Abstract

Relapsed childhood acute lymphoblastic leukemia (ALL) carries a poor prognosis, despite intensive retreatment, owing to intrinsic drug resistance1,2. The biological pathways that mediate resistance are unknown. Here, we report the transcriptome profiles of matched diagnosis and relapse bone marrow specimens from ten individuals with pediatric B-lymphoblastic leukemia using RNA sequencing. Transcriptome sequencing identified 20 newly acquired, novel nonsynonymous mutations not present at initial diagnosis, with 2 individuals harboring relapse-specific mutations in the same gene, NT5C2, encoding a 5′-nucleotidase. Full-exon sequencing of NT5C2 was completed in 61 further relapse specimens, identifying additional mutations in 5 cases. Enzymatic analysis of mutant proteins showed that base substitutions conferred increased enzymatic activity and resistance to treatment with nucleoside analog therapies. Clinically, all individuals who harbored NT5C2 mutations relapsed early, within 36 months of initial diagnosis (P = 0.03). These results suggest that mutations in NT5C2 are associated with the outgrowth of drug-resistant clones in ALL.

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Acknowledgements

We would like to thank the members of the Carroll laboratory as well as L.B. Gardner, M. Karajannis and I. Osman for their critical review of the manuscript. We gratefully acknowledge the Children's Oncology Group (COG) for patient specimens, the New York University Genome Technology Center for expert assistance with Illumina (B. Baysa) and Roche 454 (E. Venturini) deep-sequencing experiments (supported in part by US National Institutes of Health/National Center for Research Resources (NIH/NCRR) grant S10 RR026950-01), P. Grace, J.D. Ernst and M.R. Phillips (New York University School of Medicine) for expression and lentiviral vectors and F. Tsai, M.R. Phillips and S.M. Brown for technical guidance. This work was supported by US NIH grants R01 CA140729 and R21 CA152838-02 to W.L.C. and New York University Cancer Center Support Grant 5 P30 CA16087-30 in collaboration with the New York University Genome Technology Center. Additional support was provided by grants from the National Cancer Institute to COG, including U10 CA98543 (COG Chair's grant), U10 CA98413 (COG Statistical Center) and U24 CA114766 (COG Specimen Banking). J.A.M. is supported by NIH grant T32 CA009161. L.E.H. was supported by the American Society of Hematology and St. Baldrick's Foundation. S.P.H. is the Ergen Family Chair in Pediatric Cancer.

Author information

Author notes

    • Laura E Hogan

    Present address: Department of Pediatrics, Stony Brook University, Stony Brook, New York, USA.

Affiliations

  1. New York University Cancer Institute, New York University Langone Medical Center, New York, New York, USA.

    • Julia A Meyer
    • , Jinhua Wang
    • , Laura E Hogan
    • , Smita Dandekar
    • , Jiri Zavadil
    • , Elizabeth A Raetz
    • , Debra J Morrison
    •  & William L Carroll
  2. Department of Pathology, New York University Langone Medical Center, New York, New York, USA.

    • Julia A Meyer
    •  & William L Carroll
  3. New York University Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, New York, USA.

    • Jinhua Wang
    • , Zuojian Tang
    •  & Jiri Zavadil
  4. Department of Pediatrics, New York University Langone Medical Center, New York, New York, USA.

    • Laura E Hogan
    • , Smita Dandekar
    • , Elizabeth A Raetz
    • , Debra J Morrison
    •  & William L Carroll
  5. Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Jun J Yang
    •  & William E Evans
  6. Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

    • Jay P Patel
    •  & Ross L Levine
  7. Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, USA.

    • Paul Zumbo
    • , Sheng Li
    •  & Christopher E Mason
  8. HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, USA.

    • Paul Zumbo
    • , Sheng Li
    •  & Christopher E Mason
  9. Leukemia Service, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

    • Ross L Levine
  10. Department of Pharmacology, New York University Langone Medical Center, New York, New York, USA.

    • Timothy Cardozo
  11. University of Colorado School of Medicine, Aurora, Colorado, USA.

    • Stephen P Hunger
  12. Children's Hospital Colorado, Aurora, Colorado, USA.

    • Stephen P Hunger

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Contributions

J.A.M., L.E.H., J.J.Y., J.Z., R.L.L., T.C., W.E.E., D.J.M., C.E.M. and W.L.C. planned experiments. J.A.M., L.E.H., J.J.Y., S.D., J.P.P. and D.J.M. performed experiments and analyzed data. J.W., Z.T., P.Z., S.L. and C.E.M. performed sequencing and analyzed sequence data. T.C. performed molecular modeling. S.P.H. and E.A.R. provided patient samples and clinical data. J.A.M. and W.L.C. wrote the manuscript. W.L.C. coordinated the study. All authors discussed the results and reviewed the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to William L Carroll.

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DOI

https://doi.org/10.1038/ng.2558