Genome-wide molecular characterization of central nervous system primitive neuroectodermal tumor and pineoblastoma

Neuro-Oncology

Volumn 13, Issue 8, 2011, Pages 866-879

  Miller, Suzanne ^a   Rogers, Hazel A ^a   Lyon, Paul ^a   Rand, Vikki ^a,c   Adamowicz Brice, Martyna ^a   Clifford, Steven C ^c   Hayden, James T ^c   Dyer, Sara ^a,d   Pfister, Stefan ^f,h   Korshunov, Andrey ^g   Brundler, Marie Anne ^e   Lowe, James ^a,b   Coyle, Beth ^a   Grundy, Richard G ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b QUEEN S MEDICAL CENTRE   (United Kingdom)

^c NEWCASTLE UNIVERSITY   (United Kingdom)

^d BIRMINGHAM WOMEN S HOSPITAL   (United Kingdom)

^e BIRMINGHAM CHILDREN S HOSPITAL   (United Kingdom)

^f Division of Molecular Genetics   (Germany)

^g Clinical Cooperation Unit Neuropathology   (Germany)

^h UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

Author keywords

CDKN2A CDKN2B; CNS PNET; Copy number imbalance; Pineoblastoma; SNP array

Indexed keywords

ABCG5 PROTEIN; ABCG8 PROTEIN; CYCLIN DEPENDENT KINASE 4; CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; DMRTA1 PROTEIN; FAM129A PROTEIN; MICRORNA; MTAP PROTEIN; MYC PROTEIN; OR4C12 PROTEIN; PCDHGA3 PROTEIN; PDGFRA PROTEIN; PROTEIN; SALL1 PROTEIN; TRANSCRIPTION FACTOR GLI1; UNCLASSIFIED DRUG;

ADOLESCENT; AGE; ARTICLE; BRAIN TUMOR; CANCER SURVIVAL; CHILD; CHROMOSOME 10Q; CHROMOSOME 11P; CHROMOSOME 12Q; CHROMOSOME 16Q; CHROMOSOME 17Q; CHROMOSOME 18Q; CHROMOSOME 19P; CHROMOSOME 19Q; CHROMOSOME 1Q; CHROMOSOME 2P; CHROMOSOME 4P; CHROMOSOME 4Q; CHROMOSOME 5Q; CHROMOSOME 7Q; CHROMOSOME 9P; CHROMOSOME ADDITION; CHROMOSOME DELETION; CONTROLLED STUDY; COPY NUMBER VARIATION; FEMALE; GENETIC ANALYSIS; GENETIC ASSOCIATION; HUMAN; HUMAN TISSUE; INFANT; MALE; MEDULLOBLASTOMA; METASTASIS; NEUROECTODERM TUMOR; NUCLEOTIDE SEQUENCE; ONCOGENE C KIT; PINEOBLASTOMA; PRESCHOOL CHILD; PROGNOSIS; RELAPSE; SCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR LOCALIZATION; TUMOR RECURRENCE;

ADOLESCENT; BRAIN NEOPLASMS; CALCIUM-BINDING PROTEINS; CHILD; CHILD, PRESCHOOL; CYCLIN-DEPENDENT KINASE INHIBITOR P15; CYCLIN-DEPENDENT KINASE INHIBITOR P16; DNA, NEOPLASM; FEMALE; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; IMMUNOENZYME TECHNIQUES; INFANT; MALE; NEOPLASM RECURRENCE, LOCAL; NEUROECTODERMAL TUMORS, PRIMITIVE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PINEAL GLAND; PINEALOMA; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; TUMOR MARKERS, BIOLOGICAL; VESICULAR TRANSPORT PROTEINS;

EID: 80052737349     PISSN: 15228517     EISSN: 15235866     Source Type: Journal    
DOI: 10.1093/neuonc/nor070     Document Type: Article

References (54)

1. Dirks PB, Harris L, Hoffman HJ, Humphreys RP, Drake JM, Rutka JT. Supratentorial primitive neuroectodermal tumors in children. J Neurooncol. 1996;29:75-84. (Pubitemid 26193506)
2. Timmermann B, Kortmann RD, Kuhl J, et al. Role of radiotherapy in the treatment of supratentorial primitive neuroectodermal tumors in childhood: results of the prospective German brain tumor trials HIT 88/89 and 91. J Clin Oncol. 2002;20:842-849. (Pubitemid 34111394)
3. Louis DN, Ohgaki H, Wiestler O, Cavenee W. WHO Classification of Tumours of the Central Nervous System. 4th ed. Lyon: IARC; 2007.
4. Cohen BH, Zeltzer PM, Boyett JM, et al. Prognostic factors and treatment results for supratentorial primitive neuroectodermal tumors in children using radiation and chemotherapy: a Childrens Cancer Group randomized trial. J Clin Oncol. 1995;13: 1687-1696.
5. Pizer BL, Weston CL, Robinson KJ, et al. Analysis of patients with supratentorial primitive neuro-ectodermal tumours entered into the SIOP/UKCCSG PNET 3 study. Eur J Cancer. 2006;42: 1120-1128.
6. Sung KW, Yoo KH, Cho EJ, et al. High-dose chemotherapy and autologous stem cell rescue in children with newly diagnosed high-risk or relapsed medulloblastoma or supratentorial primitive neuroectodermal tumor. Pediatr Blood Cancer. 2007;48:408-415. (Pubitemid 46340106)
7. Inda MM, Perot C, Guillaud-Bataille M, et al. Genetic heterogeneity in supratentorial and infratentorial primitive neuroectodermal tumours of the central nervous system. Histopathology. 2005;47:631-637. (Pubitemid 41775187)
8. McCabe MG, Ichimura K, Liu L, et al. High-resolution array-based comparative genomic hybridization of medulloblastomas and supratentorial primitive neuroectodermal tumors. J Neuropathol Exp Neurol. 2006;65:549-561. (Pubitemid 44288939)
9. Pfister S, Remke M, Toedt G, et al. Supratentorial primitive neuroectodermal tumors of the central nervous system frequently harbor deletions of the CDKN2A locus and other genomic aberrations distinct from medulloblastomas. Genes Chromosomes Cancer. 2007;46:839-851. (Pubitemid 47106188)
10. Li M, Lee KF, Lu Y, et al. Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. Cancer Cell. 2009;16:533-546.
11. Rogers HA, Miller S, Lowe J, Brundler MA, Coyle B, Grundy RG. An investigation of WNT pathway activation and association with survival in central nervous system primitive neuroectodermal tumours (CNS PNET). Br J Cancer. 2009;100:1292-1302.
12. Batanian JR, Havlioglu N, Huang Y, Gadre B. Unusual aberration involving the short arm of chromosome 11 in an 8-month-old patient with a supratentorial primitive neuroectodermal tumor. Cancer Genet Cytogenet. 2003;141:143-147. (Pubitemid 36269214)
13. Bayani J, Zielenska M, Marrano P, et al. Molecular cytogenetic analysis of medulloblastomas and supratentorial primitive neuroectodermal tumors by using conventional banding, comparative genomic hybridization, and spectral karyotyping. J Neurosurg. 2000;93:437-448.
14. Bhattacharjee MB, Armstrong DD, Vogel H, Cooley LD. Cytogenetic analysis of 120 primary pediatric brain tumors and literature review. Cancer Genet Cytogenet. 1997;97:39-53. (Pubitemid 27318476)
15. Bigner SH, McLendon RE, Fuchs H, McKeever PE, Friedman HS. Chromosomal characteristics of childhood brain tumors. Cancer Genet Cytogenet. 1997;97:125-134. (Pubitemid 27362507)
16. Brown AE, Leibundgut K, Niggli FK, Betts DR. Cytogenetics of pineoblastoma: four new cases and a literature review. Cancer Genet Cytogenet. 2006;170:175-179. (Pubitemid 44442469)
17. Burnett ME, White EC, Sih S, von Haken MS, Cogen PH. Chromosome arm 17p deletion analysis reveals molecular genetic heterogeneity in supratentorial and infratentorial primitive neuroectodermal tumors of the central nervous system. Cancer Genet Cytogenet. 1997;97:25-31. (Pubitemid 27318473)
18. Roberts P, Chumas PD, Picton S, Bridges L, Livingstone JH, Sheridan E. A review of the cytogenetics of 58 pediatric brain tumors. Cancer Genet Cytogenet. 2001;131:1-12. (Pubitemid 33081151)
19. Sreekantaiah C, Jockin H, Brecher ML, Sandberg AA. Interstitial deletion of chromosome 11q in a pineoblastoma. Cancer Genet Cytogenet. 1989;39:125-131. (Pubitemid 19169870)
20. Uematsu Y, Takehara R, Shimizu M, Tanaka Y, Itakura T, Komai N. Pleomorphic primitive neuroectodermal tumor with glial and neuronal differentiation: clinical, pathological, cultural, and chromosomal analysisof a case. J Neurooncol. 2002;59:71-79. (Pubitemid 34918715)
21. Avet-Loiseau H, Venuat AM, Terrier-Lacombe MJ, Lellouch-Tubiana A, Zerah M, Vassal G. Comparative genomic hybridization detects many recurrent imbalances in central nervous system primitive neuroectodermal tumours in children. Br J Cancer. 1999;79:1843-1847. (Pubitemid 29133902)
22. Nicholson JC, Ross FM, Kohler JA, Ellison DW. Comparative genomic hybridization and histological variation in primitive neuroectodermal tumours. Br J Cancer. 1999;80:1322-1331. (Pubitemid 29308599)
23. Rickert CH, Simon R, Bergmann M, Dockhorn-Dworniczak B, Paulus W. Comparative genomic hybridization in pineal parenchymal tumors. Genes Chromosomes Cancer. 2001;30:99-104.
24. Affymetrix. Genechip Mapping 100K Assay Protocol. Santa Clara, USA: Affymetrix.
25. Affymetrix. Genechip Mapping 500K Assay Protocol. Santa Clara, USA: Affymetrix.
26. 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)
27. The International HapMap Project. Nature. 2003;426:789-796.
28. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29:e45.
29. Northcott PA, Nakahara Y, Wu X, et al. Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Nat Genet. 2009;41:465-472.
30. Ridley L, Rahman R, Brundler MA, et al. Multifactorial analysis of predictors of outcome in pediatric intracranial ependymoma. Neuro Oncol. 2008;10:675-689.
31. Johnson RA, Wright KD, Poppleton H, et al. Cross-species genomics matches driver mutations and cell compartments to model ependymoma. Nature. 2010; 466:632-636.
32. Gibson P, Tong Y, Robinson G, et al. Subtypes of medulloblastoma have distinct developmental origins. Nature. 2010; 468:1095-1099.
33. Ling V. Multidrug resistance: molecular mechanisms and clinical relevance. Cancer Chemother Pharmacol. 1997;40(Suppl):S3-S8.
34. Pfister S, Remke M, Castoldi M, et al.Novel genomic amplification targeting themicroRNAclusterat 19q13.42 in apediatricembryonal tumorwith abundant neuropil and true rosettes. Acta Neuropathol. 2009;117:457-464.
35. Korshunov A, Remke M, Gessi M, et al. Focal genomic amplification at 19q13.42 comprises a powerful diagnostic marker for embryonal tumors with ependymoblastic rosettes. Acta Neuropathol. 2010;120:253-260.
36. Gessi M, Giangaspero F, Lauriola L, et al. Embryonal tumors with abundant neuropil and true rosettes: a distinctive CNS primitive neuroectodermal tumor. Am J Surg Pathol. 2009;33:211-217.
37. Caren H, Erichsen J, Olsson L, et al. High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: four cases of homozygous deletions of the CDKN2A gene. BMC Genomics. 2008;9:353.
38. Mendrzyk F, Radlwimmer B, Joos S, et al. Genomic and protein expression profiling identifies CDK6 as novel independent prognostic marker in medulloblastoma. J Clin Oncol. 2005;23:8853-8862. (Pubitemid 46211532)
39. Holtkamp N, Ziegenhagen N, Malzer E, Hartmann C, Giese A, von Deimling A. Characterization of the amplicon on chromosomal segment 4q12 in glioblastoma multiforme. Neuro Oncol. 2007;9:291-297. (Pubitemid 47169661)
40. Rossi MR, Conroy J, McQuaid D, Nowak NJ, Rutka JT, Cowell JK. Array CGH analysis of pediatric medulloblastomas. Genes Chromosomes Cancer. 2006;45:290-303. (Pubitemid 43238479)
41. Schiffman JD,Wang Y, McPherson LA, et al. Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia. Cancer Genet Cytogenet. 2009;193:9-18.
42. Liggett WH, Jr, Sidransky D. Role of the p16 tumor suppressor gene in cancer. J Clin Oncol. 1998;16:1197-1206. (Pubitemid 28108758)
43. Barrow J, Adamowicz-Brice M, Cartmill M, et al. Homozygous loss of ADAM3A revealed by genome-wide analysis of pediatric high-grade glioma and diffuse intrinsic pontine gliomas. Neuro Oncol. 2011;13:212-222.
44. Taylor MD, Poppleton H, Fuller C, et al. Radial glia cells are candidate stem cells of ependymoma. Cancer Cell. 2005;8:323-335. (Pubitemid 41443417)
45. Dyer S, Prebble E, Davison V, et al. Genomic imbalances in pediatric intracranial ependymomas define clinically relevant groups. Am J Pathol. 2002;161:2133-2141. (Pubitemid 35434859)
46. Scotting PJ, Walker DA, Perilongo G. Childhood solid tumours: a developmental disorder. Nat Rev Cancer. 2005;5:481-488. (Pubitemid 40791490)
47. Biegel JA, Rorke LB, Packer RJ, et al. Isochromosome 17q in primitive neuroectodermal tumors of the central nervous system. Genes Chromosomes Cancer. 1989;1:139-147. (Pubitemid 20094558)
48. Lo KC, Rossi MR, Eberhart CG, Cowell JK. Genome wide copy number abnormalities in pediatric medulloblastomas as assessed by array comparative genome hybridization. Brain Pathol. 2007;17:282-296. (Pubitemid 47000637)
49. Michiels EM, Weiss MM, Hoovers JM, et al. Genetic alterations in childhood medulloblastoma analyzed by comparative genomic hybridization. J Pediatr Hematol Oncol. 2002;24:205-210. (Pubitemid 34297564)
50. Clifford SC, Lusher ME, Lindsey JC, et al. Wnt/Wingless pathway activation and chromosome 6 loss characterize a distinct molecular subgroup of medulloblastomas associated with a favorable prognosis. Cell Cycle. 2006;5:2666-2670.
51. Thompson MC, Fuller C, Hogg TL, et al. Genomics identifies medulloblastoma subgroups that are enriched for specific genetic alterations. J Clin Oncol. 2006;24:1924-1931. (Pubitemid 46638992)
52. Aldosari N, Bigner SH, Burger PC, et al. MYCC and MYCN oncogene amplification in medulloblastoma: a fluorescence in situ hybridization study on paraffin sections from the Children's Oncology Group. Arch Pathol Lab Med. 2002;126:540-544. (Pubitemid 34477948)
53. Eberhart CG, Kratz JE, Schuster A, et al. Comparative genomic hybridization detects an increased number of chromosomal alterations in large cell/anaplastic medulloblastomas. Brain Pathol. 2002;12:36-44. (Pubitemid 33131360)
54. Neben K, Korshunov A, Benner A, et al. Microarray-based screening for molecular markers in medulloblastoma revealed STK15 as independent predictor for survival. Cancer Res. 2004;64:3103-3111. (Pubitemid 38581410)