Gene expression profile alone is inadequate in predicting complete response in multiple myeloma

Leukemia

Volumn 28, Issue 11, 2014, Pages 2229-2234

  Amin, S B ^a,b   Yip, W K ^c   Minvielle, S ^d,e   Broyl, A ^f   Li, Y ^g   Hanlon, B ^h   Swanson, D ^c   Shah, P K ^a,c   Moreau, P ^d,e   Van Der Holt, B ^f   Van Duin, M ^f   Magrangeas, F ^d,e   Pieter Sonneveld, P ^d,e   Anderson, K C ^a   Li, C ^a,c   Avet Loiseau, H ^d,e   Munshi, N C ^a,b  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^d Service d'urologie Université et Hôpital de Nantes   (France)

^e UNIVERSITÉ DE NANTES   (France)

^f ERASMUS MEDICAL CENTER   (Netherlands)

^g UNIVERSITY OF MICHIGAN   (United States)

^h University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BORTEZOMIB; DEXAMETHASONE;

ARTICLE; AUTOLOGOUS STEM CELL TRANSPLANTATION; CANCER CELL; CANCER CHEMOTHERAPY; CANCER RECURRENCE; CANCER TRANSPLANTATION; CLINICAL TRIAL (TOPIC); GENE EXPRESSION PROFILING; GENOMICS; HUMAN; HUMAN CELL; MACHINE LEARNING; MAJOR CLINICAL STUDY; MEASUREMENT ACCURACY; MICROARRAY ANALYSIS; MULTIPLE MYELOMA; PREDICTION; PREDICTIVE VALIDITY; PREDICTIVE VALUE; PRIORITY JOURNAL; TREATMENT RESPONSE;

EID: 84999605219     PISSN: 08876924     EISSN: 14765551     Source Type: Journal    
DOI: 10.1038/leu.2014.140     Document Type: Article

References (59)

1. Laubach J, Richardson P, Anderson K. Multiple myeloma. Annu Rev Med 2011; 62: 249-264.
2. DeVita VT, Hellman S, Rosenberg SA. Cancer, Principles & Practice of Oncology. 7th edn Lippincott Williams & Wilkins: Philadelphia, PA, 2005.
3. Kyle RA, Rajkumar SV. An overview of the progress in the treatment of multiple myeloma. Expert Re Hematol 2014; 7: 5-7.
4. Anderson KC. Therapeutic advances in relapsed or refractory multiple myeloma. J Natl Compr Cancer Netw 2013; 11(5 Suppl): 676-679.
5. Ludwig H, Miguel JS, Dimopoulos MA, Palumbo A, Garcia Sanz R, Powles R et al. International Myeloma Working Group recommendations for global myeloma care. Leukemia 2014; 28: 981-992.
6. Barlogie B, Shaughnessy J, Tricot G, Jacobson J, Zangari M, Anaissie E et al. Treatment of multiple myeloma. Blood 2004; 103: 20-32.
7. Rajkumar IV SV. Initial treatment of multiple myeloma. Hematol Oncol 2013; 31(Suppl 1): 33-37.
8. Berenson JR, Yang HH, Vescio RA, Nassir Y, Mapes R, Lee SP et al. Safety and efficacy of bortezomib and melphalan combination in patients with relapsed or refractory multiple myeloma: updated results of a phase 1/2 study after longer follow-up. Ann Hematol 2008; 87: 623-631.
9. Gay F, Hayman SR, Lacy MQ, Buadi F, Gertz MA, Kumar S et al. Lenalidomide plus dexamethasone versus thalidomide plus dexamethasone in newly diagnosed multiple myeloma: a comparative analysis of 411 patients. Blood 2010; 115: 1343-1350.
10. Jagannath S, Barlogie B, Berenson JR, Siegel DS, Irwin D, Richardson PG et al. Updated survival analyses after prolonged follow-up of the phase 2, multicenter CREST study of bortezomib in relapsed or refractory multiple myeloma. Br J Haematol 2008; 143: 537-540.
11. Munshi NC, Anderson KC. New strategies in the treatment of multiple myeloma. Clin Cancer Res 2013; 19: 3337-3344.
12. McCarthy PL, Owzar K, Hofmeister CC, Hurd DD, Hassoun H, Richardson PG et al. Lenalidomide after stem-cell transplantation for multiple myeloma. N Engl J Med 2012; 366: 1770-1781.
13. Attal M, Lauwers-Cances V, Marit G, Caillot D, Moreau P, Facon T et al. Lenalidomide maintenance after stem-cell transplantation for multiple myeloma. N Engl J Med 2012; 366: 1782-1791.
14. Mateos MV, Hernandez MT, Giraldo P, de la Rubia J, de Arriba F, Lopez Corral L et al. Lenalidomide plus dexamethasone for high-risk smoldering multiple myeloma. N Engl J Med 2013; 369: 438-447.
15. Barlogie B, Kyle RA, Anderson KC, Greipp PR, Lazarus HM, Hurd DD et al. Standard chemotherapy compared with high-dose chemoradiotherapy for multiple myeloma: final results of phase III US Intergroup Trial S9321. J Clin Oncol 2006; 24: 929-936.
16. Kyle RA, Rajkumar SV. Treatment of multiple myeloma: a comprehensive review. Clin Lymphoma Myeloma 2009; 9: 278-288.
17. Kumar SK, Rajkumar SV. The current status of minimal residual disease assessment in myeloma. Leukemia 2014; 28: 239-240.
18. Bergsagel PL, Kuehl WM. Molecular pathogenesis and a consequent classification of multiple myeloma. J Clin Oncol 2005; 23: 6333-6338.
19. Hideshima T, Mitsiades C, Tonon G, Richardson PG, Anderson KC. Understanding multiple myeloma pathogenesis in the bone marrow to identify new therapeutic targets. Nat Rev Cancer 2007; 7: 585-598.
20. Ocio EM, Richardson PG, Rajkumar SV, Palumbo A, Mateos MV, Orlowski R et al. New drugs and novel mechanisms of action in multiple myeloma in 2013: a report from the International Myeloma Working Group (IMWG). Leukemia 2013; 3: 525-542.
21. Ghadimi BM, Grade M. Cancer gene profiling for response prediction. Methods Mol Biol 2010; 576: 327-339.
22. Jensen EH, McLoughlin JM, Yeatman TJ. Microarrays in gastrointestinal cancer: is personalized prediction of response to chemotherapy at hand? Curr Opin Oncol 2006; 18: 374-380.
23. Mariadason JM, Arango D, Shi Q, Wilson AJ, Corner GA, Nicholas C et al. Gene expression profiling-based prediction of response of colon carcinoma cells to 5-fluorouracil and camptothecin. Cancer Res 2003; 63: 8791-8812.
24. Nagasaki K, Miki Y. Molecular prediction of the therapeutic response to neoadjuvant chemotherapy in breast cancer. Breast Cancer 2008; 15: 117-120.
25. Schauer M, Janssen KP, Rimkus C, Raggi M, Feith M, Friess H et al. Microarraybased response prediction in esophageal adenocarcinoma. Clin Cancer Res 2010; 16: 330-337.
26. Anguiano A, Tuchman SA, Acharya C, Salter K, Gasparetto C, Zhan F et al. Gene expression profiles of tumor biology provide a novel approach to prognosis and may guide the selection of therapeutic targets in multiple myeloma. J Clin Oncol 2009; 27: 4197-4203.
27. Decaux O, Lode L, Magrangeas F, Charbonnel C, Gouraud W, Jezequel P et al. Prediction of survival in multiple myeloma based on gene expression profiles reveals cell cycle and chromosomal instability signatures in high-risk patients and hyperdiploid signatures in low-risk patients: a study of the Intergroupe Francophone du Myelome. J Clin Oncol 2008; 26: 4798-4805.
28. Moreaux J, Klein B, Bataille R, Descamps G, Maiga S, Hose D et al. A high-risk signature for patients with multiple myeloma established from the molecular classification of human myeloma cell lines. Haematologica 2011; 96: 574-582.
29. Zhan F, Huang Y, Colla S, Stewart JP, Hanamura I, Gupta S et al. The molecular classification of multiple myeloma. Blood 2006; 108: 2020-2028.
30. Zhan F, Barlogie B, Arzoumanian V, Huang Y, Williams DR, Hollmig K et al. Geneexpression signature of benign monoclonal gammopathy evident in multiple myeloma is linked to good prognosis. Blood 2007; 109: 1692-1700.
31. Zhan F, Barlogie B, Mulligan G, Shaughnessy Jr JD, Bryant B. High-risk myeloma: a gene expression based risk-stratification model for newly diagnosed multiple myeloma treated with high-dose therapy is predictive of outcome in relapsed disease treated with single-agent bortezomib or high-dose dexamethasone. Blood 2008; 111: 968-969.
32. Mulligan G, Mitsiades C, Bryant B, Zhan F, Chng WJ, Roels S et al. Gene expression profiling and correlation with outcome in clinical trials of the proteasome inhibitor bortezomib. Blood 2007; 109: 3177-3188.
33. Minna JD, Girard L, Xie Y. Tumor mRNA expression profiles predict responses to chemotherapy. J Clin Oncol 2007; 25: 4329-4336.
34. Kumar SGP, Haug J, Kline M, Chng WJ, Blood E, Bergsagel L et al. Gene expression profiling of myeloma cells at diagnosis can predict response to therapy with thalidomide and dexamethasone combination. Blood 2005 508.
35. Broyl A, Hose D, Lokhorst H, de Knegt Y, Peeters J, Jauch A et al. Gene expression profiling for molecular classification of multiple myeloma in newly diagnosed patients. Blood 2010; 116: 2543-2553.
36. Blade J, Samson D, Reece D, Apperley J, Bjorkstrand B, Gahrton G et al. Criteria for evaluating disease response and progression in patients with multiple myeloma treated by high-dose therapy and haemopoietic stem cell transplantation. Myeloma Subcommittee of the EBMT. European Group for Blood and Marrow Transplant. Br J Haematol 1998; 102: 1115-1123.
37. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 2001; 98: 31-36.
38. Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, Speed TP. FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics 2008; 24: 1707-1714.
39. Dimitriadou E HK, Leisch F, Meyer D, Weingessel A. CRAN - Package e1071 Webcite 2005.
40. Yip WK, Amin SB, Li C. A survey of classification techniques for microarray data analysis. In: HH-S Lu, B Scholkopf, H Zhao (eds). Handbook of Computational Statistics: Statistical Bioinformatics, 2011, pp 193-224 (Chapter 10). http://www.springer.com/statistics/book/978-3-642-16344-9.
41. Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 1999; 96: 9212-9217.
42. Munshi NC, Anderson KC, Bergsagel PL, Shaughnessy J, Palumbo A, Durie B et al. Consensus recommendations for risk stratification in multiple myeloma: report of the International Myeloma Workshop Consensus Panel 2. Blood 2011; 117: 4696-4700.
43. Avet-Loiseau H, Attal M, Moreau P, Charbonnel C, Garban F, Hulin C et al. Genetic abnormalities and survival in multiple myeloma: the experience of the Intergroupe Francophone du Myelome. Blood 2007; 109: 3489-3495.
44. Dimopoulos M, Kyle R, Fermand JP, Rajkumar SV, San Miguel J, Chanan-Khan A et al. Consensus recommendations for standard investigative workup: report of the International Myeloma Workshop Consensus Panel 3. Blood 2011; 117: 4701-4705.
45. Sorlie T, Perou CM, Fan C, Geisler S, Aas T, Nobel A et al. Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer. Mol Cancer Ther 2006; 5: 2914-2918.
46. Simon R, Radmacher MD, Dobbin K, McShane LM. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003; 95: 14-18.
47. Kuiper R, Broyl A, de Knegt Y, van Vliet MH, van Beers EH, van der Holt B et al. A gene expression signature for high-risk multiple myeloma. Leukemia 2012; 26: 2406-2413.
48. Shaughnessy Jr JD, Zhan F, Burington BE, Huang Y, Colla S, Hanamura I et al. A validated gene expression model of high-risk multiple myeloma is defined by deregulated expression of genes mapping to chromosome 1. Blood 2007; 109: 2276-2284.
49. Chen Z, Yan B, Van Waes C. The role of the NF-kappaB transcriptome and proteome as biomarkers in human head and neck squamous cell carcinomas. Biomark Med 2008; 2: 409-426.
50. Zheng PZ, Wang KK, Zhang QY, Huang QH, Du YZ, Zhang QH et al. Systems analysis of transcriptome and proteome in retinoic acid/arsenic trioxide-induced cell differentiation/apoptosis of promyelocytic leukemia. Proc Natl Acad Sci USA 2005; 102: 7653-7658.
51. Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 2003; 72: 291-336.
52. David CJ, Manley JL. Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev 2010; 24: 2343-2364.
53. Venables JP. Aberrant and alternative splicing in cancer. Cancer Res 2004; 64: 7647-7654.
54. Avet-Loiseau H, Li C, Magrangeas F, Gouraud W, Charbonnel C, Harousseau JL et al. Prognostic significance of copy-number alterations in multiple myeloma. J Clin Oncol 2009; 27: 4585-4590.
55. Walker BA, Leone PE, Chiecchio L, Dickens NJ, Jenner MW, Boyd KD et al. A compendium of myeloma-associated chromosomal copy number abnormalities and their prognostic value. Blood 2010; 116: e56-e65.
56. Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I et al. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun 2014; 5: 2997.
57. Lohr JG, Stojanov P, Carter SL, Cruz-Gordillo P, Lawrence MS, Auclair D et al. Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy. Cancer Cell 2014; 25: 91-101.
58. Catchpoole DR, Kennedy P, Skillicorn DB, Simoff S. The curse of dimensionality: a blessing to personalized medicine. J Clin Oncol 2010; 28: e723-e724; author reply e725.
59. Michiels S, Kramar A, Koscielny S. Multidimensionality of microarrays: statistical challenges and (im)possible solutions. Mol Oncol 2011; 5: 190-196.