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Acute Leukemias

A genome-wide approach identifies that the aspartate metabolism pathway contributes to asparaginase sensitivity

Abstract

Asparaginase is an important component for treatment of childhood acute lymphoblastic leukemia (ALL). The basis for interindividual differences in asparaginase sensitivity remains unclear. To comprehensively identify genetic variants important in the cytotoxicity of asparaginase, we used a genome-wide association approach using the HapMap lymphoblastoid cell lines (87 CEU trio members) and 54 primary ALL leukemic blast samples at diagnosis. Asparaginase sensitivity was assessed as the drug concentration necessary to inhibit 50% of growth (inhibitory concentration (IC)50). In CEU lines, we tested 2 390 203 single-nucleotide polymorphism (SNP) genotypes at the individual SNP (P<0.001) and gene level (P<0.05), and identified 329 SNPs representing 94 genes that were associated with asparaginase IC50. The aspartate metabolism pathway was the most overrepresented among 199 pathways evaluated (P=8.1 × 10−3), with primary involvement of adenylosuccinate lyase and aspartyl-tRNA synthetase genes. We validated that SNPs in the aspartate metabolism pathway were also associated with asparaginase sensitivity in primary ALL leukemic blast samples (P=5.5 × 10−5). Our genome-wide interrogation of CEU cell lines and primary ALL blasts revealed that inherited genomic interindividual variation in a plausible candidate pathway can contribute to asparaginase sensitivity.

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References

  1. Pui CH, Evans WE . Treatment of acute lymphoblastic leukemia. N Engl J Med 2006; 354: 166–178.

    Article  CAS  PubMed  Google Scholar 

  2. Pui CH, Jeha S . New therapeutic strategies for the treatment of acute lymphoblastic leukaemia. Nat Rev Drug Discov 2007; 6: 149–165.

    Article  CAS  PubMed  Google Scholar 

  3. Schrappe M, Reiter A, Ludwig WD, Harbott J, Zimmermann M, Hiddemann W et al. Improved outcome in childhood acute lymphoblastic leukemia despite reduced use of anthracyclines and cranial radiotherapy: results of trial ALL-BFM 90 German-Austrian-Swiss ALL-BFM Study Group. Blood 2000; 95: 3310–3322.

    CAS  PubMed  Google Scholar 

  4. Silverman LB, Gelber RD, Dalton VK, Asselin BL, Barr RD, Clavell LA et al. Improved outcome for children with acute lymphoblastic leukemia: results of Dana-Farber Consortium Protocol 91-01. Blood 2001; 97: 1211–1218.

    Article  CAS  PubMed  Google Scholar 

  5. Hongo T, Yajima S, Sakurai M, Horikoshi Y, Hanada R . In vitro drug sensitivity testing can predict induction failure and early relapse of childhood acute lymphoblastic leukemia. Blood 1997; 89: 2959–2965.

    CAS  PubMed  Google Scholar 

  6. Kaspers GJ, Veerman AJ, Pieters R, Van Zantwijk CH, Smets LA, Van Wering ER et al. In vitro cellular drug resistance and prognosis in newly diagnosed childhood acute lymphoblastic leukemia. Blood 1997; 90: 2723–2729.

    CAS  PubMed  Google Scholar 

  7. Pieters R, Huismans DR, Loonen AH, Hahlen K, van der Does-van den Berg A, van Wering ER et al. Relation of cellular drug resistance to long-term clinical outcome in childhood acute lymphoblastic leukaemia. Lancet 1991; 338: 399–403.

    Article  CAS  PubMed  Google Scholar 

  8. Asselin BL, Kreissman S, Coppola DJ, Bernal SD, Leavitt PR, Gelber RD et al. Prognostic significance of early response to a single dose of asparaginase in childhood acute lymphoblastic leukemia. J Pediatr Hematol Oncol 1999; 21: 6–12.

    Article  CAS  PubMed  Google Scholar 

  9. Appel IM, Kazemier KM, Boos J, Lanvers C, Huijmans J, Veerman AJ et al. Pharmacokinetic, pharmacodynamic and intracellular effects of PEG-asparaginase in newly diagnosed childhood acute lymphoblastic leukemia: results from a single agent window study. Leukemia 2008; 22: 1665–1679.

    Article  CAS  PubMed  Google Scholar 

  10. Capizzi RL, Bertino JR, Skeel RT, Creasey WA, Zanes R, Olayon C et al. L-asparaginase: clinical, biochemical, pharmacological, and immunological studies. Ann Intern Med 1971; 74: 893–901.

    Article  CAS  PubMed  Google Scholar 

  11. Haskell CM, Canellos GP . l-asparaginase resistance in human leukemia—asparagine synthetase. Biochem Pharmacol 1969; 18: 2578–2580.

    Article  CAS  PubMed  Google Scholar 

  12. Horowitz B, Madras BK, Meister A, Old LJ, Boyes EA, Stockert E . Asparagine synthetase activity of mouse leukemias. Science 1968; 160: 533–535.

    Article  CAS  PubMed  Google Scholar 

  13. Kiriyama Y, Kubota M, Takimoto T, Kitoh T, Tanizawa A, Akiyama Y et al. Biochemical characterization of U937 cells resistant to L-asparaginase: the role of asparagine synthetase. Leukemia 1989; 3: 294–297.

    CAS  PubMed  Google Scholar 

  14. Aslanian AM, Fletcher BS, Kilberg MS . Asparagine synthetase expression alone is sufficient to induce l-asparaginase resistance in MOLT-4 human leukaemia cells. Biochem J 2001; 357: 321–328.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Hutson RG, Kitoh T, Moraga Amador DA, Cosic S, Schuster SM, Kilberg MS . Amino acid control of asparagine synthetase: relation to asparaginase resistance in human leukemia cells. Am J Physiol 1997; 272: C1691–C1699.

    Article  CAS  PubMed  Google Scholar 

  16. Asselin BL, Ryan D, Frantz CN, Bernal SD, Leavitt P, Sallan SE et al. In vitro and in vivo killing of acute lymphoblastic leukemia cells by L-asparaginase. Cancer Res 1989; 49: 4363–4368.

    CAS  PubMed  Google Scholar 

  17. Estes DA, Lovato DM, Khawaja HM, Winter SS, Larson RS . Genetic alterations determine chemotherapy resistance in childhood T-ALL: modelling in stage-specific cell lines and correlation with diagnostic patient samples. Br J Haematol 2007; 139: 20–30.

    Article  CAS  PubMed  Google Scholar 

  18. Fine BM, Kaspers GJ, Ho M, Loonen AH, Boxer LM . A genome-wide view of the in vitro response to l-asparaginase in acute lymphoblastic leukemia. Cancer Res 2005; 65: 291–299.

    CAS  PubMed  Google Scholar 

  19. Iwamoto S, Mihara K, Downing JR, Pui CH, Campana D . Mesenchymal cells regulate the response of acute lymphoblastic leukemia cells to asparaginase15. JClinInvest 2007; 117: 1049–1057.

    CAS  Google Scholar 

  20. Krejci O, Starkova J, Otova B, Madzo J, Kalinova M, Hrusak O et al. Upregulation of asparagine synthetase fails to avert cell cycle arrest induced by L-asparaginase in TEL/AML1-positive leukaemic cells. Leukemia 2004; 18: 434–441.

    Article  CAS  PubMed  Google Scholar 

  21. Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L et al. A gene expression database for the molecular pharmacology of cancer. Nat Genet 2000; 24: 236–244.

    Article  CAS  PubMed  Google Scholar 

  22. Stams WA, den Boer ML, Beverloo HB, Meijerink JP, Stigter RL, van Wering ER et al. Sensitivity to L-asparaginase is not associated with expression levels of asparagine synthetase in t(12;21)+ pediatric ALL. Blood 2003; 101: 2743–2747.

    Article  CAS  PubMed  Google Scholar 

  23. Stams WA, den Boer ML, Holleman A, Appel IM, Beverloo HB, van Wering ER et al. Asparagine synthetase expression is linked with L-asparaginase resistance in TEL-AML1-negative but not TEL-AML1-positive pediatric acute lymphoblastic leukemia. Blood 2005; 105: 4223–4225.

    Article  CAS  PubMed  Google Scholar 

  24. Holleman A, Cheok MH, den Boer ML, Yang W, Veerman AJ, Kazemier KM et al. Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment. N Engl J Med 2004; 351: 533–542.

    Article  CAS  PubMed  Google Scholar 

  25. Abshire TC, Pollock BH, Billett AL, Bradley P, Buchanan GR . Weekly polyethylene glycol conjugated L-asparaginase compared with biweekly dosing produces superior induction remission rates in childhood relapsed acute lymphoblastic leukemia: a Pediatric Oncology Group Study. Blood 2000; 96: 1709–1715.

    CAS  PubMed  Google Scholar 

  26. Holleman A, den Boer ML, de Menezes RX, Cheok MH, Cheng C, Kazemier KM et al. The expression of 70 apoptosis genes in relation to lineage, genetic subtype, cellular drug resistance, and outcome in childhood acute lymphoblastic leukemia. Blood 2006; 107: 769–776.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Pui CH, Campana D, Pei D, Bowman WP, Sandlund JT, Kaste SC et al. Treating childhood acute lymphoblastic leukemia without cranial irradiation. N Engl J Med 2009; 360: 2730–2741.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. French D, Yang W, Hamilton LH, Neale G, Fan Y, Downing JR et al. Concordant gene expression in leukemia cells and normal leukocytes is associated with germline cis-SNPs. PLoS ONE 2008; 3: e2144.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Pieters R, Loonen AH, Huismans DR, Broekema GJ, Dirven MW, Heyenbrok MW et al. In vitro drug sensitivity of cells from children with leukemia using the MTT assay with improved culture conditions. Blood 1990; 76: 2327–2336.

    CAS  PubMed  Google Scholar 

  30. Pottier N, Cheok MH, Yang W, Assem M, Tracey L, Obenauer JC et al. Expression of SMARCB1 modulates steroid sensitivity in human lymphoblastoid cells: identification of a promoter SNP that alters PARP1 binding and SMARCB1 expression. Hum Mol Genet 2007; 16: 2261–2271.

    Article  CAS  PubMed  Google Scholar 

  31. D'Argenio DZ, Schumitzky A . Adapt II User's Guide: Pharmacokinetic/Pharmacodynamic Systems Analysis Software. Biomedical Simulations Resource: Los Angeles, 1997.

    Google Scholar 

  32. Pieters R, Huismans DR, Leyva A, Veerman AJ . Adaptation of the rapid automated tetrazolium dye based (MTT) assay for chemosensitivity testing in childhood leukemia. Cancer Lett 1988; 41: 323–332.

    Article  CAS  PubMed  Google Scholar 

  33. Beesley AH, Palmer ML, Ford J, Weller RE, Cummings AJ, Freitas JR et al. Authenticity and drug resistance in a panel of acute lymphoblastic leukaemia cell lines. Br J Cancer 2006; 95: 1537–1544.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Breiman L . Random forests. Mach Learn 2001; 45: 5–32.

    Article  Google Scholar 

  35. Huang RS, Duan S, Shukla SJ, Kistner EO, Clark TA, Chen TX et al. Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach. Am J Hum Genet 2007; 81: 427–437.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Engel K, Hohne W, Haberle J . Mutations and polymorphisms in the human argininosuccinate synthetase (ASS1) gene. Hum Mutat 2009; 30: 300–307.

    Article  CAS  PubMed  Google Scholar 

  37. Ohno T, Kimura Y, Sakurada K, Sugimura K, Fujiyoshi T, Saheki T et al. Argininosuccinate synthetase gene expression in leukemias: potential diagnostic marker for blastic crisis of chronic myelocytic leukemia. Leuk Res 1992; 16: 475–483.

    Article  CAS  PubMed  Google Scholar 

  38. Piga A, Sylwestrowicz T, Ganeshaguru K, Breatnach F, Amos R, Prentice HG et al. Nucleoside incorporation into DNA and RNA in acute leukaemia: differences between the various leukaemia sub-types. Br J Haematol 1982; 52: 195–204.

    Article  CAS  PubMed  Google Scholar 

  39. Scholar EM, Calabresi P . Identification of the enzymatic pathways of nucleotide metabolism in human lymphocytes and leukemia cells. Cancer Res 1973; 33: 94–103.

    CAS  PubMed  Google Scholar 

  40. Pui CH, Evans WE . Acute lymphoblastic leukemia. N Engl J Med 1998; 339: 605–615.

    Article  CAS  PubMed  Google Scholar 

  41. Bhojwani D, Kang H, Moskowitz NP, Min DJ, Lee H, Potter JW et al. Biologic pathways associated with relapse in childhood acute lymphoblastic leukemia: a Children's Oncology Group Study. Blood 2006; 108: 711–717.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Bhojwani D, Kang H, Menezes RX, Yang W, Sather H, Moskowitz NP et al. Gene expression signatures predictive of early response and outcome in high-risk childhood acute lymphoblastic leukemia: A Children's Oncology Group Study [corrected]. J Clin Oncol 2008; 26: 4376–4384.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Bardot V, Dutrillaux AM, Delattre JY, Vega F, Poisson M, Dutrillaux B et al. Purine and pyrimidine metabolism in human gliomas: relation to chromosomal aberrations. Br J Cancer 1994; 70: 212–218.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Reed VL, Mack DO, Smith LD . Adenylosuccinate lyase as an indicator of breast and prostate malignancies: a preliminary report. Clin Biochem 1987; 20: 349–351.

    Article  CAS  PubMed  Google Scholar 

  45. Weber G . Enzymes of purine metabolism in cancer. Clin Biochem 1983; 16: 57–63.

    Article  CAS  PubMed  Google Scholar 

  46. Su N, Pan YX, Zhou M, Harvey RC, Hunger SP, Kilberg MS . Correlation between asparaginase sensitivity and asparagine synthetase protein content, but not mRNA, in acute lymphoblastic leukemia cell lines. Pediatr Blood Cancer 2008; 50: 274–279.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Kaspers GJ, Smets LA, Pieters R, Van Zantwijk CH, Van Wering ER, Veerman AJ . Favorable prognosis of hyperdiploid common acute lymphoblastic leukemia may be explained by sensitivity to antimetabolites and other drugs: results of an in vitro study. Blood 1995; 85: 751–756.

    CAS  PubMed  Google Scholar 

  48. Ramakers-van Woerden NL, Pieters R, Loonen AH, Hubeek I, van Drunen E, Beverloo HB et al. TEL/AML1 gene fusion is related to in vitro drug sensitivity for L- asparaginase in childhood acute lymphoblastic leukemia. Blood 2000; 96: 1094–1099.

    CAS  PubMed  Google Scholar 

  49. Pieters R, den Boer ML, Durian M, Janka G, Schmiegelow, Kaspers GJ et al. Relation between age, immunophenotype and in vitro drug resistance in 395 children with acute lymphoblastic leukemia—implications for treatment of infants. Leukemia 1998; 12: 1344–1348.

    Article  CAS  PubMed  Google Scholar 

  50. Tai HL, Krynetski EY, Schuetz EG, Yanishevski Y, Evans WE . Enhanced proteolysis of thiopurine S-methyltransferase (TPMT) encoded by mutant alleles in humans (TPMT*3A, TPMT*2): mechanisms for the genetic polymorphism of TPMT activity. Proc Natl Acad Sci USA 1997; 94: 6444–6449.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Loennechen T, Yates CR, Fessing MY, Relling MV, Krynetski EY, Evans WE . Isolation of a human thiopurine S-methyltransferase (TPMT) complementary DNA with a single nucleotide transition A719G (TPMT*3C) and its association with loss of TPMT protein and catalytic activity in humans. Clin Pharmacol Ther 1998; 64: 46–51.

    Article  CAS  PubMed  Google Scholar 

  52. Cao A, Galanello R . Beta-thalassemia. Genet Med 2010; 12: 61–76.

    Article  CAS  PubMed  Google Scholar 

  53. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL et al. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 2008; 4: e1000287.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Hartford CM, Duan S, Delaney SM, Mi S, Kistner EO, Lamba JK et al. Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity. Blood 2009; 113: 2145–2153.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Jones TS, Yang W, Evans WE, Relling MV . Using HapMap tools in pharmacogenomic discovery: the thiopurine methyltransferase polymorphism. Clin Pharmacol Ther 2007; 81: 729–734.

    Article  CAS  PubMed  Google Scholar 

  56. Welsh M, Mangravite L, Medina MW, Tantisira K, Zhang W, Huang RS et al. Pharmacogenomic discovery using cell-based models. Pharmacol Rev 2009; 61: 413–429.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. French D, Yang W, Cheng C, Raimondi SC, Mullighan CG, Downing JR et al. Acquired variation outweighs inherited variation in whole genome analysis of methotrexate polyglutamate accumulation in leukemia. Blood 2009; 113: 4512–4520.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank the patients and their families, and our research faculty and staff for participating. We also thank Nancy Kornegay and Mark Wilkinson for database and computer expertise, and Yaqin Chu, May Chung, Natalya Lenchik, Margaret Needham, Emily Melton and Siamac Salehy for outstanding technical assistance. This work was supported by NCI CA78224, CA36401 and the NIH/NIGMS Pharmacogenomics Research Network (U01GM92666) and by ALSAC.

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Correspondence to M V Relling.

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Chen, SH., Yang, W., Fan, Y. et al. A genome-wide approach identifies that the aspartate metabolism pathway contributes to asparaginase sensitivity. Leukemia 25, 66–74 (2011). https://doi.org/10.1038/leu.2010.256

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