Insights revealed by high-throughput genomic arrays in nonglial primary brain tumors

Expert Review of Molecular Diagnostics

Volumn 12, Issue 3, 2012, Pages 265-277

  Alentorn, Agustí ^a,b   Sanson, Marc ^a,b   Mokhtari, Karima ^a,b   Marie, Yannick ^c   Hoang Xuan, Khê ^a,b   Delattre, Jean Yves ^a,b   Idbaih, Ahmed ^a,b  

^a INSTITUT DU CERVEAU ET DE LA MOELLE ÉPINIÈRE   (France)

^b PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

^c ICM   (France)

Author keywords

biomarker; brain cancer; genetics; genomics; microarray; nonglial tumor; oncogenesis

Indexed keywords

B RAF KINASE; CYCLIN DEPENDENT KINASE INHIBITOR 2A; GENOMIC DNA; TISSUE INHIBITOR OF METALLOPROTEINASE 3;

BRAIN TUMOR; CARCINOGENESIS; CHROMOSOME; CHROMOSOME DELETION; CLINICAL PRACTICE; CRANIOPHARYNGIOMA; GENE DOSAGE; GENE FREQUENCY; GENOMICS; GLIOMA; HUMAN; HYPOPHYSIS ADENOMA; MEDULLOBLASTOMA; MENINGIOMA; NEUROEPITHELIOMA; NONHODGKIN LYMPHOMA; PRIMARY CENTRAL NERVOUS SYSTEM TUMOR; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

BRAIN NEOPLASMS; CELL TRANSFORMATION, NEOPLASTIC; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; GENETIC VARIATION; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; TUMOR MARKERS, BIOLOGICAL;

EID: 84859404398     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/erm.12.17     Document Type: Review

References (91)

1. Louis D, Ohgaki H, Wiestler O, Cavenee W. WHO classification of tumours of the central nervous system. In: IARC WHO Classification of Tumours. WHO, Geneva, Switzerland (2007). The current classification of CNS brain tumors.
2. Kieran MW, Walker D, Frappaz D, Prados M. Brain tumors: from childhood through adolescence into adulthood. J. Clin. Oncol. 32, 4783-4789 (2010).
3. Jeuken J, Cornelissen S, Boots-Sprenger S, Gijsen S, Wesseling P. Multiplex ligation-dependent probe amplification: a diagnostic tool for simultaneous identification of different genetic markers in glial tumors. J. Mol. Diagn. 4, 433-443 (2006).
4. Schröck E, Thiel G, Lozanova T et al. Comparative genomic hybridization of human malignant gliomas reveals multiple amplification sites and nonrandom chromosomal gains and losses. Am. J. Pathol. 6, 1203-1218 (1994).
5. Shapiro JR, Yung WK, Shapiro WR. Isolation, karyotype, and clonal growth of heterogeneous subpopulations of human malignant gliomas. Cancer Res. 6, 2349-2359 (1981).
6. Smith JS, Perry A, Borell TJ et al. Alterations of chromosome arms 1p and 19q as predictors of survival in oligodendrogliomas, astrocytomas, and mixed oligoastrocytomas. J. Clin. Oncol. 3, 636-645 (2000).
7. Idbaih A, Crinière E, Ligon KL, Delattre O, Delattre JY. Array-based genomics in glioma research. Brain Pathol. 1, 28-38 (2010). Focused on genomic imbalances in gliomas.
8. Horbinski C, Miller CR, Perry A. Gone FISHing: clinical lessons learned in brain tumor molecular diagnostics over the last decade. Brain Pathol. 1, 57-73 (2011).
9. Pfister S, Janzarik WG, Remke M et al. BRAF gene duplication constitutes a mechanism of MAPK pathway activation in low-grade astrocytomas. J. Clin. Invest. 118, 1739-1749 (2008). Describes BRAF rearrangements in pilocytic astrocytomas using high-throughput genomic technologies.
10. Jones DTW, Kocialkowski S, Liu L, Pearson DM, Ichimura K, Collins VP. Oncogenic RAF1 rearrangement and a novel BRAF mutation as alternatives to KIAA1549: BRAF fusion in activating the MAPK pathway in pilocytic astrocytoma. Oncogene 20, 2119-2123 (2009).
11. Sievert AJ, Jackson EM, Gai X et al. Duplication of 7q34 in pediatric low-grade astrocytomas detected by high-density single-nucleotide polymorphism-based genotype arrays results in a novel BRAF fusion gene. Brain Pathol. 3, 449-458 (2009).
12. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 7216, 1061-1068 (2008). Comprehensive genomic study depicting genetic abnormalities in glioblastoma and their consequences in intracellular signaling pathways.
13. Riemenschneider MJ, Perry A, Reifenberger G. Histological classification and molecular genetics of meningiomas. Lancet Neurol. 12, 1045-1054 (2006). In-depth review of molecular portraits of meningioma.
14. Ho DMT, Hsu CY, Ting LT, Chiang H. Histopathology and MIB-1 labeling index predicted recurrence of meningiomas: a proposal of diagnostic criteria for patients with atypical meningioma. Cancer 5, 1538-1547 (2002).
15. Gabeau-Lacet D, Engler D, Gupta S et al. Genomic profiling of atypical meningiomas associates gain of 1q with poor clinical outcome. J. Neuropathol. Exp. Neurol. 10, 1155-1165 (2009).
16. Dumanski JP, Carlbom E, Collins VP, Nordenskjöld M. Deletion mapping of a locus on human chromosome 22 involved in the oncogenesis of meningioma. Proc. Natl Acad. Sci. USA 24, 9275-9279 (1987).
17. Ruttledge MH, Sarrazin J, Rangaratnam S et al. Evidence for the complete inactivation of the NF2 gene in the majority of sporadic meningiomas. Nat. Genet. 2, 180-184 (1994).
18. Wellenreuther R, Kraus JA, Lenartz D et al. Analysis of the neurofibromatosis 2 gene reveals molecular variants of meningioma. Am. J. Pathol. 4, 827-832 (1995).
19. Rouleau GA, Merel P, Lutchman M et al. Alteration in a new gene encoding a putative membrane-organizing protein causes neuro-fibromatosis type 2. Nature 6429, 515-521 (1993).
20. Trofatter JA, MacCollin MM, Rutter JL et al. A novel moesin-, ezrin-, radixin-like gene is a candidate for the neurofibromatosis 2 tumor suppressor. Cell 5, 791-800 (1993).
21. Peyrard M, Fransson I, Xie YG et al. Characterization of a new member of the human β-adaptin gene family from chromosome 22q12, a candidate meningioma gene. Hum. Mol. Genet. 8, 1393-1399 (1994).
22. Barski D, Wolter M, Reifenberger G, Riemenschneider MJ. Hypermethylation and transcriptional downregulation of the TIMP3 gene is associated with allelic loss on 22q12.3 and malignancy in meningiomas. Brain Pathol. 3, 623-631 (2010).
23. Weber RG, Boström J, Wolter M et al. Analysis of genomic alterations in benign, atypical, and anaplastic meningiomas: toward a genetic model of meningioma progression. Proc. Natl Acad. Sci. USA 26, 14719-14724 (1997). Pivotal study investigating the molecular pattern of progression in meningioma.
24. Ketter R, Henn W, Niedermayer I et al. Predictive value of progression-associated chromosomal aberrations for the prognosis of meningiomas: a retrospective study of 198 cases. J. Neurosurg. 4, 601-607 (2001).
25. Ketter R, Rahnenführer J, Henn W et al. Correspondence of tumor localization with tumor recurrence and cytogenetic progression in meningiomas. Neurosurgery 1, 61-69 (2008).
26. Pfisterer WK, Hank NC, Preul MC et al. Diagnostic and prognostic significance of genetic regional heterogeneity in meningiomas. Neuro. Oncol. 4, 290-299 (2004).
27. Lamszus K, Kluwe L, Matschke J, Meissner H, Laas R, Westphal M. Allelic losses at 1p, 9q, 10q, 14q, and 22q in the progression of aggressive meningiomas and undifferentiated meningeal sarcomas. Cancer Genet. Cytogenet. 2, 103-110 (1999).
28. Carvalho LH, Smirnov I, Baia GS et al. Molecular signatures define two main classes of meningiomas. Mol. Cancer 6, 64 (2007).
29. Buckley PG, Jarbo C, Menzel U et al. Comprehensive DNA copy number profiling of meningioma using a chromosome 1 tiling path microarray identifies novel candidate tumor suppressor loci. Cancer Res. 7, 2653-2661 (2005).
30. Shen Y, Nunes F, Stemmer-Rachamimov A et al. Genomic profiling distinguishes familial multiple and sporadic multiple meningiomas. BMC Med. Genomics 2, 42 (2009).
31. Pérez-Magán E, Rodríguez de Lope A, Ribalta T et al. Differential expression profiling analyses identifies downregulation of 1p, 6q, and 14q genes and overexpression of 6p histone cluster 1 genes as markers of recurrence in meningiomas. Neuro. Oncol. 12, 1278-1290 (2010).
32. DeLellis R, Lloyd R, Heitz P, Eng C. Pathology and genetics of tumours of endocrine organs. In: IARC WHO Classification of Tumours. WHO, Geneva, Switzerland, 14-36 (2004).
33. Ezzat S, Asa SL, Couldwell WT et al. The prevalence of pituitary adenomas: a systematic review. Cancer 3, 613-619 (2004).
34. Herman V, Fagin J, Gonsky R, Kovacs K, Melmed S. Clonal origin of pituitary adenomas. J. Clin. Endocrinol. Metab. 6, 1427-1433 (1990).
35. Trautmann K, Thakker RV, Ellison DW et al. Chromosomal aberrations in sporadic pituitary tumors. Int. J. Cancer 6, 809-814 (2001).
36. Hui AB, Pang JC, Ko CW, Ng HK. Detection of chromosomal imbalances in growth hormone-secreting pituitary tumors by comparative genomic hybridization. Hum. Pathol. 9, 1019-1023 (1999).
37. Harada K, Nishizaki T, Ozaki S et al. Cytogenetic alterations in pituitary adenomas detected by comparative genomic hybridization. Cancer Genet. Cytogenet. 1, 38-41 (1999).
38. Metzger AK, Mohapatra G, Minn YA et al. Multiple genetic aberrations including evidence of chromosome 11q13 rearrangement detected in pituitary adenomas by comparative genomic hybridization. J. Neurosurg. 2, 306-314 (1999).
39. Rickert CH, Dockhorn-Dworniczak B, Busch G et al. Increased chromosomal imbalances in recurrent pituitary adenomas. Acta Neuropathol. 6, 615-620 (2001).
40. Daly AF, Rixhon M, Adam C, Dempegioti A, Tichomirowa MA, Beckers A. High prevalence of pituitary adenomas: a cross-sectional study in the province of Liege, Belgium. J. Clin. Endocrinol. Metab. 12, 4769-4775 (2006).
41. Garnett MR, Puget S, Grill J, Sainte-Rose C. Craniopharyngioma. Orphanet. J. Rare Dis. 2, 18 (2007).
42. Bunin GR, Surawicz TS, Witman PA, Preston-Martin S, Davis F, Bruner JM. The descriptive epidemiology of craniopharyngioma. J. Neurosurg. 4, 547-551 (1998).
43. Rickert CH, Paulus W. Lack of chromosomal imbalances in adamantinomatous and papillary craniopharyngiomas. J. Neurol. Neurosurg. Psychiatr. 2, 260-261 (2003).
44. Yoshimoto M, de Toledo SRC, da Silva NS et al. Comparative genomic hybridization analysis of pediatric adamantinomatous craniopharyngiomas and a review of the literature. J. Neurosurg. 101(Suppl. 1), 85-90 (2004).
45. Gerstner ER, Batchelor TT. Primary central nervous system lymphoma. Arch. Neurol. 3, 291-297 (2010).
46. Sierra del Rio M, Rousseau A, Soussain C, Ricard D, Hoang-Xuan K. Primary CNS lymphoma in immunocompetent patients. Oncologist 5, 526-539 (2009).
47. Camilleri-Broët S, Martin A, Moreau A et al. Primary central nervous system lymphomas in 72 immunocompetent patients: pathologic findings and clinical correlations. Groupe Ouest Est d'étude des Leucénies et Autres Maladies du Sang (GOELAMS). Am. J. Clin. Pathol. 5, 607-612 (1998).
48. Swerdlow S, Campo E, Lee N et al. WHO classification of tumours of haematopoietic and lymphoid tissue. In: IARC WHO Classification of Tumours. WHO, Geneva, Switzerland, 236-237 (2008).
49. Chen W, Houldsworth J, Olshen AB. Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas. Blood 6, 2477-2485 (2006).
50. Beà S, Colomo L, López-Guillermo A et al. Clinicopathologic significance and prognostic value of chromosomal imbalances in diffuse large B-cell lymphomas. J. Clin. Oncol. 17, 3498-3506 (2004).
51. Robledo C, García JL, Caballero D et al. Array comparative genomic hybridization identifies genetic regions associated with outcome in aggressive diffuse large B-cell lymphomas. Cancer 16, 3728-3737 (2009).
52. Lin CH, Kuo KT, Chuang SS et al. Comparison of the expression and prognostic significance of differentiation markers between diffuse large B-cell lymphoma of central nervous system origin and peripheral nodal origin. Clin. Cancer Res. 4, 1152-1156 (2006).
53. Braaten KM, Betensky PA, de Leval L et al. BCL-6 expression predicts improved survival in patients with primary central nervous system lymphoma. Clin. Cancer Res. 3, 1063-1069 (2003).
54. Weber T, Weber RG, Kaulich K et al. Characteristic chromosomal imbalances in primary central nervous system lymphomas of the diffuse large B-cell type. Brain Pathol. 1, 73-84 (2000).
55. Harada K, Nishizaki T, Kubota H, Harada K, Suzuki M, Sasaki K. Distinct primary central nervous system lymphoma defined by comparative genomic hybridization and laser scanning cytometry. Cancer Genet. Cytogenet. 2, 147-150 (2001).
56. Schwindt H, Vater I, Kreuz M et al. Chromosomal imbalances and partial uniparental disomies in primary central nervous system lymphoma. Leukemia 10, 1875-1884 (2009).
57. Sung CO, Kim SC, Karnan S et al. Genomic profiling combined with gene expression profiling in primary central nervous system lymphoma. Blood 4, 1291-1300 (2011).
58. Cady FM, O'Neill BP, Law ME et al. Del(6)(q22) and BCL6 rearrangements in primary CNS lymphoma are indicators of an aggressive clinical course. J. Clin. Oncol. 29, 4814-4819 (2008).
59. Luyken C, Blümcke I, Fimmers R, Urbach H, Wiestler OD, Schramm J. Supratentorial gangliogliomas: histopathologic grading and tumor recurrence in 184 patients with a median follow-up of 8 years. Cancer 1, 146-155 (2004).
60. Jay V, Squire J, Becker LE, Humphreys R. Malignant transformation in a ganglioglioma with anaplastic neuronal and astrocytic components. Report of a case with flow cytometric and cytogenetic analysis. Cancer 11, 2862-2868 (1994).
61. Pandita A, Balasubramaniam A, Perrin R, Shannon P, Guha A. Malignant and benign ganglioglioma: a pathological and molecular study. Neuro. Oncol. 2, 124-134 (2007).
62. Yin XL, Hui ABY, Pang JCS, Poon WS, Ng HK. Genome-wide survey for chromosomal imbalances in ganglioglioma using comparative genomic hybridization. Cancer Genet. Cytogenet. 1, 71-76 (2002).
63. Hoischen A, Ehrler M, Fassunke J et al. Comprehensive characterization of genomic aberrations in gangliogliomas by CGH, array-based CGH and interphase FISH. Brain Pathol. 3, 326-337 (2008).
64. Suresh TN, Santosh V, Yasha TC et al. Medulloblastoma with extensive nodularity: a variant occurring in the very young - clinicopathological and immunohistochemical study of four cases. Childs Nerv. Syst. 1, 55-60 (2004).
65. Padovani L, Sunyach M, Perol D et al. Common strategy for adult and pediatric medulloblastoma: a multicenter series of 253 adults. Int. J. Radiat. Oncol. Biol. Phys. 2, 433-440 (2007).
66. Brandes AA, Franceschi E, Tosoni A et al. Adult neuroectodermal tumors of posterior fossa (medulloblastoma) and of supratentorial sites (stPNET). Crit. Rev. Oncol. Hematol. 2, 165-179 (2009).
67. 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. 3, 437-448 (2000).
68. Hui ABY, Takano H, Lo K et al. Identification of a novel homozygous deletion region at 6q23.1 in medulloblastomas using high-resolution array comparative genomic hybridization analysis. Clin. Cancer Res. 13, 4707-4716 (2005).
69. 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. 6, 549-561 (2006).
70. Michiels EMC, Weiss MM, Hoovers JMN et al. Genetic alterations in childhood medulloblastoma analyzed by comparative genomic hybridization. J. Pediatr. Hematol. Oncol. 3, 205-210 (2002).
71. Pan E, Pellarin M, Holmes E et al. Isochromosome 17q is a negative prognostic factor in poor-risk childhood medulloblastoma patients. Clin. Cancer Res. 13, 4733-4740 (2005).
72. Rossi MR, Conroy J, McQuaid D, Nowak NJ, Rutka JT, Cowell JK. Array CGH analysis of pediatric medulloblastomas. Genes Chromosomes Cancer 3, 290-303 (2006).
73. Remke M, Hielscher T, Northcott PA et al. Adult medulloblastoma comprises three major molecular variants. J. Clin. Oncol. 19, 2717-2723 (2011). This study identified signaling pathways disrupted in adult medulloblastoma and showed that they are different from pediatric tumors using genome-wide technologies.
74. Korshunov A, Remke M, Werft W et al. Adult and pediatric medulloblastomas are genetically distinct and require different algorithms for molecular risk stratification. J. Clin. Oncol. 18, 3054-3060 (2010).
75. 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. 34, 8853-8862 (2005).
76. Pfister S, Remke M, Benner A et al. Outcome prediction in pediatric medulloblastoma based on DNA copy-number aberrations of chromosomes 6q and 17q and the MYC and MYCN loci. J. Clin. Oncol. 10, 1627-1636 (2009).
77. Bjornsson J, Scheithauer BW, Okazaki H, Leech RW. Intracranial germ cell tumors: pathobiological and immunohistochemical aspects of 70 cases. J. Neuropathol. Exp. Neurol. 1, 32-46 (1985).
78. Hoffman HJ, Otsubo H, Hendrick EB et al. Intracranial germ-cell tumors in children. J. Neurosurg. 4, 545-551 (1991).
79. Jennings MT, Gelman R, Hochberg F. Intracranial germ-cell tumors: natural history and pathogenesis. J. Neurosurg. 2, 155-167 (1985).
80. Ho DM, Liu HC. Primary intracranial germ cell tumor. Pathologic study of 51 patients. Cancer 6, 1577-1584 (1992).
81. Matsutani M, Sano K, Takakura K et al. Primary intracranial germ cell tumors: a clinical analysis of 153 histologically verified cases. J. Neurosurg. 3, 446-455 (1997).
82. Schneider DT, Calaminus G, Koch S et al. Epidemiologic analysis of 1,442 children and adolescents registered in the German germ cell tumor protocols. Pediatr. Blood Cancer 2, 169-175 (2004).
83. Calaminus G, Bamberg M, Baranzelli MC et al. Intracranial germ cell tumors: a comprehensive update of the European data. Neuropediatrics 1, 26-32 (1994).
84. Schneider DT, Zahn S, Sievers S et al. Molecular genetic analysis of central nervous system germ cell tumors with comparative genomic hybridization. Mod. Pathol. 6, 864-873 (2006).
85. Hassoun J, Gambarelli D, Grisoli F et al. Central neurocytoma. An electron-microscopic study of two cases. Acta Neuropathol. 2, 151-156 (1982).
86. Schmidt MH, Gottfried ON, von Koch CS, Chang SM, McDermott MW. Central neurocytoma: a review. J. Neurooncol. 3, 377-384 (2004).
87. Cerdá-Nicolás M, López-Ginés C, Peydro-Olaya A, Llombart-Bosch A. Central neurocytoma: a cytogenetic case study. Cancer Genet. Cytogenet. 2, 173-174 (1993).
88. Jay V, Edwards V, Hoving E et al. Central neurocytoma: morphological, flow cytometric, polymerase chain reaction, fluorescence in situ hybridization, and karyotypic analyses. Case report. J. Neurosurg. 2, 348-354 (1999).
89. Yin XL, Pang JC, Hui AB, Ng HK. Detection of chromosomal imbalances in central neurocytomas by using comparative genomic hybridization. J. Neurosurg. 1, 77-81 (2000).
90. Korshunov A, Sycheva R, Golanov A. Recurrent cytogenetic aberrations in central neurocytomas and their biological relevance. Acta Neuropathol. 3, 303-312 (2007). Unique study that investigated genomic aberrations in central neurocytomas.
91. CBTRUS: Reports and Tables.www.cbtrus.org/reports/reports.html