Subclassification and individual survival time prediction from gene expression data of neuroblastoma patients by using CASPAR

Clinical Cancer Research

Volumn 14, Issue 20, 2008, Pages 6590-6601

  Oberthuer, Andreacute ^a   Kaderali, Lars ^b   Kahlert, Yvonne ^a   Hero, Barbara ^a   Westermann, Frank ^b   Berthold, Frank ^a   Brors, Benedikt ^b   Eils, Roland ^b   Fischer, Matthias ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ADULT; ARTICLE; CANCER RISK; CANCER SURVIVAL; CHILD; CLASSIFICATION ALGORITHM; DISEASE MARKER; GENE EXPRESSION; GENE EXPRESSION PROFILING; HIGH RISK PATIENT; HUMAN; INFANT; MAJOR CLINICAL STUDY; NEUROBLASTOMA; NEWBORN; PRESCHOOL CHILD; PRIORITY JOURNAL; RISK ASSESSMENT; SCHOOL CHILD; SURVIVAL TIME; TUMOR CLASSIFICATION; ALGORITHM; CANCER STAGING; CLINICAL TRIAL; COHORT ANALYSIS; DNA MICROARRAY; GENE AMPLIFICATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MORTALITY; MULTICENTER STUDY; PROGNOSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SURVIVAL RATE; TIME;

MESSENGER RNA; MYCN PROTEIN, HUMAN; NUCLEAR PROTEIN; ONCOPROTEIN; RNA; TUMOR MARKER; UNCLASSIFIED DRUG;

ADOLESCENT; ALGORITHMS; CHILD; CHILD, PRESCHOOL; COHORT STUDIES; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; INFANT; NEOPLASM STAGING; NEUROBLASTOMA; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ONCOGENE PROTEINS; PROGNOSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RISK ASSESSMENT; RNA, MESSENGER; RNA, NEOPLASM; SURVIVAL RATE; TIME FACTORS; TUMOR MARKERS, BIOLOGICAL;

EID: 58149190788     PISSN: 10780432     EISSN: None     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-07-4377     Document Type: Article

References (55)

1. Castleberry RP. Neuroblastoma. Eur J Cancer 1997;33:1430-8.
2. Evans AE, D'Angio GJ, Randolph J; Children's cancer study group A. A proposed staging for children with neuroblastoma. Cancer 1971;27:374-8.
3. Brodeur GM, Pritchard J, Berthold F, et al. Revisions of the international criteria for neuroblastoma diagnosis, staging, and response to treatment. J Clin Oncol 1993;11:1466-77.
4. Brodeur GM, Seeger RC, Schwab M, Varmus HE, Bishop JM. Amplification of N-myc in untreated human neuroblastomas correlates with advanced disease stage. Science 1984;224:1121-4.
5. Brodeur GM, Fong CT, Morita M, Griffith R, Hayes FA, Seeger RC. Molecular analysis and clinical significance of N-myc amplification and chromosome 1p monosomy in human neuroblastomas. Prog Clin Biol Res 1988;271:3-15.
6. Spitz R, Hero B, Ernestus K, Berthold F. Deletions in chromosome arms 3p and 11q are new prognostic markers in localized and 4s neuroblastoma. Clin Cancer Res 2003;9:52-8.
7. Bown N, Cotterill S, Lastowska M, et al. Gain of chro-mosome arm 17q and adverse outcome in patients with neuroblastoma. N Engl J Med 1999;340:1954-61.
8. Nakagawara A, Arima-Nakagawara M, Scavarda NJ, Azar CG, Cantor AB, Brodeur GM. Association between high levels of expression of the TRK gene and favorable outcome in human neuroblastoma. N Engl J Med 1993;328:847-54.
9. Favrot MC, Combaret V, Lasset C. CD44-a new prognostic marker for neuroblastoma. N Engl J Med 1993;329:1965.
10. Ohira M, Oba S, Nakamura Y, et al. Expression profiling using a tumor-specific cDNA microarray predicts the prognosis of intermediate risk neuroblastomas. Cancer Cell 2005;7:337-50.
11. Oberthuer A, Berthold F,Warnat P, et al. Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol 2006;24:5070-8.
12. Asgharzadeh S, Pique-Regi R, Sposto R, et al. Prognostic significance of gene expression profiles of metastatic neuroblastomas lacking MYCN gene amplification. J Natl Cancer Inst 2006;98:1193-203.
13. Wei JS, Greer BT, Westermann F, et al. Prediction of clinical outcome using gene expression profiling and artificial neural networks for patients with neuroblastoma. Cancer Res 2004;64:6883-91.
14. Kaderali L, Zander T, Faigle U, Wolf J, Schultze JL, Schrader R. CASPAR: a hierarchical Bayesian approach to predict survival times in cancer from gene expression data. Bioinformatics 2006;22:1495-502.
15. Spitz R, Hero B, Ernestus K, Berthold F. FISH analyses for alterations in chromosomes 1, 2, 3, and 11 define high-risk groups in neuroblastoma. Med Pediatr Oncol 2003;41:30-5.
16. Spitz R, Hero B, Ernestus K, Berthold F. Gain of distal chromosome arm 17q is not associated with poor prognosis in neuroblastoma. Clin Cancer Res 2003;9:4835-40.
17. Ambros PF, Ambros IM. Pathology and biology guidelines for resectable and unresectable neuroblastic tumors and bone marrow examination guidelines. Med Pediatr Oncol 2001;37:492-504.
18. Cheung NKV, Cohn S, editors. Neuroblastoma. New York: Springer; 2005.
19. Gentleman RC, Carey VJ, Bates DM, et al. Biocon-ductor: open software development for computational biology and bioinformatics. Genome Biol 2004;5:R80.
20. Buness A, Huber W, Steiner K, Sultmann H, Poustka A. array Magic: two-colour cDNA microarray quality control and preprocessing. Bio-informatics 2005;21:554-6.
21. Huber W, von Heydebreck A, Sultmann H, Poustka A,Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002;18 Suppl 1:S96-104.
22. Heagerty PJ, Lumley T, Pepe MS. Time-dependent ROC curves for censored survival data and a diagnostic marker. Biometrics 2000;56:337-44.
23. Schramm A, Schulte JH, Klein-Hitpass L, et al. Prediction of clinical outcome and biological characterization of neuroblastoma by expression profiling. Oncogene 2005;24:7902-12.
24. McArdle L, McDermott M, Purcell R, et al. Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q. Carcinogenesis 2004;25:1599-609.
25. Schwab M, Westermann F, Hero B, Berthold F. Neuroblastoma: biology and molecular and chromosomal pathology. Lancet Oncol 2003;4:472-80.
26. Wang Q, Diskin S, Rappaport E, et al. Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number. Cancer Res 2006;66:6050-62.
27. Fong CT, Dracopoli NC,White PS, et al. Loss of heterozygosity for the short arm of chromosome1 in human neuroblastomas: correlation with N-myc amplification. Proc Natl Acad Sci U S A 1989;86:3753-7.
28. Attiyeh EF, London WB, Mosse YP, et al. Chromo-some1p and 11q deletions and outcome in neuroblastoma. N Engl J Med 2005;353:2243-53.
29. Vandesompele J, Baudis M, De Preter K, et al.Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma. J Clin Oncol 2005;23:2280-99.
30. George RE, Attiyeh EF, Li S, et al. Genome-wide analysis of neuroblastomas using high-density single nucleotide polymorphism arrays. PLoS ONE 2007;2:e255.
31. Lastowska M, Cotterill S, Bown N, et al. Breakpoint position on 17q identifies the most aggressive neuroblastoma tumors. Genes Chromosomes Cancer 2002;34:428-36.
32. Chavakis T, Cines DB, Rhee JS, et al. Regulation of neovascularization by human neutrophil peptides (α-defensins): a link between inflammation and angiogenesis. FASEB J 2004;18:1306-8.
33. Huang S, Mills L, Mian B, et al. Fully humanized neutralizing antibodies to interleukin-8 (ABX-IL8) inhibit angiogenesis, tumor growth, and metastasis of human melanoma. Am J Pathol 2002;161:125-34.
34. Sharma MR, Koltowski L, Ownbey RT, Tuszynski GP, Sharma MC. Angiogenesis-associated protein Annexin II in breast cancer: selective expression in invasive breast cancer and contribution to tumor invasion and progression. Exp Mol Pathol 2006;81:146-56.
35. Tahara E, Jr., Tahara H, Kanno M, et al. G1P3,aninterferon inducible gene 6-16, is expressed in gastric cancers and inhibits mitochondrial-mediated apoptosis in gastric cancer cell lineTMK-1 cell. Cancer Immunol Immunother 2005;54:729-40.
36. Huang J, Tan PH, Thiyagarajan J, Bay BH. Prognostic significance of glutathione S-transferase-pi in invasive breast cancer. Mod Pathol 2003;16:558-65.
37. Shureiqi I, Jiang W, Fischer SM, et al. GATA-6 transcriptional regulation of 15-lipoxygenase-1 during NSAID-induced apoptosis in colorectal cancer cells. Cancer Res 2002;62:1178-83.
38. Niakan KK, McCabe ER. DAX1 origin, function, and novel role. Mol Genet Metab 2005;86:70-83.
39. Fujita T, Maturana AD, Ikuta J, et al. Axonal guidance protein FEZ1associates with tubulin and kinesin motor protein to transport mitochondria in neurites of NGF-stimulated PC12 cells. Biochem Biophys Res Commun 2007;361:605-10.
40. IkutaJ, Maturana A, FujitaT, et al. Fasciculation and elongation protein ζ-1 (FEZ1) participates in the polarization of hippocampal neuron bycontrolling the mitochondrial motility. Biochem Biophys Res Commun 2007;353:127-32.
41. Tonini GP, Casalaro A, Cara A, Di Martino D. Inducible expression of calcyclin, a gene with strong homology to S-100 protein, during neuroblastoma cell differentiation and its prevalent expression in Schwann-like cell lines. Cancer Res1991;51:1733-7.
42. Obata T, Toyota M, Satoh A, et al. Identification of HRK as a target of epigenetic inactivation in colorectal and gastric cancer. Clin Cancer Res 2003;9:6410-8.
43. Lang SH, Hyde C, Reid IN, et al. Enhanced expression of vimentin in motile prostate cell lines and in poorly differentiated and metastatic prostate carcinoma. Prostate 2002;52:253-63.
44. Che Y, Luo A, Wang H, Qi J, Guo J, Liu Z. The differential expression of SPARC in esophageal squamous cell carcinoma. Int J Mol Med 2006;17:1027-33.
45. Wang CS, Lin KH, Chen SL, Chan YF, Hsueh S. Overexpression of SPARC gene in human gastric carcinoma and its clinic-pathologic significance. Br J Cancer 2004;91:1924-30.
46. Watkins G, Douglas-Jones A, Bryce R, Mansel RE, Jiang WG. Increased levels of SPARC (osteonectin) in human breast cancer tissues and its association with clinical outcomes. Prostaglandins Leukot Essent Fatty Acids 2005;72:267-72.
47. Shureiqi I, Zuo X, Broaddus R, et al. The transcription factor GATA-6 is overexpressed in vivo and contributes to silencing 15-LOX-1 in vitro in human colon cancer. FASEB J 2007;21:743-53.
48. Huang G, Mills L,Worth LL. Expression of human glutathione S-transferase P1 mediates the chemosensitivity of osteosarcoma cells. Mol Cancer Ther 2007;6:1610-9.
49. Benoy IH, Salgado R, Van Dam P, et al. Increased serum interleukin-8 in patients with early and metastatic breast cancer correlates with early dissemination and survival. Clin Cancer Res 2004;10:7157-62.
50. Oberthuer A, Hero B, Spitz R, Berthold F, Fischer M. The tumor-associated antigen PRAME is universally expressed in high-stage neuroblastoma and associated with poor outcome. Clin Cancer Res 2004;10:4307-13.
51. Osajima-Hakomori Y, Miyake I, Ohira M, Nakagawara A, Nakagawa A, Sakai R. Biological role of anaplastic lymphoma kinase in neuroblastoma. Am J Pathol 2005;167:213-22.
52. Lamant L, Pulford K, Bischof D, et al. Expression of the ALK tyrosine kinase gene in neuroblastoma. Am J Pathol 2000;156:1711-21.
53. Calvet L, Geoerger B, Regairaz M, et al. Pleiotrophin, a candidate gene for poor tumor vasculature and in vivo neuroblastoma sensitivity to irinotecan. Oncogene 2006;25:3150-9.
54. Nakagawara A, Milbrandt J, Muramatsu T, et al. Differential expression of pleiotrophin and midkine in advanced neuroblastomas. Cancer Res 1995;55:1792-7.
55. Pulford K, Lamant L, Espinos E, et al. The emerging normal and disease-related roles of anaplastic lymphoma kinase. Cell Mol Life Sci 2004;61:2939-53.