Gene expression signature of primary imatinib-resistant chronic myeloid leukemia patients

Leukemia

Volumn 20, Issue 8, 2006, Pages 1400-1407

  Frank, Oliver ^a   Brors, B ^b   Fabarius, A ^a   Li, L ^c   Haak, M ^c   Merk, S ^d   Schwindel, U ^a   Zheng, C ^a   Muller M C ^a   Gretz, N ^c   Hehlmann, R ^a   Hochhaus, A ^a   Seifarth, W ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c MEDICAL FACULTY MANNHEIM HEIDELBERG UNIVERSITY   (Germany)

^d UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

CML; Cytogenetic response; Gene expression profiling; Imatinib; Microarray; Primary resistance

Indexed keywords

ALPHA INTERFERON; ANTIOXIDANT; ARYLDIALKYLPHOSPHATASE; ARYLDIALKYLPHOSPHATASE 2; BCR ABL PROTEIN; CASPASE 9; GLUTATHIONE SYNTHASE; IMATINIB; INHIBITOR OF DIFFERENTIATION 1; PROTEIN MSH3; PROTEIN TYROSINE KINASE INHIBITOR; RNA; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR 1; UNCLASSIFIED DRUG; VANIN 1;

APOPTOSIS; ARTICLE; CENTROSOME; CHRONIC MYELOID LEUKEMIA; CLASSIFICATION; CLINICAL ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; CYTOGENETICS; DISEASE COURSE; DNA REPAIR; GENE EXPRESSION PROFILING; HUMAN; INTERMETHOD COMPARISON; LEUKEMIA REMISSION; LEUKOCYTE; METAPHASE; MICROARRAY ANALYSIS; OXIDATIVE STRESS; PHILADELPHIA 1 CHROMOSOME; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RETROSPECTIVE STUDY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; TREATMENT OUTCOME;

EID: 33746143590     PISSN: 08876924     EISSN: 14765551     Source Type: Journal    
DOI: 10.1038/sj.leu.2404270     Document Type: Article

References (56)

1. Calabretta B, Perrotti D. The biology of CML blast crisis. Blood 2004; 103: 4010-4022.
2. Bonifazi F, de Vivo A, Rosti G, Guilhot F, Guilhot J, Trabacchi E et al. Chronic myeloid leukemia and interferon-alpha: A study of complete cytogenetic responders. Blood 2001; 98: 3074-3081.
3. O'Brien SG, Guilhot F, Larson RA, Gathmann I, Baccarani M, Cervantes F et al. Imatinib compared with interferon and low-dose cytarabine for newly diagnosed chronic-phase chronic myeloid leukemia. N Engl J Med 2003; 348: 994-1004.
4. Kantarjian H, Sawyers C, Hochhaus A, Guilhot F, Schiffer C, Gambacorti-Passerini C et al. Hematologic and cytogenetic responses to imatinib mesylate in chronic myelogenous leukemia. N Engl J Med 2002; 346: 645-652.
5. Kantarjian HM, Cortes JE, O'Brien S, Luthra R, Giles F, Verstovsek S et al. Long-term survival benefit and improved complete cytogenetic and molecular response rates with imatinib mesylate in Philadelphia chromosome-positive chronic-phase chronic myeloid leukemia after failure of interferon-alpha. Blood 2004; 104: 1979-1988.
6. Hochhaus A, La Rosée P. Imatinib therapy in chronic myelogenous leukemia: Strategies to avoid and overcome resistance. Leukemia 2004; 18: 1321-1331.
7. Thomas J, Wang L, Clark RE, Pirmohamed M. Active transport of imatinib into and out of cells: Implications for drug resistance. Blood 2004; 104: 3739-3745.
8. McLean LA, Gathmann I, Capdeville R, Polymeropoulos MH, Dressman M. Pharmacogenomic analysis of cytogenetic response in chronic myeloid leukemia patients treated with imatinib. Clin Cancer Res 2004; 10 (Part 1): 155-165.
9. Crossman LC, Druker BJ, Deininger MW, Pirmohamed M, Wang L, Clark RE. hOCT 1 and resistance to imatinib. Blood 2005; 106: 1133-1134.
10. Wadlow R, Ramaswamy S. DNA microarrays in clinical cancer research. Curr Mol Med 2005; 5: 111-120.
11. Haferlach T, Kohlmann A, Schnittger S, Dugas M, Hiddemann W, Kern W et al. Global approach to the diagnosis of leukemia using gene expression profiling. Blood 2005; 106: 1189-1198.
12. Kohlmann A, Schoch C, Dugas M, Rauhut S, Weninger F, Schnittger S et al. Pattern robustness of diagnostic gene expression signatures in leukemia. Genes Chromosomes Cancer 2005; 42: 299-307.
13. Hofmann WK, de Vos S, Elashoff D, Gschaidmeier H, Hoelzer D, Koeffler HP et al. Relation between resistance of Philadelphia-chromosome-positive acute lymphoblastic leukaemia to the tyrosine kinase inhibitor STI571 and gene-expression profiles: A gene-expression study. Lancet 2002; 359: 481-486.
14. Yong AS, Szydlo RM, Goldman JM, Apperley JF, Melo JV. Molecular profiling of CD34+ cells identifies low expression of CD7, along with high expression of proteinase 3 or elastase, as predictors of longer survival in patients with CML. Blood 2006; 107: 205-212.
15. Fonatsch C, Schaadt M, Kirchner H, Diehl V. A possible correlation between the degree of karyotype aberrations and the rate of sister chromatid exchanges in lymphoma lines. Int J Cancer 1980; 26: 749-756.
16. Cross NC, Melo JV, Feng L, Goldman JM. An optimized multiplex polymerase chain reaction (PCR) for detection of BCR-ABL fusion mRNAs in haematological disorders. Leukemia 1994; 8: 186-189.
17. Emig M, Saussele S, Wittor H, Weisser A, Reiter A, Willer A et al. Accurate and rapid analysis of residual disease in patients with CML using specific fluorescent hybridization probes for real time quantitative RT-PCR. Leukemia 1999; 13: 1825-1832.
18. Hochhaus A, Kreil S, Corbin AS, La Rosée P, Müller MC, Lahaye T et al. Molecular and chromosomal mechanisms of resistance to imatinib (STI571) therapy. Leukemia 2002; 16: 2190-2196.
19. Cross NC, Feng L, Bungey J, Goldman JM. Minimal residual disease after bone marrow transplant for chronic myeloid leukaemia detected by the polymerase chain reaction. Leuk Lymphoma 1993; 11 (Suppl 1): 39-43.
20. Auer H, Lyianarachchi S, Newsom D, Klisovic MI, Marcucci G, Kornacker K. Chipping away at the chip bias: RNA degradation in microarray analysis. Nat Genet 2003; 35: 292-293.
21. Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002; 18 (Suppl 1): S96-S104.
22. Vapnik VN. Statistical Learning Theory. John Wiley & Sons Inc.: New York, NY, 1998.
23. Guyon I, Weston J, Barnhill S, Vapnik V. Gene selection for cancer classification using support vector machines. Mach Learn 2002; 46: 389-422.
24. Beillard E, Pallisgaard N, van der Valden VH, Bi W, Dee R, van der Schoot E et al. Evaluation of candidate control genes for diagnosis and residual disease detection in leukemic patients using 'real-time' quantitative reverse-transcriptase polymerase chain reaction (RQ-PCR) - a Europe against cancer program. Leukemia 2003; 17: 2474-2486.
25. Aerts JL, Gonzales MI, Topalian SL. Selection of appropriate control genes to assess expression of tumor antigens using real-time RT-PCR. Biotechniques 2004; 36: 84-86, 88, 90-91.
26. Hochhaus A, Hughes T. Clinical resistance to imatinib: Mechanisms and implications. Hematol Oncol Clin N Am 2004; 18: 641-656, ix.
27. Dallas PB, Gottardo NG, Firth MJ, Beesley AH, Hoffmann K, Terry PA et al. Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR - how well do they correlate? BMC Genom 2005; 6: 59.
28. Melo JV, Deininger MW. Biology of chronic myelogenous leukemia - signaling pathways of initiation and transformation. Hematol Oncol Clin N Am 2004; 18: 545, viii.
29. Kuwahara D, Tsutsumi K, Oyake D, Ohta T, Nishikawa H, Koizuka I. Inhibition of caspase-9 activity and Apaf-1 expression in cisplatin-resistant head and neck squamous cell carcinoma cells. Auris Nasus Larynx 2003; 30 (Suppl): S85-S88.
30. Vallat L, Magdelenat H, Merle-Beral H, Masdehors P, Potocki DM, Davi F et al. The resistance of B-CLL cells to DNA damage-induced apoptosis defined by DNA microarrays. Blood 2003; 101: 4598-4606.
31. Masuda Y, Shima G, Aiuchi T, Horie M, Hori K, Nakajo S et al. involvement of tumor necrosis factor receptor-associated protein 1 (TRAP1) in apoptosis induced by beta-hydroxyisovalerylshikonin. J Biol Chem 2004; 279: 42503-42515.
32. Shet AS, Jahagirdar BN, Verfaillie CM. Chronic myelogenous leukemia: mechanisms underlying disease progression. Leukemia 2002; 16: 1402-1411.
33. Evans PC, Smith TS, Lai MJ, Williams MG, Burke DF, Heyninck K et al. A novel type of deubiquitinating enzyme. J Biol Chem 2003; 278: 23180-23186.
34. Chen F. Endogenous inhibitors of nuclear factor-kappaB, an opportunity for cancer control. Cancer Res 2004; 64: 8135-8138.
35. Sattler M, Griffin JD. Molecular mechanisms of transformation by the BCR-ABL oncogene. Semin Hematol 2003; 40 (Suppl 2): 4-10.
36. Wurmbach E, Yuen T, Ebersole BJ, Sealfon SC. Gonadotropin-releasing hormone receptor-coupled gene network organization. J Biol Chem 2001; 276: 47195-47201.
37. Nam SW, Clair T, Campo CK, Lee HY, Liotta LA, Stracke ML. Autotaxin (ATX), a potent tumor motogen, augments invasive and metastatic potential of ras-transformed cells. Oncogene 2000; 19: 241-247.
38. Nowicki MO, Pawlowski P, Fischer T, Hess G, Pawlowski T, Skorski T. Chronic myelogenous leukemia molecular signature. Oncogene 2003; 22: 3952-3963.
39. Talpaz M, Silver RT, Druker BJ, Goldman JM, Gambacorti-Passerini C, Guilhot F et al. Imatinib induces durable hematologic and cytogenetic responses in patients with accelerated phase chronic myeloid leukemia: results of a phase 2 study. Blood 2002; 99: 1928-1937.
40. Weng Z, Fluckiger AC, Nisitani S, Wahl MI, Le LQ, Hunter CA et al. A DNA damage and stress inducible G protein-coupled receptor blocks cells in G2/M. Proc Natl Acad Sci USA 1998; 95: 12334-12339.
41. Chuang JI, Chang TY, Liu HS. Glutathione depletion-induced apoptosis of Ha-ras-transformed NIH3T3 cells can be prevented by melatonin. Oncogene 2003; 22: 1349-1357.
42. Berruyer C, Martin FM, Castellano R, Macone A, Malergue F, Garrido-Urbani S et al. Vanin-1-/- mice exhibit a glutathione-mediated tissue resistance to oxidative stress. Mol Cell Biol 2004; 24: 7214-7224.
43. Shiner M, Fuhrman B, Aviram M. Paraoxonase 2 (PON2) expression is upregulated via a reduced-nicotinamide-adenine-dinucleotide-phosphate (NADPH)-oxidase-dependent mechanism during monocytes differentiation into macrophages. Free Radic Biol Med 2004; 37: 2052-2063.
44. Cong F, Tang J, Hwang BJ, Vuong BQ, Chu G, Goff SP. Interaction between UV-damaged DNA binding activity proteins and the c-Abl tyrosine kinase. J Biol Chem 2002; 277: 34870-34878.
45. Giehl M, Fabarius A, Frank O, Hochhaus A, Hafner M, Hehlmann R et al. Centrosome aberrations in chronic myeloid leukemia correlate with stage of disease and chromosomal instability. Leukemia 2005; 19: 1192-1197.
46. Hasskarl J, Duensing S, Manuel E, Munger K. The helix-loop-helix protein ID1 localizes to centrosomes and rapidly induces abnormal centrosome numbers. Oncogene 2004; 23: 1930-1938.
47. Takai N, Miyazaki T, Fujisawa K, Nasu K, Miyakawa I. Id1 expression is associated with histological grade and invasive behavior in endometrial carcinoma. Cancer Lett 2001; 165: 185-193.
48. Polsky D, Young AZ, Busam KJ, Alani RM. The transcriptional repressor of p16/Ink4a, Id1, is up-regulated in early melanomas. Cancer Res 2001; 61: 6008-6011.
49. Cohen N, Rozenfeld-Granot G, Hardan I, Brok-Simoni F, Amariglio N, Rechavi G et al. Subgroup of patients with Philadelphia-positive chronic myelogenous leukemia characterized by a deletion of 9q proximal to ABL gene: Expression profiling, resistance to interferon therapy, and poor prognosis. Cancer Genet Cytogenet 2001; 128: 114-119.
50. Ohmine K, Ota J, Ueda M, Ueno S, Yoshida K, Yamashita Y et al. Characterization of stage progression in chronic myeloid leukemia by DNA microarray with purified hematopoietic stem cells. Oncogene 2001; 20: 8249-8257.
51. Ohno R, Nakamura Y. Prediction of response to imatinib by cDNA microarray analysis. Semin Hematol 2003; 40 (Suppl 2): 42-49.
52. Crossman LC, Mori M, Hsieh YC, Lange T, Paschka P, Harrington CA et al. In chronic myeloid leukemia white to cells from cytogenetic responders and non-responders to imatinib have very similar gene expression signatures. Haematologica 2005; 90: 459-464.
53. Man MZ, Dyson G, Johnson K, Liao B. Evaluating methods for classifying expression data. J Biopharm Stat 2004; 14: 1065-1084.
54. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 2002; 30: E48.
55. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S et al. Within the fold: Assessing differential expression measures and reproducibility in microarray assays. Genome Biol 2002; 3: Research 0062.1-13.
56. Yao B, Rakhade SN, Li Q, Ahmed S, Krauss R, Draghici S et al. Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells. BMC Bioinformatics 2004; 5: 99.