High-resolution genomic copy number profiling of glioblastoma multiforme by single nucleotide polymorphism DNA microarray

Molecular Cancer Research

Volumn 7, Issue 5, 2009, Pages 665-677

  Yin, Dong ^a   Ogawa, Seishi ^b   Kawamata, Norihiko ^a   Tunici, Patrizia ^a   Finocchiaro, Gaetano ^c   Eoli, Marica ^c   Ruckert, Christian ^e   Huynh, Thien ^a   Liu, Gentao ^a   Kato, Motohiro ^b   Sanada, Masashi ^b   Jauch, Anna ^d   Dugas, Martin ^e   Black, Keith L ^a   Koeffler, H Phillip ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF TOKYO   (Japan)

^c DEPARTMENT OF NEUROSURGERY   (Italy)

^d UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^e UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE 4; CYCLIN DEPENDENT KINASE 6; CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; EPIDERMAL GROWTH FACTOR RECEPTOR; GENOMIC DNA; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PLATELET DERIVED GROWTH FACTOR ALPHA RECEPTOR; PROTEIN MDM2; PROTEIN MDMX; PROTEIN P14; PROTEIN P53; RETINOBLASTOMA PROTEIN; VASCULOTROPIN;

ADULT; AGED; ARTICLE; CHROMOSOME 13Q; CHROMOSOME 17P; CHROMOSOME 1P; CHROMOSOME 6Q; CHROMOSOME DELETION; CONTROLLED STUDY; DNA MICROARRAY; EXPLANT; FEMALE; GENE AMPLIFICATION; GENE DELETION; GENE DUPLICATION; GENE EXPRESSION; GENE FREQUENCY; GENE MUTATION; GLIOBLASTOMA; HETEROZYGOSITY LOSS; HOMOZYGOSITY; HUMAN; HUMAN CELL; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; MICROSATELLITE MARKER; MITOTIC RECOMBINATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION; SIGNAL TRANSDUCTION; SINGLE STRAND CONFORMATION POLYMORPHISM; SURVIVAL TIME; TUMOR SUPPRESSOR GENE; UNIPARENTAL DISOMY;

ADOLESCENT; ADULT; AGED; AMINO ACID SEQUENCE; BASE SEQUENCE; CELL LINE, TUMOR; FEMALE; GENE AMPLIFICATION; GENE DOSAGE; GLIOBLASTOMA; HUMANS; LOSS OF HETEROZYGOSITY; MALE; MIDDLE AGED; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; SIGNAL TRANSDUCTION; UNIPARENTAL DISOMY; YOUNG ADULT;

EID: 66349133436     PISSN: 15417786     EISSN: None     Source Type: Journal    
DOI: 10.1158/1541-7786.MCR-08-0270     Document Type: Article

References (63)

1. Schmidt EE, Ichimura K, Reifenberger G, Collins VP. CDKN2 (p16/MTS1) gene deletion or CDK4 amplification occurs in the majority of glioblastomas. Cancer Res 1994;54:6321-6324
2. Ueki K, Ono Y, Henson JW, Efird JT, von Deimling A, Louis DN. CDKN2/ p16 or RB alterations occur in the majority of glioblastomas and are inversely correlated. Cancer Res 1996;56:150-153 (Pubitemid 26010393)
3. Ohgaki H, Dessen P, Jourde B, et al. Genetic pathways to glioblastoma: a population-based study. Cancer Res 2004;64:6892-6899 (Pubitemid 39330996)
4. McLendon R, Friedman A, Bigner D, et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008;1061-1068
5. Merlo A, Herman JG, Mao L, et al. 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nat Med 1995;1:686-692
6. Nishikawa R, Furnari FB, Lin H, et al. Loss of P16INK4 expression is frequent in high grade gliomas. Cancer Res 1995;55:1941-1945
7. Arap W, Nishikawa R, Furnari FB, Cavenee WK, Huang HJ. Replacement of the p16/CDKN2 gene suppresses human glioma cell growth. Cancer Res 1995; 55:1351-1354
8. Henson JW, Schnitker BL, Correa KM, et al. The retinoblastoma gene is involved in malignant progression of astrocytomas. Ann Neurol 1994;36:714-721 (Pubitemid 24337629)
9. von Deimling A, Louis DN, von Ammon K, et al. Association of epidermal growth factor receptor gene amplification with loss of chromosome 10 in human glioblastoma multiforme. J Neurosurg 1992;77:295-301.
10. Duerr EM, Rollbrocker B, Hayashi Y, et al. PTEN mutations in gliomas and glioneuronal tumors. Oncogene 1998;16:2259-2264 (Pubitemid 28220656)
11. Li J, Yen C, Liaw D, et al. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 1997;275:1943-1947 (Pubitemid 27148818)
12. Steck PA, Pershouse MA, Jasser SA, et al. Identification of a candidate tumour suppressor gene, MMAC1, at chromosome 10q23.3 that is mutated in multiple advanced cancers. Nat Genet 1997;15:356-362 (Pubitemid 27147102)
13. Narita Y, Nagane M, Mishima K, Huang HJ, Furnari FB, Cavenee WK. Mutant epidermal growth factor receptor signaling down-regulates p27 through activation of the phosphatidylinositol 3-kinase/Akt pathway in glioblastomas. Cancer Res 2002;62:6764-6769 (Pubitemid 35364149)
14. Hayashi Y, Ueki K, Waha A, Wiestler OD, Louis DN, von Deimling A. Association of EGFR gene amplification and CDKN2 (p16/MTS1) gene deletion in glioblastoma multiforme. Brain Pathol 1997;7:871-875 (Pubitemid 27346731)
15. Roerig P, Nessling M, Radlwimmer B, et al. Molecular classification of human gliomas using matrix-based comparative genomic hybridization. Int J Cancer 2005;117:95-103. (Pubitemid 41262763)
16. Bourdon V, Plessis G, Chapon F, Guarnieri J, Derlon JM, Jonveaux P. Chromosome imbalances in oligodendroglial tumors detected by comparative genomic hybridization. Ann Genet 2004;47:105-111 (Pubitemid 38748492)
17. Paunu N, Sallinen SL, Karhu R, et al. Chromosome imbalances in familial gliomas detected by comparative genomic hybridization. Genes Chromosomes Cancer 2000;29:339-346
18. Kotliarov Y, Steed ME, Christopher N, et al. High-resolution global genomic survey of 178 gliomas reveals novel regions of copy number alteration and allelic imbalances. Cancer Res 2006;66:9428-9436 (Pubitemid 44623639)
19. Zhao X, Li C, Paez JG, et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004;64:3060-3071 (Pubitemid 38581405)
20. Blagosklonny MV. p53 from complexity to simplicity: mutant p53 stabilization, gain-of-function, and dominant-negative effect. FASEB J 2000;14:1901-1907
21. Kim E, Deppert W. Transcriptional activities of mutant p53: when mutations are more than a loss. J Cell Biochem 2004;93:878-886 (Pubitemid 44264143)
22. Lang GA, Iwakuma T, Suh YA, et al. Gain of function of a p53 hot spot mutation in a mouse model of Li-Fraumeni syndrome. Cell 2004;119:861-872 (Pubitemid 40017691)
23. Bossi G, Lapi E, Strano S, Rinaldo C, Blandino G, Sacchi A. Mutant p53 gain of function: reduction of tumor malignancy of human cancer cell lines through abrogation of mutant p53 expression. Oncogene 2006;25:304-309 (Pubitemid 43083692)
24. Olive KP, Tuveson DA, Ruhe ZC, et al. Mutant p53 gain of function in two mouse models of Li-Fraumeni syndrome. Cell 2004;119:847-860 (Pubitemid 40017690)
25. Heinlein C, Krepulat F, Lohler J, Speidel D, Deppert W, Tolstonog GV. Mutant p53(R270H) gain of function phenotype in a mouse model for oncogene-induced mammary carcinogenesis. Int J Cancer 2008;122:1701-1709
26. Scian MJ, Stagliano KE, Anderson MA, et al. Tumor-derived p53 mutants induce NF-κB2 gene expression. Mol Cell Biol 2005;25:10097-10110 (Pubitemid 41572755)
27. Jarvinen TA, Liu ET. Simultaneous amplification of HER-2 (ERBB2) and topoisomerase IIα (TOP2A) genes - molecular basis for combination chemotherapy in cancer. Curr Cancer Drug Targets 2006;6:579-602.
28. Carrano AC, Eytan E, Hershko A, Pagano M. SKP2 is required for ubiquitin-mediated degradation of the CDK inhibitor p27. Nat Cell Biol 1999;1:193-199 (Pubitemid 129500937)
29. Saigusa K, Hashimoto N, Tsuda H, et al. Overexpressed Skp2 within 5p amplification detected by array-based comparative genomic hybridization is associated with poor prognosis of glioblastomas. Cancer Sci 2005;96:676-683 (Pubitemid 41723544)
30. Chiappetta G, De Marco C, Quintiero A, et al. Overexpression of the Sphase kinase-associated protein 2 in thyroid cancer. Endocr Relat Cancer 2007;14:405-420 (Pubitemid 47242639)
31. Zhu CQ, Blackhall FH, Pintilie M, et al. Skp2 gene copy number aberrations are common in non-small cell lung carcinoma, and its overexpression in tumors with ras mutation is a poor prognostic marker. Clin Cancer Res 2004;10:1984-1991 (Pubitemid 38375557)
32. Salon C, Merdzhanova G, Brambilla C, Brambilla E, Gazzeri S, Eymin B. E2F-1, Skp2 and cyclin E oncoproteins are upregulated and directly correlated in high-grade neuroendocrine lung tumors. Oncogene 2007;26:6927-6936
33. Westermann F, Henrich KO, Wei JS, et al. High Skp2 expression characterizes high-risk neuroblastomas independent of MYCN status. Clin Cancer Res 2007;13:4695-4703 (Pubitemid 47294775)
34. Mori N, Morosetti R, Mizoguchi H, Koeffler HP. Progression of myelodysplastic syndrome: allelic loss on chromosomal arm 1p. Br J Haematol 2003;122:226-230 (Pubitemid 36859607)
35. Mori N, Morosetti R, Spira S, et al. Chromosome band 1p36 contains a putative tumor suppressor gene important in the evolution of chronic myelocytic leukemia. Blood 1998;92:3405-3409 (Pubitemid 28492351)
36. Kleer CG, Bryant BR, Giordano TJ, Sobel M, Merino MJ. Genetic changes in chromosomes 1p and 17p in thyroid cancer progression. Endocr Pathol 2000;11:137-143 (Pubitemid 30610123)
37. Cheung TH, Lo KW, Yim SF, et al. Clinicopathologic significance of loss of heterozygosity on chromosome 1 in cervical cancer. Gynecol Oncol 2005;96:510-515 (Pubitemid 40127157)
38. White PS, Thompson PM, Gotoh T, et al. Definition and characterization of a region of 1p36.3 consistently deleted in neuroblastoma. Oncogene 2005;24:2684-2694 (Pubitemid 40593096)
39. Piaskowski S, Rieske P, Szybka M, et al. GADD45A and EPB41 as tumor suppressor genes in meningioma pathogenesis. Cancer Genet Cytogenet 2005;162:63-67 (Pubitemid 41278472)
40. Mulholland PJ, Fiegler H, Mazzanti C, et al. Genomic profiling identifies discrete deletions associated with translocations in glioblastoma multiforme. Cell Cycle 2006;5:783-791
41. Barbashina V, Salazar P, Holland EC, Rosenblum MK, Ladanyi M. Allelic losses at 1p36 and 19q13 in gliomas: correlation with histologic classification, definition of a 150-kb minimal deleted region on 1p36, and evaluation of CAMTA1 as a candidate tumor suppressor gene. Clin Cancer Res 2005;11:1119-1128 (Pubitemid 40175761)
42. Cengiz B, Gunduz M, Nagatsuka H, et al. Fine deletion mapping of chromosome 2q21-37 shows three preferentially deleted regions in oral cancer. Oral Oncol 2007;43:241-247 (Pubitemid 46228008)
43. Langbein S, Szakacs O, Wilhelm M, et al. Alteration of the LRP1B gene region is associated with high grade of urothelial cancer. Lab Invest 2002;82:639-643 (Pubitemid 34522376)
44. Liu CX, Musco S, Lisitsina NM, Yaklichkin SY, Lisitsyn NA. Genomic organization of a new candidate tumor suppressor gene, LRP1B. Genomics 2000;69:271-274
45. Nakagawa T, Pimkhaokham A, Suzuki E, Omura K, Inazawa J, Imoto I. Genetic or epigenetic silencing of low density lipoprotein receptor-related protein 1B expression in oral squamous cell carcinoma. Cancer Sci 2006;97:1070-1074 (Pubitemid 44322556)
46. Roversi G, Pfundt R, Moroni RF, et al. Identification of novel genomic markers related to progression to glioblastoma through genomic profiling of 25 primary glioma cell lines. Oncogene 2006;25:1571-1583 (Pubitemid 43361942)
47. Sonoda I, Imoto I, Inoue J, et al. Frequent silencing of low density lipoprotein receptor-related protein 1B (LRP1B) expression by genetic and epigenetic mechanisms in esophageal squamous cell carcinoma. Cancer Res 2004;64:3741-3747 (Pubitemid 38697280)
48. Agirre X, Roman-Gomez J, Vazquez I, et al. Abnormal methylation of the common PARK2 and PACRG promoter is associated with downregulation of gene expression in acute lymphoblastic leukemia and chronic myeloid leukemia. Int J Cancer 2006;118:1945-1953
49. Denison SR, Callahan G, Becker NA, Phillips LA, Smith DI. Characterization of FRA6E and its potential role in autosomal recessive juvenile parkinsonism and ovarian cancer. Genes Chromosomes Cancer 2003;38:40-52. (Pubitemid 36994883)
50. Letessier A, Garrido-Urbani S, Ginestier C, et al. Correlated break at PARK2/FRA6E and loss of AF-6/Afadin protein expression are associated with poor outcome in breast cancer. Oncogene 2007;26:298-307. (Pubitemid 46095741)
51. Wang SI, Puc J, Li J, et al. Somatic mutations of PTEN in glioblastoma multiforme. Cancer Res 1997;57:4183-4186 (Pubitemid 27413419)
52. Ghimenti C, Fiano V, Chiado-Piat L, Chio A, Cavalla P, Schiffer D. Deregulation of the p14ARF/Mdm2/p53 pathway and G1/S transition in two glioblastoma sets. J Neurooncol 2003;61:95-102. (Pubitemid 36253654)
53. Riemenschneider MJ, Knobbe CB, Reifenberger G. Refined mapping of 1q32 amplicons in malignant gliomas confirms MDM4 as the main amplification target. Int J Cancer 2003;104:752-757 (Pubitemid 36418513)
54. Riemenschneider MJ, Buschges R, Wolter M, et al. Amplification and overexpression of the MDM4 (MDMX) gene from 1q32 in a subset of malignant gliomas without TP53 mutation or MDM2 amplification. Cancer Res 1999;59:6091-6096 (Pubitemid 30035626)
55. Mellinghoff IK, Wang MY, Vivanco I, et al. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N Engl J Med 2005;353:2012-2024 (Pubitemid 41609094)
56. Fan QW, Cheng CK, Nicolaides TP, et al. A dual phosphoinositide-3-kinase α/mTOR inhibitor cooperates with blockade of epidermal growth factor receptor in PTEN-mutant glioma. Cancer Res 2007;67:7960-7965 (Pubitemid 47395125)
57. Cloughesy TF, Yoshimoto K, Nghiemphu P, et al. Antitumor activity of rapamycin in a phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med 2008;5:e8.
58. Yang L, Clarke MJ, Carlson BL, et al. PTEN loss does not predict for response to RAD001 (Everolimus) in a glioblastoma orthotopic xenograft test panel. Clin Cancer Res 2008;14:3993-4001.
59. Yin D, Zhou H, Kumagai T, et al. Proteasome inhibitor PS-341 causes cell growth arrest and apoptosis in human glioblastoma multiforme (GBM). Oncogene 2005;24:344-354 (Pubitemid 40188583)
60. Nannya Y, Sanada M, Nakazaki K, et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 2005;65:6071-6079 (Pubitemid 40994391)
61. Yamamoto G, Nannya Y, Kato M, et al. Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of Affymetrix single-nucleotide-polymorphism genotyping microarrays. Am J Hum Genet 2007;81:114-126 (Pubitemid 47001161)
62. Imai Y, Strohmeyer TG, Fleischhacker M, Slamon DJ, Koeffler HP. p53 mutations and MDM-2 amplification in renal cell cancers. Mod Pathol 1994;7:766-770
63. Mori N, Morosetti R, Lee S, et al. Allelotype analysis in the evolution of chronic myelocytic leukemia. Blood 1997;90:2010-2014 (Pubitemid 27377313)