Perspectives of gene expression profiling for diagnosis and therapy in haematological malignancies

Briefings in Functional Genomics and Proteomics

Volumn 8, Issue 3, 2009, Pages 184-193

  Bacher, Ulrike ^a   Kohlmann, Alexander ^b   Haferlach, Torsten ^c  

^a UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

^c MLL MUNICH LEUKEMIA LABORATORY   (Germany)

Author keywords

Acute lymphoblastic leukaemia (ALL); Acute myeloid leukaemia (AML); Gene expression profiling (GEP); Lymphatic malignancies; MILE study

Indexed keywords

ANTINEOPLASTIC AGENT; BCR ABL PROTEIN; CD135 ANTIGEN; IMATINIB; MIXED LINEAGE LEUKEMIA PROTEIN; MULTIDRUG RESISTANCE PROTEIN 1; MYC PROTEIN; PROTEIN FARNESYLTRANSFERASE INHIBITOR; TIPIFARNIB; TRANSCRIPTION FACTOR GATA 2;

ACUTE GRANULOCYTIC LEUKEMIA; ACUTE LYMPHOCYTIC LEUKEMIA; ARTICLE; BURKITT LYMPHOMA; CANCER CLASSIFICATION; CANCER DIAGNOSIS; CANCER RESEARCH; CANCER RESISTANCE; CANCER SURVIVAL; CANCER THERAPY; DIFFERENTIAL DIAGNOSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE MUTATION; GENE REARRANGEMENT; HEMATOLOGIC MALIGNANCY; HUMAN; LARGE CELL LYMPHOMA; LYMPHATIC LEUKEMIA; LYMPHOMA; PROGNOSIS; SURVIVAL TIME; TREATMENT RESPONSE;

ANIMALS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, LEUKEMIC; HEMATOLOGIC NEOPLASMS; HUMANS;

EID: 70349089080     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/elp011     Document Type: Article

References (90)

1. Swerdlow S, Campo E, Lee Harris N, et al. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues. 4th edn. Lyon: WHO Press, 2008.
2. Haferlach T, Bacher U, Kern W, et al. Diagnostic pathways in acute leukemias: A proposal for a multimodal approach. Ann Hematol 2007;86:311-27.
3. Bloomfield CD, Shuma C, Regal L, et al. Long-term survival of patients with acute myeloid leukemia: A third follow-up of the Fourth International Workshop on Chromosomes in Leukemia. Cancer 1997; 80:2191-8.
4. Grimwade D, Walker H, Oliver F, et al. The importance of diagnostic cytogenetics on outcome in AML: Analysis of 1,612 patients entered into the MRC AML 10 trial. The Medical Research Council Adult and Children's Leukaemia Working Parties. Blood 1998;92 2322-33.
5. Swansbury GJ, Lawler SD, Alimena G, et al. Long-term survival in acute myelogenous leukemia: A second follow-up of the Fourth International Workshop on Chromosomes in Leukemia. Cancer Genet Cytogen 1994;73:1-7.
6. Schoch C, Haferlach T, Haase D, et al. Patients with de novo acute myeloid leukaemia and complex karyotype aberrations show a poor prognosis despite intensive treatment: A study of 90 patients. Brit J Haematol 2001;112:118-26.
7. Schoch C, Kern W, Kohlmann A, et al. Acute myeloid leukemia with a complex aberrant karyotype is a distinct biological entity characterized by genomic imbalances and a specific gene expression profile. Gene Chromosome Canc 2005;43:227-38.
8. Gokbuget N, Hoelzer D. Treatment of adult acute lymphoblastic leukemia. Semin Hematol 2009;46:64-75.
9. + AML): Biologic and clinical features. Blood 2007;109:874-85.
10. Dave SS, Fu K, Wright GW, et al. Molecular diagnosis of Burkitt's lymphoma. New Engl J Med 2006;354:2431-42.
11. Rosenwald A, Ott G. Burkitt lymphoma versus diffuse large B-cell lymphoma. Ann Oncol 2008;19(Suppl):iV67-iv69.
12. Haferlach T. Molecular genetic pathways as therapeutic targets in acute myeloid leukemia. Hematology Am Soc Hematol Educ Program 2008;400-11.
13. Golub TR, Slonim DK, Tamayo P, et al. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 1999;286:531-7.
14. Wouters BJ, Lowenberg B, Delwel R. A decade of genome-wide gene expression profiling in acute myeloid leukemia: Flashback and prospects. Blood 2009;113:291-8.
15. Valk PJ, Verhaak RG, Beijen MA, et al. Prognostically useful gene-expression profiles in acute myeloid leukemia. New Engl J Med 2004;350:1617-28.
16. Yeoh EJ, Ross ME, Shurtleff SA, et al. Classification, sub-type discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 2002;1 133-43.
17. Haferlach T, Kohlmann A, Schnittger S, et al. Global approach to the diagnosis of leukemia using gene expression profiling. Blood 2005;106:1189-98.
18. Bullinger L, Dohner K, Bair E, et al. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. New Engl J Med 2004;350: 1605-16.
19. Radmacher MD, Marcucci G, Ruppert AS, et al. Independent confirmation of a prognostic gene-expression signature in adult acute myeloid leukemia with a normal karyotype: A Cancer and Leukemia Group B study. Blood 2006;108:1677-83.
20. Mullighan CG, Goorha S, Radtke I, et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 2007;446:758-64.
21. Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503-11.
22. Rosenwald A, Wright G, Chan WC, et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. New Engl J Med 2002; 346:1937-47.
23. Lenz G, Wright G, Dave SS, et al. Stromal gene signatures in large-B-cell lymphomas. New Engl J Med 2008;359: 2313-23.
24. Staal FJ, Cario G, Cazzaniga G, et al. Consensus guidelines for microarray gene expression analyses in leukemia from three European leukemia networks. Leukemia 2006;20: 1385-92.
25. Kohlmann A, Schoch C, Dugas M, et al. Pattern robustness of diagnostic gene expression signatures in leukemia. Gene Chromosome Canc 2005;42:299-307.
26. Southern E, Mir K, Shchepinov M. Molecular interactions on microarrays. Nat Genet 1999;21:5-9.
27. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays. Nat Genet 1999;21: 20-4.
28. Simon R. Roadmap for developing and validating therapeutically relevant genomic classifiers. J Clin Oncol 2005;23: 7332-41.
29. Ioannidis JP. Is molecular profiling ready for use in clinical decision making? Oncologist 2007;12:301-11.
30. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998;95:14863-8.
31. Mardia K, Kent J, Bibby J. Multivariate Analysis. London: Academic Press, 1979.
32. Schoch C, Kohlmann A, Schnittger S, et al. Acute myeloid leukemias with reciprocal rearrangements can be distinguished by specific gene expression profiles. Proc Natl Acad Sci USA 2002;99:10008-15.
33. Debernardi S, Lillington DM, Chaplin T, et al. Genomewide analysis of acute myeloid leukemia with normal karyotype reveals a unique pattern of homeobox gene expression distinct from those with translocation-mediated fusion events. Gene Chromosome Canc 2003; 37:149-58.
34. Ross ME, Mahfouz R, Onciu M, et al. Gene expression profiling of pediatric acute myelogenous leukemia. Blood 2004;104:3679-87.
35. Verhaak RG, Wouters BJ, Erpelinck CA, et al. Prediction of molecular subtypes in acute myeloid leukemia based on gene expression profiling. Haematologica 2009;94:131-4.
36. Kohlmann A, Schoch C, Dugas M, et al. New insights into MLL gene rearranged acute leukemias using gene expression profiling: Shared pathways, lineage commitment, and partner genes. Leukemia 2005; 19:953-64.
37. Camos M, Esteve J, Jares P, et al. Gene expression profiling of acute myeloid leukemia with translocation t(8;16)(p11;p13) and MYST3-CREBBP rearrangement reveals a distinctive signature with a specific pattern of HOX gene expression. Cancer Res 2006;66 6947-54.
38. Haferlach T, Kohlmann A, Klein HU, et al. AML with translocation t(8;16)(p11;p13) demonstrates unique cytomorphological, cytogenetic, molecular and prognostic features. Leukemia 2009; doi:10.1038/ leu.2008.388.
39. Murati A, Gervais C, Carbuccia N, et al. Genome profiling of acute myelomonocytic leukemia: Alteration of the MYB locus in MYST3-linked cases. Leukemia 2009;23:85-94.
40. Schoch C, Haferlach T, Bursch S, et al. Loss of genetic material is more common than gain in acute myeloid leukemia with complex aberrant karyotype: A detailed analysis of 125 cases using conventional chromosome analysis and fluorescence in situ hybridization including 24-color FISH. Gene Chromosome Canc 2002;35:20-9.
41. Lindvall C, Furge K, Bjorkholm M, et al. Combined genetic and transcriptional profiling of acute myeloid leukemia with normal and complex karyotypes. Haematologica 2004;89: 1072-81.
42. Rucker FG, Bullinger L, Schwaenen C, et al. Disclosure of candidate genes in acute myeloid leukemia with complex karyotypes using microarray-based molecular characterization. J Clin Oncol 2006; 24:3887-94.
43. Falini B, Mecucci C, Tiacci E, et al. Cytoplasmic nucleophosmin in acute myelogenous leukemia with a normal karyotype. New Engl J Med 2005;352:254-66.
44. Verhaak RG, Goudswaard CS, van PW, et al. Mutations in nucleophosmin (NPM1) in acute myeloid leukemia (AML): Association with other gene abnormalities and previously established gene expression signatures and their favorable prognostic significance. Blood 2005;106:3747-54.
45. + AML) shows a distinct gene expression profile characterized by up-regulation of genes involved in stem-cell maintenance. Blood 2005;106:899-902.
46. Mullighan CG, Kennedy A, Zhou X, et al. Pediatric acute myeloid leukemia with NPM1 mutations is characterized by a gene expression profile with dysregulated HOX gene expression distinct from MLL-rearranged leukemias. Leukemia 2007;21:2000-9.
47. Wilson CS, Davidson GS, Martin SB, et al. Gene expression profiling of adult acute myeloid leukemia identifies novel biologic clusters for risk classification and outcome prediction. Blood 2006;108:685-96.
48. Neben K, Schnittger S, Brors B, et al. Distinct gene expression patterns associated with FLT3- and NRAS-activating mutations in acute myeloid leukemia with normal karyotype. Oncogene 2005;24 1580-8.
49. Whitman SP, Ruppert AS, Radmacher MD, et al. FLT3 D835/I836 mutations are associated with poor disease-free survival and a distinct gene-expression signature among younger adults with de novo cytogenetically normal acute myeloid leukemia lacking FLT3 internal tandem duplications. Blood 2008;111:1552-9.
50. Lacayo NJ, Meshinchi S, Kinnunen P, et al. Gene expression profiles at diagnosis in denovo childhood AML patients identify FLT3 mutations with good clinical outcomes. Blood 2004;104 2646-54.
51. Bullinger L, Dohner K, Kranz R, et al. An FLT3 gene-expression signature predicts clinical outcome in normal karyotype AML. Blood 2008;111:4490-5.
52. Heuser M, Wingen LU, Steinemann D, et al. Gene-expression profiles and their association with drug resistance in adult acute myeloid leukemia. Haematologica 2005;90: 1484-92.
53. Langer C, Radmacher MD, Ruppert AS, et al. High BAALC expression associates with other molecular prognostic markers, poor outcome, and a distinct gene-expression signature in cytogenetically normal patients younger than 60 years with acute myeloid leukemia: A Cancer and Leukemia Group B (CALGB) study. Blood 2008;111:5371-9.
54. Raponi M, Lancet JE, Fan H, et al. A 2-gene classifier for predicting response to the farnesyltransferase inhibitor tipifarnib in acute myeloid leukemia. Blood 2008;111:2589-96.
55. Kohlmann A, Schoch C, Schnittger S, et al. Molecular characterization of acute leukemias by use of microarray technology. Gene Chromosome Canc 2003;37:396-405.
56. Willenbrock H, Juncker AS, Schmiegelow K, et al. Prediction of immunophenotype, treatment response, and relapse in childhood acute lymphoblastic leukemia using DNA microarrays. Leukemia 2004;18 1270-7.
57. Moos PJ, Raetz EA, Carlson MA, et al. Identification of gene expression profiles that segregate patients with childhood leukemia. Clin Cancer Res 2002;8:3118-30.
58. Kern W, Kohlmann A, Wuchter C, et al. Correlation of protein expression and gene expression in acute leukemia. Cytom Part B-Clin Cy 2003;55:29-36.
59. van Delft FW, Bellotti T, Luo Z, et al. Prospective gene expression analysis accurately subtypes acute leukaemia in children and establishes a commonality between hyperdiploidy and t(12;21) in acute lymphoblastic leukaemia. Brit J Haematol 2005;130:26-35.
60. Armstrong SA, Staunton JE, Silverman LB, et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet 2002;30:41-7.
61. Ross ME, Zhou X, Song G, et al. Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood 2003; 102:2951-9.
62. Chiaretti S, Li X, Gentleman R, et al. Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation. Clin Cancer Res 2005; 11:7209-19.
63. Mullighan CG, Su X, Zhang J, et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. New Engl J Med 2009; 360:470-80.
64. Den Boer ML, Van SM, De Menezes RX, et al. A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: A genome-wide classification study. Lancet Oncol 2009;10:125-34.
65. Bueno MJ, de Castro PI, de Cedron GM, et al. Genetic and epigenetic silencing of microRNA-203 enhances ABL1 and BCR-ABL1 oncogene expression. Cancer Cell 2008; 13:496-506.
66. Faber J, Gregory RI, Armstrong SA. Linking miRNA regulation to BCR-ABL expression: The next dimension. Cancer Cell 2008;13:467-9.
67. Bhojwani D, Kang H, Menezes RX, et al. Gene expression signatures predictive of early response and outcome in high-risk childhood acute lymphoblastic leukemia: A Children's Oncology Group Study. J Clin Oncol 2008;26:4376-84.
68. Hoffmann K, Firth MJ, Beesley AH, et al. Prediction of relapse in paediatric pre-B acute lymphoblastic leukaemia using a three-gene risk index. Brit J Haematol 2008;140: 656-64.
69. Hofmann WK, de Vos S, Elashoff D, 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;359:481-6.
70. Chiaretti S, Li X, Gentleman R, et al. Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood 2004;103:2771-8.
71. Lenz G, Wright GW, Emre NC, etal. Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Proc Natl Acad Sci USA 2008;105:13520-5.
72. Perkins AS, Friedberg JW. Burkitt lymphoma in adults. Hematology Am Soc Hematol Educ Program 2008;341-8.
73. Hummel M, Bentink S, Berger H, et al. A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling. New Engl J Med 2006;354:2419-30.
74. Klapper W, Szczepanowski M, Burkhardt B, et al. Molecular profiling of pediatric mature B-cell lymphoma treated in population-based prospective clinical trials. Blood 2008;112 1374-81.
75. Wellmann A, Thieblemont C, Pittaluga S, et al. Detection of differentially expressed genes in lymphomas using cDNA arrays: identification of clusterin as a new diagnostic marker for anaplastic large-cell lymphomas. Blood 2000;96:398-404.
76. Haferlach T, Kohlmann A, Basso G, et al. The clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: Final report on 3252 cases from the international MILE study group. ASH annual meeting abstracts,. Blood 2008;112:753.
77. Kohlmann A, Haschke-Becher E, Wimmer B, et al. Intraplatform reproducibility and technical precision of gene expression profiling in 4 laboratories investigating 160 leukemia samples: The DACH study. Clin Chem 2008; 54:1705-15.
78. Willman CL. Has gene expression profiling improved diagnosis, classification, and outcome prediction in AML? Best Pract Res Cl Ha 2008;21:21-8.
79. Kearney L, Horsley SW. Molecular cytogenetics in haematological malignancy: Current technology and future prospects. Chromosoma 2005;114:286-94.
80. Chen JS, Coustan-Smith E, Suzuki T, et al. Identification of novel markers for monitoring minimal residual disease in acute lymphoblastic leukemia. Blood 2001;97: 2115-20.
81. Steinbach D, Schramm A, Eggert A, et al. Identification of a set of seven genes for the monitoring of minimal residual disease in pediatric acute myeloid leukemia. Clin Cancer Res 2006;12 2434-41.
82. Baldus CD, Bullinger L. Gene expression with prognostic implications in cytogenetically normal acute myeloid leukemia. Semin Oncol 2008; 35:356-64.
83. Schlenk RF, Dohner K, Krauter J, et al. Mutations and treatment outcome in cytogenetically normal acute myeloid leukemia. New Engl J Med 2008;358:1909-18.
84. Stapnes C, Ryningen A, Hatfield K, et al. Functional characteristics and gene expression profiles of primary acute myeloid leukaemia cells identify patient subgroups that differ in susceptibility to histone deacetylase inhibitors. Int J Oncol 2007;31 1529-38.
85. Zembutsu H, Yanada M, Hishida A, et al. Prediction of risk of disease recurrence by genome-wide cDNA microarray analysis in patients with Philadelphia chromosome-positive acute lymphoblastic leukemia treated with imatinib-combined chemotherapy. Int J Oncol 2007; 31:313-22.
86. Holleman A, Cheok MH, den Boer ML, et al. Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment. New Engl J Med 2004;351:533-42.
87. Kohlmann A, Kipps TJ, Rassenti LZ, et al. An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: The Microarray Innovations in LEukemia study prephase. Br J Haematol 2008;142:802-7.
88. Maher CA, Kumar-Sinha C, Cao X, et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009; 458:97-101.
89. Gnirke A, Melnikov A, Maguire J, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009;27:182-9.
90. Ley TJ, Mardis ER, Ding L, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008;456:66-72.