Integrated genomic profiling identifies two distinct molecular subtypes with divergent outcome in neuroblastoma with loss of chromosome 11q

Oncogene

Volumn 29, Issue 6, 2010, Pages 865-875

  Fischer, M ^a   Bauer, T ^b,c   Oberthur A ^a   Hero, B ^a   Theissen, J ^a   Ehrich, M ^d   Spitz, R ^a   Eils, R ^b,c   Westermann, F ^c   Brors, B ^c   Konig R ^b,c   Berthold, F ^a  

^a UNIVERSITY HOSPITAL OF COLOGNE   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^d SEQUENOM INC   (United States)

Author keywords

Cancer; Gene expression; Integrative genomics; Loss of 11q; Neuroblastoma; Outcome

Indexed keywords

MESSENGER RNA;

ARTICLE; CHROMOSOME 11Q; CHROMOSOME 1P; CHROMOSOME LOSS; GENE AMPLIFICATION; GENE CONTROL; GENE DELETION; GENE EXPRESSION PROFILING; HUMAN; MAJOR CLINICAL STUDY; METHYLATION; NEUROBLASTOMA; ONCOGENE C MYB; PHENOTYPIC PLASTICITY; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTOMICS;

CHILD, PRESCHOOL; CHROMOSOME DELETION; CHROMOSOMES, HUMAN, PAIR 11; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HUMANS; METHYLATION; NEUROBLASTOMA; PROGNOSIS; PROMOTER REGIONS, GENETIC;

EID: 76849106660     PISSN: 09509232     EISSN: 14765594     Source Type: Journal    
DOI: 10.1038/onc.2009.390     Document Type: Article

References (40)

1. Alaminos M, Mora J, Cheung NK, Smith A, Qin J, Chen L et al. (2003). Genome-wide analysis of gene expression associated with MYCN in human neuroblastoma. Cancer Res 63: 4538-4546.
2. Ambros PF, Ambros IM. (2001). Pathology and biology guidelines for resectable and unresectable neuroblastic tumors and bone marrow examination guidelines. Med Pediatr Oncol 37: 492-504.
3. Asgharzadeh S, Pique-Regi R, Sposto R, Wang H, Yang Y, Shimada H et al. (2006). Prognostic significance of gene expression profiles of metastatic neuroblastomas lacking MYCN gene amplification. J Natl Cancer Inst 98: 1193-1203.
4. Attiyeh EF, London WB, Mosse YP, Wang Q, Winter C, Khazi D et al. (2005). Chromosome 1p and 11q deletions and outcome in neuroblastoma. N Engl J Med 353: 2243-2253.
5. Berwanger B, Hartmann O, Bergmann E, Bernard S, Nielsen D, Krause M et al. (2002). Loss of a FYN-regulated differentiation and growth arrest pathway in advanced stage neuroblastoma. Cancer Cell 2: 377-386.
6. Bilke S, Chen QR, Westerman F, Schwab M, Catchpoole D, Khan J. (2005). Inferring a tumor progression model for neuroblastoma from genomic data. J Clin Oncol 23: 7322-7331.
7. Boon K, Caron HN, van Asperen R, Valentijn L, Hermus MC, van Sluis P et al. (2001). N-myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis. EMBO J 20: 1383-1393.
8. Brodeur GM. (2003). Neuroblastoma: biological insights into a clinical enigma. Nat Rev Cancer 3: 203-216.
9. Chen W, Salto-Tellez M, Palanisamy N, Ganesan K, Hou Q, Tan LK et al. (2007). Targets of genome copy number reduction in primary breast cancers identified by integrative genomics. Genes Chromosomes Cancer 46: 288-301.
10. Classen S, Zander T, Eggle D, Chemnitz JM, Brors B, Buchmann I et al. (2007). Human resting CD4+ T cells are constitutively inhibited by TGF beta under steady-state conditions. J Immunol 178: 6931-6940.
11. Cohn SL, Pearson AD, London WB, Monclair T, Ambros PF, Brodeur GM et al. (2009). The International Neuroblastoma Risk Group (INRG) classification system: an INRG Task Force report. J Clin Oncol 27: 289-297.
12. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G et al. (2005). Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 102: 15785-15790.
13. Fischer M, Oberthuer A, Brors B, Kahlert Y, Skowron M, Voth H et al. (2006). Differential expression of neuronal genes defines subtypes of disseminated neuroblastoma with favorable and unfavorable outcome. Clin Cancer Res 12: 5118-5128.
14. Fischer M, Spitz R, Oberthur A, Westermann F, Berthold F. (2008). Risk estimation of neuroblastoma patients using molecular markers. Klin Padiatr 220: 137-146.
15. Gallegos Ruiz MI, Floor K, Roepman P, Rodriguez JA, Meijer GA, Mooi WJ et al. (2008). Integration of gene dosage and gene expression in non-small cell lung cancer, identification of HSP90 as potential target. PLoS ONE 3: e0001722.
16. Henrich KO, Fischer M, Mertens D, Benner A, Wiedemeyer R, Brors B et al. (2006). Reduced expression of CAMTA1 correlates with adverse outcome in neuroblastoma patients. Clin Cancer Res 12: 131-138.
17. Huang J, Sheng HH, Shen T, Hu YJ, Xiao HS, Zhang Q et al. (2006). Correlation between genomic DNA copy number alterations and transcriptional expression in hepatitis B virus-associated hepatocel-lular carcinoma. FEBS Lett 580: 3571-3581.
18. Janoueix-Lerosey I, Schleiermacher G, Michels E, Mosseri V, Ribeiro A, Lequin D et al. (2009). Overall genomic pattern is a predictor of outcome in neuroblastoma. J Clin Oncol 27: 1026-1033.
19. Lastowska M, Viprey V, Santibanez-Koref M, Wappler I, Peters H, Cullinane C et al. (2007). Identification of candidate genes involved in neuroblastoma progression by combining genomic and expression microarrays with survival data. Oncogene 26: 7432-7444.
20. Maris JM, Hogarty MD, Bagatell R, Cohn SL. (2007). Neuroblastoma. Lancet 369: 2106-2120.
21. McArdle L, McDermott M, Purcell R, Grehan D, O'Meara A, Breatnach F et al. (2004). Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q. Carcinogenesis 25: 1599-1609.
22. Mosse YP, Diskin SJ, Wasserman N, Rinaldi K, Attiyeh EF, Cole K et al. (2007). Neuroblastomas have distinct genomic DNA profiles that predict clinical phenotype and regional gene expression. Genes Chromosomes Cancer 46: 936-949.
23. Mosse YP, Laudenslager M, Longo L, Cole KA, Wood A, Attiyeh EF et al. (2008). Identification of ALK as a major familial neuroblas-toma predisposition gene. Nature 455: 930-935.
24. Nigro JM, Misra A, Zhang L, Smirnov I, Colman H, Griffin C et al. (2005). Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma. Cancer Res 65: 1678-1686.
25. Oberthuer A, Berthold F, Warnat P, Hero B, Kahlert Y, Spitz R et al. (2006). Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol 24: 5070-5078.
26. Oberthuer A, Kaderali L, Kahlert Y, Hero B, Westermann F, Berthold F et al. (2008). Subclassification and individual survival time prediction from gene expression data of neuroblastoma patients by using CASPAR. Clin Cancer Res 14: 6590-6601.
27. Ohira M, Oba S, Nakamura Y, Isogai E, Kaneko S, Nakagawa A et al. (2005). Expression profiling using a tumor-specific cDNA micro-array predicts the prognosis of intermediate risk neuroblastomas. Cancer Cell 7: 337-350.
28. Platzer P, Upender MB, Wilson K, Willis J, Lutterbaugh J, Nosrati A et al. (2002). Silence of chromosomal amplifications in colon cancer. Cancer Res 62: 1134-1138.
29. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE et al. (2002). Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 99: 12963-12968.
30. Potter N, Karakoula A, Phipps KP, Harkness W, Hayward R, Thompson DN et al. (2008). Genomic deletions correlate with underexpression of novel candidate genes at six loci in pediatric pilocytic astrocytoma. Neoplasia 10: 757-772.
31. Savelyeva L, Schwab M. (2001). Amplification of oncogenes revisited: from expression profiling to clinical application. Cancer Lett 167: 115-123.
32. Spitz R, Hero B, Ernestus K, Berthold F. (2003). Deletions in chromosome arms 3p and 11q are new prognostic markers in localized and 4s neuroblastoma. Clin Cancer Res 9: 52-58.
33. Spitz R, Hero B, Simon T, Berthold F. (2006a). Loss in chromosome 11q identifies tumors with increased risk for metastatic relapses in localized and 4S neuroblastoma. Clin Cancer Res 12: 3368-3373.
34. Spitz R, Oberthuer A, Zapatka M, Brors B, Hero B, Ernestus K et al. (2006b). Oligonucleotide array-based comparative genomic hybridization (aCGH) of 90 neuroblastomas reveals aberration patterns closely associated with relapse pattern and outcome. Genes Chromosomes Cancer 45: 1130-1142.
35. Stallings RL. (2007). Origin and functional significance of large-scale chromosomal imbalances in neuroblastoma. Cytogenet Genome Res 118: 110-115.
36. Stallings RL, Nair P, Maris JM, Catchpoole D, McDermott M, O'Meara A et al. (2006). High-resolution analysis of chromosomal breakpoints and genomic instability identifies PTPRD as a candidate tumor suppressor gene in neuroblastoma. Cancer Res 66: 3673-3680.
37. Tusher VG, Tibshirani R, Chu G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121.
38. Wang Q, Diskin S, Rappaport E, Attiyeh E, Mosse Y, Shue D et al. (2006). Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number. Cancer Res 66: 6050-6062.
39. Westermann F, Muth D, Benner A, Bauer T, Henrich KO, Oberthuer A et al. (2008). Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. Genome Biol 9: R150.
40. Yoshimoto T, Matsuura K, Karnan S, Tagawa H, Nakada C, Tanigawa M et al. (2007). High-resolution analysis of DNA copy number alterations and gene expression in renal clear cell carcinoma. J Pathol 213: 392-401.