure 3: Activating PRPS1 mutations reduce nucleotide feedback inhibition.
Figure 4: Elevated HX directly inhibits 6-MP conversion, which can be reversed by the GART inhibitor lometrexol.

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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.).

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Author notes

  1. Benshang Li, Hui Li and Yun Bai: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Hematology and Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China

    Benshang Li, Hui Li, Yao Chen, Tongmin Wu, Lixia Ding, Huanhuan Liang, Xiaohang Huang, Shuhong Shen, Jing Chen, Longjun Gu, Jingyan Tang & Bin-Bing S Zhou

  2. Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China

    Benshang Li, Yun Bai, Gang Lu, Minjun Yang, Lei Jin, Hui Kang, Shuting Chen & Shengyue Wang

  3. Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China

    Benshang Li, Hui Li, Yao Chen, Tongmin Wu, Lixia Ding, Shuhong Shen & Bin-Bing S Zhou

  4. Department of Pharmacology, School of Basic Medicine and Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China

    Hui Li, Tongmin Wu, Hongzhuan Chen & Bin-Bing S Zhou

  5. Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany

    Renate Kirschner-Schwabe & Arend von Stackelberg

  6. German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany

    Renate Kirschner-Schwabe

  7. St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Jun J Yang, Xiaotu Ma & Jinghui Zhang

  8. Institute for Cancer Genetics, Columbia University, New York, New York, USA

    Gannie Tzoneva & Adolfo Ferrando

  9. National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China

    Wenjing Li & Jianping Ding

  10. ChemPartner Co., Shanghai, China

    Haisong Lu & Alicia Du

  11. Collaborative Innovation Center of Systems Biomedicine, National Research Center for Translational Medicine, Shanghai, China

    Hongzhuan Chen, Shengyue Wang & Bin-Bing S Zhou

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  1. Benshang Li
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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

Correspondence to Jingyan Tang, Shengyue Wang or Bin-Bing S Zhou.

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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

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