BTECH: A platform to integrate genomic, transcriptomic and epigenomic alterations in brain tumors

Neuroinformatics

Volumn 9, Issue 1, 2011, Pages 59-67

  Wang, Min ^a   Xie, Hehuang ^a   Stellpflug, Wendy ^a   Rajaram, Veena ^a   De Fatima Bonaldo, Maria ^a   Goldman, Stewart ^a   Tomita, Tadanori ^a   Soares, Marcelo Bento ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Brain tumor; Database; DNA methylation; Epigenomics; Gene expression; Genome browser; Genomics

Indexed keywords

ARTICLE; BRAIN TUMOR; DATA BASE; FACTUAL DATABASE; GENE EXPRESSION PROFILING; GENETIC EPIGENESIS; GENETICS; GENOMICS; HUMAN; METHODOLOGY; ORGANIZATION AND MANAGEMENT;

BRAIN NEOPLASMS; DATABASES AS TOPIC; DATABASES, FACTUAL; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENOMICS; HUMANS;

EID: 79953791086     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-010-9091-9     Document Type: Article

References (73)

1. Abo-Dalo, B., Kutsche, K., Mautner, V., & Kluwe, L. (2010). Large intragenic deletions of the NF2 gene: breakpoints and associated phenotypes. Genes Chromosom Cancer, 49(2), 171-175.
2. Bandres, E., Andion, E., Escalada, A., Honorato, B., Catalan, V., Cubedo, E., et al. (2005). Gene expression profile induced by BCNU in human glioma cell lines with differential MGMT expression. J Neurooncol, 73(3), 189-198. (Pubitemid 40974013)
3. Batzer, M. A., Rubin, C. M., Hellmann-Blumberg, U., Alegria-Hartman, M., Leeflang, E. P., Stern, J. D., et al. (1995). Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J Mol Biol, 247(3), 418-427.
4. Bird, A. P., & Wolffe, A. P. (1999). Methylation-induced repression - belts, braces, and chromatin. Cell, 99(5), 451-454. (Pubitemid 129746827)
5. Boon, K., Osorio, E. C., Greenhut, S. F., Schaefer, C. F., Shoemaker, J., Polyak, K., et al. (2002). An anatomy of normal and malignant gene expression. Proc Natl Acad Sci USA, 99(17), 11287-11292. (Pubitemid 34920918)
6. Bozinov, O., Kohler, S., Samans, B., Benes, L., Miller, D., Ritter, M., et al. (2008). Candidate genes for the progression of malignant gliomas identified by microarray analysis. Neurosurg Rev, 31(1), 83-89. discussion 89-90.
7. Bredel, M., Bredel, C., Juric, D., Duran, G. E., Yu, R. X., Harsh, G. R., et al. (2006). Tumor necrosis factor-alpha-induced protein 3 as a putative regulator of nuclear factor-kappaB-mediated resistance to O6-alkylating agents in human glioblastomas. J Clin Oncol, 24(2), 274-287. (Pubitemid 46622056)
8. Bredel, M., Bredel, C., Juric, D., Harsh, G. R., Vogel, H., Recht, L. D., et al. (2005). High-resolution genome-wide mapping of genetic alterations in human glial brain tumors. Cancer Res, 65 (10), 4088-4096. (Pubitemid 40775645)
9. Brennan, C., Momota, H., Hambardzumyan, D., Ozawa, T., Tandon, A., Pedraza, A., et al. (2009). Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations. PLoS ONE, 4(11), e7752.
10. Brito-Babapulle, V., & Atkin, N. B. (1981). Break points in chromosome #1 abnormalities of 218 human neoplasms. Cancer Genet Cytogenet, 4(3), 215-225. (Pubitemid 12251425)
11. Chen, J., Heerdt, B. G., & Augenlicht, L. H. (1995). Presence and instability of repetitive elements in sequences the altered expression of which characterizes risk for colonic cancer. Cancer Res, 55(1), 174-180.
12. Cho, N. Y., Kim, B. H., Choi, M., Yoo, E. J., Moon, K. C., Cho, Y. M., et al. (2007). Hypermethylation of CpG island loci and hypomethylation of LINE-1 and Alu repeats in prostate adenocarcinoma and their relationship to clinicopathological features. J Pathol, 211(3), 269-277. (Pubitemid 46172702)
13. Cordaux, R., Srikanta, D., Lee, J., Stoneking, M., & Batzer, M. A. (2007). In search of polymorphic Alu insertions with restricted geographic distributions. Genomics, 90(1), 154-158.
14. Deshmukh, H., Yeh, T. H., Yu, J., Sharma, M. K., Perry, A., Leonard, J. R., et al. (2008). High-resolution, dual-platform aCGH analysis reveals frequent HIPK2 amplification and increased expression in pilocytic astrocytomas. Oncogene, 27(34), 4745-4751.
15. Dong, S., Nutt, C. L., Betensky, R. A., Stemmer-Rachamimov, A. O., Denko, N. C., Ligon, K. L., et al. (2005a). Histology-based expression profiling yields novel prognostic markers in human glioblastoma. J Neuropathol Exp Neurol, 64(11), 948-955. (Pubitemid 41668924)
16. Dong, H., Wade, M., Williams, A., Lee, A., Douglas, G. R., & Yauk, C. (2005b). Molecular insight into the effects of hypothyroidism on the developing cerebellum. Biochem Biophys Res Commun, 330(4), 1182-1193.
17. Donson, A. M., Birks, D. K., Barton, V. N., Wei, Q., Kleinschmidt- Demasters, B. K., Handler, M. H., et al. (2009). Immune gene and cell enrichment is associated with a good prognosis in ependymoma. J Immunol, 183(11), 7428-7440.
18. Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V. K., Attwood, J., Burger, M., et al. (2006). DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet, 38(12), 1378-1385.
19. Estecio, M. R., Yan, P. S., Ibrahim, A. E., Tellez, C. S., Shen, L., Huang, T. H., et al. (2007). High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res, 17(10), 1529-1536. (Pubitemid 47529437)
20. Fathallah-Shaykh, H. M. (2005). Logical networks inferred from highly specific discovery of transcriptionally regulated genes predict protein states in cultured gliomas. Biochem Biophys Res Commun, 336(4), 1278-1284.
21. Feinberg, A. P., & Tycko, B. (2004). The history of cancer epigenetics. Nat Rev Cancer, 4(2), 143-153. (Pubitemid 38198742)
22. Freije, W. A., Castro-Vargas, F. E., Fang, Z., Horvath, S., Cloughesy, T., Liau, L. M., et al. (2004). Gene expression profiling of gliomas strongly predicts survival. Cancer Res, 64(18), 6503-6510. (Pubitemid 39297907)
23. Gad, S., Caux-Moncoutier, V., Pages-Berhouet, S., Gauthier-Villars, M., Coupier, I., Pujol, P., et al. (2002). Significant contribution of large BRCA1 gene rearrangements in 120 French breast and ovarian cancer families. Oncogene, 21(44), 6841-6847. (Pubitemid 35221927)
24. Gravendeel, L. A., Kouwenhoven, M. C., Gevaert, O., de Rooi, J. J., Stubbs, A. P., Duijm, J. E., et al. (2009). Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. Cancer Res, 69(23), 9065-9072.
25. Hegi, M. E., Diserens, A. C., Gorlia, T., Hamou, M. F., de Tribolet, N., Weller, M., et al. (2005). MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med, 352(10), 997-1003. (Pubitemid 40349502)
26. Hoelzinger, D. B., Mariani, L., Weis, J., Woyke, T., Berens, T. J., McDonough, W. S., et al. (2005). Gene expression profile of glioblastoma multiforme invasive phenotype points to new therapeutic targets. Neoplasia, 7(1), 7-16. (Pubitemid 40209466)
27. Iskow, R. C., McCabe, M. T., Mills, R. E., Torene, S., Pittard, W. S., Neuwald, A. F., et al. (2010). Natural mutagenesis of human genomes by endogenous retrotransposons. Cell, 141(7), 1253-1261.
28. Jemal, A., Siegel, R., Ward, E., Hao, Y., Xu, J., Murray, T., et al. (2008). Cancer statistics, 2008. CA Cancer J Clin, 58(2), 71-96.
29. Jordan, I. K., Rogozin, I. B., Glazko, G. V., & Koonin, E. V. (2003). Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet, 19(2), 68-72. (Pubitemid 36120660)
30. Kazazian, H. H., Jr. (2004). Mobile elements: drivers of genome evolution. Science, 303(5664), 1626-1632.
31. Kikuchi, T., Daigo, Y., Ishikawa, N., Katagiri, T., Tsunoda, T., Yoshida, S., et al. (2006). Expression profiles of metastatic brain tumor from lung adenocarcinomas on cDNA microarray. Int J Oncol, 28(4), 799-805.
32. Kim, J., Kollhoff, A., Bergmann, A., & Stubbs, L. (2003). Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3. Hum Mol Genet, 12(3), 233-245.
33. Kolomietz, E., Al-Maghrabi, J., Brennan, S., Karaskova, J., Minkin, S., Lipton, J., et al. (2001). Primary chromosomal rearrangements of leukemia are frequently accompanied by extensive submicroscopic deletions and may lead to altered prognosis. Blood, 97 (11), 3581-3588.
34. Kotliarov, Y., Steed, M. E., Christopher, N., Walling, J., Su, Q., Center, A., et al. (2006). High-resolution Global Genomic Survey of 178 Gliomas Reveals Novel Regions of Copy Number Alteration and Allelic Imbalances. Cancer Res, 66(19), 9428-9436. (Pubitemid 44623639)
35. Lee, J., Kotliarova, S., Kotliarov, Y., Li, A., Su, Q., Donin, N. M., et al. (2006). Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines. Cancer Cell, 9(5), 391-403. (Pubitemid 43668737)
36. Lev-Maor, G., Sorek, R., Shomron, N., & Ast, G. (2003). The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science, 300(5623), 1288-1291. (Pubitemid 36618239)
37. Lin, C. S., Goldthwait, D. A., & Samols, D. (1988). Identification of Alu transposition in human lung carcinoma cells. Cell, 54(2), 153-159.
38. Ljubimova, J. Y., Lakhter, A. J., Loksh, A., Yong, W. H., Riedinger, M. S., Miner, J. H., et al. (2001). Overexpression of alpha4 chain-containing laminins in human glial tumors identified by gene microarray analysis. Cancer Res, 61(14), 5601-5610. (Pubitemid 32694948)
39. Ma, D., Nutt, C. L., Shanehsaz, P., Peng, X., Louis, D. N., & Kaetzel, D. M. (2005). Autocrine platelet-derived growth factor-dependent gene expression in glioblastoma cells is mediated largely by activation of the transcription factor sterol regulatory element binding protein and is associated with altered genotype and patient survival in human brain tumors. Cancer Res, 65(13), 5523-5534. (Pubitemid 40911152)
40. Mariani, L., Beaudry, C., McDonough, W. S., Hoelzinger, D. B., Demuth, T., Ross, K. R., et al. (2001). Glioma cell motility is associated with reduced transcription of proapoptotic and proliferation genes: a cDNA microarray analysis. J Neurooncol, 53(2), 161-176. (Pubitemid 33034689)
41. Mauillon, J. L., Michel, P., Limacher, J. M., Latouche, J. B., Dechelotte, P., Charbonnier, F., et al. (1996). Identification of novel germline hMLH1 mutations including a 22 kb Alu-mediated deletion in patients with familial colorectal cancer. Cancer Res, 56(24), 5728-5733. (Pubitemid 26422180)
42. Mehrian Shai, R., Reichardt, J. K., Ya-Hsuan, H., Kremen, T. J., Liau, L. M., Cloughesy, T. F., et al. (2005). Robustness of gene expression profiling in glioma specimen samplings and derived cell lines. Brain Res Mol Brain Res, 136(1-2), 99-103. (Pubitemid 40704613)
43. Mendrzyk, F., Korshunov, A., Benner, A., Toedt, G., Pfister, S., Radlwimmer, B., et al. (2006). Identification of gains on 1q and epidermal growth factor receptor overexpression as independent prognostic markers in intracranial ependymoma. Clin Cancer Res, 12(7 Pt 1), 2070-2079.
44. Miki, Y., Katagiri, T., Kasumi, F., Yoshimoto, T., & Nakamura, Y. (1996). Mutation analysis in the BRCA2 gene in primary breast cancers. Nat Genet, 13(2), 245-247. (Pubitemid 26000446)
45. Mueller, W., Hartmann, C., Hoffmann, A., Lanksch, W., Kiwit, J., Tonn, J., et al. (2002). Genetic signature of oligoastrocytomas correlates with tumor location and denotes distinct molecular subsets. Am J Pathol, 161(1), 313-319. (Pubitemid 34760797)
46. Pachiappan, A., Thwin,M.M.,Manikandan, J.,& Gopalakrishnakone, P. (2005). Glial inflammation and neurodegeneration induced by candoxin, a novel neurotoxin from Bungarus candidus venom: global gene expression analysis using microarray. Toxicon, 46(8), 883-899.
47. Park, P. C., Taylor, M. D., Mainprize, T. G., Becker, L. E., Ho, M., Dura, W. T., et al. (2003). Transcriptional profiling of medulloblastoma in children. J Neurosurg, 99(3), 534-541. (Pubitemid 37040416)
48. Rand, V., Prebble, E., Ridley, L., Howard, M., Wei, W., Brundler, M. A., et al. (2008). Investigation of chromosome 1q reveals differential expression of members of the S100 family in clinical subgroups of intracranial paediatric ependymoma. Br J Cancer, 99(7), 1136-1143.
49. Raza, S. M., Fuller, G. N., Rhee, C. H., Huang, S., Hess, K., Zhang, W., et al. (2004). Identification of necrosis-associated genes in glioblastoma by cDNA microarray analysis. Clin Cancer Res, 10 (1 Pt 1), 212-221. (Pubitemid 38114182)
50. Rich, J. N., Hans, C., Jones, B., Iversen, E. S., McLendon, R. E., Rasheed, B. K., et al. (2005). Gene expression profiling and genetic markers in glioblastoma survival. Cancer Res, 65(10), 4051-4058. (Pubitemid 40775641)
51. Riggs, A. D., & Jones, P. A. (1983). 5-methylcytosine, gene regulation, and cancer. Adv Cancer Res, 40, 1-30.
52. Rollins, R. A., Haghighi, F., Edwards, J. R., Das, R., Zhang, M. Q., Ju, J., et al. (2006). Large-scale structure of genomic methylation patterns. Genome Res, 16(2), 157-163. (Pubitemid 43200263)
53. Roman-Gomez, J., Jimenez-Velasco, A., Agirre, X., Castillejo, J. A., Navarro, G., San Jose-Eneriz, E., et al. (2008). Repetitive DNA hypomethylation in the advanced phase of chronic myeloid leukemia. Leuk Res, 32(3), 487-490. (Pubitemid 351308023)
54. Schumacher, A., Kapranov, P., Kaminsky, Z., Flanagan, J., Assadzadeh, A., Yau, P., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res, 34(2), 528-542. (Pubitemid 43240241)
55. Smith, L. T.,Otterson,G. A.,&Plass, C. (2007). Unraveling the epigenetic code of cancer for therapy. Trends Genet, 23(9), 449-456.
56. Sorek, R., Lev-Maor, G., Reznik, M., Dagan, T., Belinky, F., Graur, D., et al. (2004). Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons. Mol Cell, 14(2), 221-231. (Pubitemid 38515649)
57. Stein, L. D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., et al. (2002). The generic genome browser: a building block for a model organismsystemdatabase. Genome Res, 12(10), 1599-1610. (Pubitemid 35175099)
58. Strout,M. P., Marcucci, G., Bloomfield, C. D., & Caligiuri,M. A. (1998). The partial tandem duplication of ALL1 (MLL) is consistently generated by Alu-mediated homologous recombination in acute myeloid leukemia. Proc Natl Acad Sci USA, 95(5), 2390-2395. (Pubitemid 28145951)
59. Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., et al. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA, 101(16), 6062-6067. (Pubitemid 38520528)
60. Sun, L., Hui, A.M., Su, Q., Vortmeyer, A., Kotliarov, Y., Pastorino, S., et al. (2006). Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer Cell, 9(4), 287-300.
61. Takai, D., & Jones, P. A. (2002). Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA, 99(6), 3740-3745. (Pubitemid 34252176)
62. Taylor, M. D., Poppleton, H., Fuller, C., Su, X., Liu, Y., Jensen, P., et al. (2005). Radial glia cells are candidate stem cells of ependymoma. Cancer Cell, 8(4), 323-335. (Pubitemid 41443417)
63. Teugels, E., De Brakeleer, S., Goelen, G., Lissens, W., Sermijn, E., & De Greve, J. (2005). De novo Alu element insertions targeted to a sequence common to the BRCA1 and BRCA2 genes. Hum Mutat, 26(3), 284.
64. Tso, C. L., Shintaku, P., Chen, J., Liu, Q., Liu, J., Chen, Z., et al. (2006). Primary glioblastomas express mesenchymal stem-like properties. Mol Cancer Res, 4(9), 607-619. (Pubitemid 44497214)
65. Turkheimer, F. E., Roncaroli, F., Hennuy, B., Herens, C., Nguyen, M., Martin, D., et al. (2006). Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas. BMC Bioinform, 7, 526.
66. Verhaak, R. G., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., et al. (2010). Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell, 17(1), 98-110.
67. Vogelstein, B., & Kinzler, K. W. (1993). The multistep nature of cancer. Trends Genet, 9(4), 138-141. (Pubitemid 23098782)
68. Whang-Peng, J., Kao-Shan, C. S., Lee, E. C., Bunn, P. A., Carney, D. N., Gazdar, A. F., et al. (1982). Specific chromosome defect associated with human small-cell lung cancer; deletion 3p(14-23). Science, 215(4529), 181-182. (Pubitemid 12178106)
69. Wu, X., Rauch, T. A., Zhong, X., Bennett, W. P., Latif, F., Krex, D., et al. (2010). CpG island hypermethylation in human astrocytomas. Cancer Res, 70(7), 2718-2727.
70. Xie H,Wang M, Bonaldo MD, Smith C, Rajaram V, Goldman S, Tomita T, Soares MB (2009) High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res
71. Xie, H.,Wang, M., Bonaldo Mde, F., Rajaram, V., Stellpflug,W., Smith, C., et al. (2010). Epigenomic analysis of Alu repeats in human ependymomas. Proc Natl Acad Sci USA, 107(15), 6952-6957.
72. Xing, J., Zhang, Y., Han, K., Salem, A. H., Sen, S. K., Huff, C. D., et al. (2009). Mobile elements create structural variation: analysis of a complete human genome. Genome Res, 19(9), 1516-1526.
73. Zlatescu, M. C., TehraniYazdi, A., Sasaki, H., Megyesi, J. F., Betensky, R. A., Louis, D. N., et al. (2001). Tumor location and growth pattern correlate with genetic signature in oligodendroglial neoplasms. Cancer Res, 61(18), 6713-6715. (Pubitemid 32896492)