Differential proteome analysis of human gliomas stratified for loss of heterozygosity on chromosomal arms 1p and 19q

Neuro-Oncology

Volumn 12, Issue 3, 2010, Pages 243-256

  Grzendowski, Michael ^a   Wolter, Marietta ^b   Riemenschneider, Markus J ^b   Knobbe, Christiane B ^b   Schlegel, Uwe ^c   Meyer, Helmut E ^a   Reifenberger, Guido ^b   Stühler, Kai ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b HEINRICH HEINE UNIVERSITY   (Germany)

^c RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

1p 19q LOH; 2D DIGE; Glioma; Loss of heterozygosity; Proteomics

Indexed keywords

EZRIN; GLIAL FIBRILLARY ACIDIC PROTEIN; LIPOCORTIN 1; VIMENTIN;

ARTICLE; ASTROCYTOMA; CHROMOSOME 19Q; CHROMOSOME 1P; CHROMOSOME DELETION; CPG ISLAND; GEL ELECTROPHORESIS; GENE SEQUENCE; GLIOMA; HETEROZYGOSITY; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; PROTEOMICS; BRAIN TUMOR; CHROMOSOME 1; CHROMOSOME 19; DNA METHYLATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HETEROZYGOSITY LOSS; IMAGE PROCESSING; PROGNOSIS; PROTEIN MICROARRAY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TWO DIMENSIONAL GEL ELECTROPHORESIS; WESTERN BLOTTING;

BLOTTING, WESTERN; BRAIN NEOPLASMS; CHROMOSOMES, HUMAN, PAIR 1; CHROMOSOMES, HUMAN, PAIR 19; DNA METHYLATION; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GLIOMA; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; IMMUNOHISTOCHEMISTRY; LOSS OF HETEROZYGOSITY; PROGNOSIS; PROTEIN ARRAY ANALYSIS; PROTEOMICS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 77952311163     PISSN: 15228517     EISSN: 15235866     Source Type: Journal    
DOI: 10.1093/neuonc/nop025     Document Type: Article

References (64)

1. Louis DN, Ohgakl H, Wiestier OD, et al., eds. WHO Classification of Tumours of the Central Nervous System. Lyon: IARC Press; 2007.
2. Hegi ME, Diserens AC, Gorlia T, et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med. 2005;352:997-1003. (Pubitemid 40349502)
3. Cairncross JG, Ueki K, Zlatescu MC, et al. Specific genetic predictors of chemotherapeutic response and survival in patients with anaplastic oligodendrogliomas. J Natl Cancer Inst. 1998; 90:1473-1479. (Pubitemid 28482012)
4. Louis DN. Molecular pathology of malignant gliomas. Annu Rev Path Mech Dis. 2006; 1:97-117.
5. Cairncross G, Berkey B, Shaw E, et al. Phase III trial of chemotherapy plus radiotherapy compared with radiotherapy alone for pure and mixed anaplastic oligodendroglioma: intergroup radiation therapy oncology group trial 9402. J Clin Oncol. 2006; 24:2707-2714. (Pubitemid 46630566)
6. van den Bent MJ, Carpentier AF, Brandes AA, et al. Adjuvant procarbazine, lomustine, and vincristine improves progression-free survival but not overall survival in newly diagnosed anaplastic oligodendrogliomas and oligoastrocytomas: a randomized European Organisation for Research and Treatment of Cancer phase III trial. J Clin Oncol. 2006; 24:2715-2722.
7. Yip S, lafrate AJ, Louis DN. Molecular diagnostic testing in malignant gliomas: a practical update on predictive markers. J Neuropathol Exp Neurol. 2008; 67:1-15.
8. Dong S, Pang JC, Hu J, et al. Transcriptional inactivation of TP73 expression in Oligodendroglial tumors. Int J Cancer 2002; 98:370-375. (Pubitemid 34188680)
9. BarbashinaV, Salazar P, Holland EC, et al. Allelic losses at1p36 and 19q13 in gliomas: correlation with histologic classification, definition of a 150-kb minimal deleted region on 1 p36, and evaluation of CAMTA1 as a candidate tumor suppressor gene. Clin Cancer Res. 2005; 11:1119-1128.
10. McDonald JM, Dunmire V, Taylor E, et al. Attenuated expression of DFFB is a hallmark of oligodendrogliomas with 1p-allelic loss. Mol Cancer. 2005;4:35. (Pubitemid 41461189)
11. McDonald JM, Dunlap S, Cogdell D, et al. The SHREW1 gene, frequently deleted in oligodendrogliomas, functions to inhibit cell adhesion and migration. Cancer Biol Ther. 2006; 5:300-304.
12. Tews B, Roerig P, Hartmann C, et al. Hypermethylation and transcriptional downregulation of the CITED4 gene at 1 p34.2 in Oligodendroglial tumours with allelic losses on 1p and 19q. Oncogene. 2007; 26:5010-5016. (Pubitemid 47172644)
13. Pohl U, Cairncross JG, Louis DN. Homozygous deletions of the CDKN2C/p18INK4C gene on the short arm of chromosome 1 in anaplastic oligodendrogliomas. Brain Pathol 1999; 9:639-643. (Pubitemid 29470956)
14. Riemenschneider MJ, Reifenberger J, Reifenberger G. Frequent biallelic inactivation and transcriptional silencing of the DIRAS3 gene at 1 p31 in Oligodendroglial tumors with 1p loss. Int J Cancer. 2008; 122:2503-2510. (Pubitemid 351590483)
15. Wolf MR, Draghi N, Liang X, et al. 190RhoGAP can act to inhibit PDGF-induced gliomas in mice: a putative tumor suppressor encoded on human Chromosome 19q13.3. Cenes Dev. 2003; 17:476-487. (Pubitemid 36258762)
16. Kunitz A, Wolter M, van den Boom J, et al. DNA hypermethylation and aberrant expression of the EMP3 gene at 19q13.3 in human gliomas. Brain Pathol. 2007; 17:363-370. (Pubitemid 47537593)
17. Ünlü M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis. 1997; 18:2071-2077. (Pubitemid 27501267)
18. van den Boom J, Wolter M, Kuick R, et al. Characterization of gene expression profiles associated with glioma progression using oligonucleotide-based microarray analysis and real-time reverse transcriptionpolymerase chain reaction. Am J Pathol. 2003; 163:1033-1043. (Pubitemid 37040139)
19. Felsberg J, Erkwoh A, Sabei M, et al. Oligodendroglial tumors: refinement of candidate regions on chromosome arm 1p and correlation of 1p/19q status with survival. Brain Pathol. 2004;14:121-130. (Pubitemid 38656383)
20. 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)
21. Nesterenko MV, Tilley M, Upton SJ. A simple modification of Blum's sliver stain method allows for 30 minute detection of proteins in Polyacrylamide gels. J Biochem Biophys Methods. 1994; 28:239-242. (Pubitemid 24131336)
22. Klose J. Large-gel 2-Delectrophoresis. Methods Mol Biol. 1999; 112:147-172.
23. Klose J, Kobalz U. Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis. 1995; 16:1034-1059.
24. Sitek B, Sipos B, Pfeiffer K, et al. Establishment of one-piece large-gel 2-DE for high-resolution analysis of small amounts of sample using difference gel electrophoresis saturation labeling. Anal Bioanal Chem. 2008; 391:361-365. (Pubitemid 351572429)
25. Marcus K, immler D, Sternberger J, et al. Identification of platelet proteins separated by two-dimensional gel elctrophoresis and analyzed by matrix assisted laser desorption/ionization-time of flight-mass spectrometry and detection of tyrosine-phosphorylated proteins. Electrophoresis, 2000; 21:2622-2636. (Pubitemid 30646297)
26. Ehrbrecht A, Muller U, Wolter M, et al. Comprehensive genomic analysis of desmoplastic medulloblastomas: identification of novel amplified genes and separate evaluation of the different histological components. J Pathol. 2006; 208:554-563. (Pubitemid 43329342)
27. Herman JG, Graff JR, Myöhänen S, et al. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA. 1996; 18:9821-9826.
28. Konings H. Use of Deming regression in method-comparison studies. Surv Immunol Res. 1982; 1:371-374.
29. Peri S, Navarro JD, Amanchy R, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003; 13:2363-2371.
30. Zweig MH, Campbell G. Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin Chem. 1993; 39:561-577.
31. Takizawa T, Nakashima K, Namihira M, et al. DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev Cell. 2001; 1:749-758.
32. Stupp R, Hegi M. Neuro-oncology: oligodendroglioma and molecular markers. Lancet Neurol. 2007; 6:10-12.
33. Okamoto H, Li J, Gläsker S, et al. Proteomic comparison of oligodendrogliomas with and without 1p LOH. Cancer Biol Ther. 2007; 6:391-396.
34. Ejeskär K, Krona C, Carén H, et al. Introduction of in vitro transcribed ENO1 mRNA in to neuroblastoma cells induce cell death. BMC Cancer. 2005; 16:161.
35. Subramanian A, Miller DM. Structural analysis of alpha-enolase. Mapping the functional domains involved in down-regulation of the c-myc protooncogene. J Biol Chem. 2000; 275:5958-5965.
36. Tews B, Felsberg J, Hartmann C, et al. Identification of novel oligodendroglioma-associated candidate tumor suppressor genes in 1p36 and 19q13 using microarray-based expression profiling. Int J Cancer. 2006; 119:792-800.
37. Quinlan RA, Brenner M, Goldman JE, et al. GFAP and its role in Alexander disease. Exp Cell Res. 2007; 313:2077-2087.
38. Brat DJ, Shehata BM, Castellano-Sanchez AA, et al. Congenital glioblastoma: a clinicopathologic and genetic analysis. Brain Pathol. 2007; 17:276-281.
39. Herpers MJ, Budka H. Glial fibrillary acidic protein (GFAP) in Oligodendroglial tumors: gliofibrillary oligodendroglioma and transitional oligoastrocytoma as subtypes of oligodendroglioma. Acta Neuropathol. 1984; 64:265-272.
40. Aldape K, Burger PC, Perry A. Clinicopathologic aspects of 1p/19q loss and the diagnosis of oligodendroglioma. Arch Pathol Lab Med. 2007; 131:242-251.
41. Maintz D, Fiedler K, Koopmann J, et al. Molecular genetic evidence for subtypes of oligoastrocytomas. J Neuropathol Exp Neurol. 1997; 56:1098-1104.
42. Gopalan SM, Wilczynska KM, Konik BS, et al. Nuclear factor-1-X regulates astrocyte-specific expression of the alphal -antichymotrypsin and glial fibrillary acidic protein genes. J Biol Chem. 2006; 281:13126-13133.
43. Laping NJ, Teter B, Nichols NR, et al. Glial fibrillary acidic protein: regulation by hormones, cytokines, and growth factors. Brain Pathol. 1994;4:259-275.
44. Fukuyama K, Matsuzawa K, Hubbard SL, et al. Analysis of glial fibrillary acidic protein gene methylation in human malignant gliomas. Anticancer Res. 1996; 16:1251-1257.
45. Reifenberger G, Szymas J, Wechsler W. Differential expression of glialand neuronal-associated antigens in human tumors of the central and peripheral nervous system. Acta Neuropathol. 1987; 74:105-123.
46. Perentes E, Rubinstein LJ. Recent applications of immunoperoxidase histochemistry in human neuro-oncology. An update. Arch Pathol Lab Med. 1987; 111:796-812.
47. Dehghani F, Schachenmayr W, Laun A, et al. Prognostic implication of histopathological, immunohistochemical and clinical features of oligodendrogliomas: a study of 89 cases. Acta Neuropathol. 1998; 95:493-504.
48. Izmailova ES, Wieczorek E, Perkins EB, et al. A GC-box is required for expression of the human vimentin gene. Gene. 1999; 235:69-75.
49. Chen WD, Han ZJ, Skoletsky J, et al. Detectioninfecal DNA of colon cancer-specific methylation of the nonexpressed vimentin gene. J Natl Cancer Inst. 2005; 97:1124-1132.
50. Hughes SC, Fehon RG. Understanding ERM proteins- the awesome power of genetics finally brought to bear. Curr Opin Cell Biol. 2007;19:51-56.
51. Geiger KD, Stoldt P, Schlote W, et al. Ezrin immunoreactivity is associated with increasing malignancy of astrocytic tumors but is absent in oligodendrogliomas. Am J Pathol. 2000; 157:1785-1793.
52. Tynninen O, Carpén O, Jääskelälnen J, et al. Ezrin expression in tissue microarray of primary and recurrent gliomas. Neuropathol Appl Neurobiol. 2004; 30:472-477.
53. Lim LH, Pervaiz S. Annexin 1: the new face of an old molecule. FASEB J. 2007; 21:968-975.
54. Castro-Caldas M. Annexin-1: 2nd messanger of the anti-inflammatory actions of glucocorticoids. Acta Reumatol Port. 2006; 31:293-302.
55. Shen J, Person MD, Zhu J, et al. Protein expression profiles in pancreatic adenocarcinoma compared with normal pancreatic tissue and tissue affected by pancreatitis as detected by two-dimensional gel electrophoresis and mass spectrometry. Cancer Res. 2004;64:9018-9026.
56. Garcia Pedrero JM, Fernandez MP, Morgan RO, et al. Annexin A1 down-regulationinhead and neck cancer is associated with epithelial differentiation status. Am J Pathol. 2004; 164:73-79.
57. Yu G, Wang J, Chen Y, et al. Tissue microarray analysis reveals strong clinical evidence for a close association between loss of annexin A1 expression and nodal metastasis in gastric cancer. Clin Exp Metastasis. 2008;25:695-702.
58. de Bont JM, den Boer ML, Kros JM, et al. Identification of novel biomarkers in pediatric primitive neuroectodermal tumors and ependymomas by proteome-wide analysis. J Neuropathol Exp Neurol. 2007; 66:505-516.
59. Johnson MD, Kamso-Pratt J, Pepinsky RB, et al. Lipocortin-1 immunoreactivity in central and peripheral nervous system glial tumors. Hum Pathol. 1989; 20:772-776. (Pubitemid 19203639)
60. Ruano Y, Mollejo M, Camacho Fl, et al. Identification of survival-related genes of the phosphatidylinositol 3'-kinase signaling pathway in glioblastoma multiforme. Cancer. 2008; 112:1575-1584.
61. Wolter M, Reifenberger J, Blaschke B, et al. Oligodendroglial tumors frequently demonstrate hypermethylation of the CDKN2A (MTS1, p16INK4a), p14ARF, and CDKN2B (MTS2, p15INK4b) tumor suppressor genes. J Neuropathol Exp Neurol. 2001; 60:1170-1180.
62. Dong SM, Pang JC, Poon WS, et al. Concurrent hypermethylation of multiple genes is associated with grade of Oligodendroglial tumors. J Neuropathol Exp Neurol. 2001;60:808-816.
63. Alonso ME, Bello MJ, Gonzalez-Gomez P, et al. Aberrant promoter methylation of multiple genes in oligodendrogliomas and ependymomas. Cancer Genet Cytogenet. 2003;144:134-142.
64. Reifenberger G, Kros JM, Louis DN, et al. Oligodendroglioma. in: Louis, DN, Ohgaki, H, Wiestler, OD, Cavenee, WK, eds. WHO Classification of Tumours of the Central Nervous System. Lyon: IARC; 2007: 54-59.