Discovering gene-environment interactions in Glioblastoma through a comprehensive data integration bioinformatics method

NeuroToxicology

Volumn 35, Issue 1, 2013, Pages 1-14

  Kunkle, Brian ^a   Yoo, Changwon ^a   Roy, Deodutta ^a  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

Author keywords

Bioinformatics; Comparative Toxicology Database; Copy number variation; DAVID; Environmental exposure; Gene variation; Gene environment interaction; Glioblastoma; Nerve growth factor; Single nucleotide polymorphism

Indexed keywords

ARACHIDONIC ACID; DNA; INTEGRIN; NERVE GROWTH FACTOR;

APOPTOSIS; ARACHIDONIC ACID METABOLISM; ARTICLE; BIOINFORMATICS; CARCINOGENESIS; CELL CYCLE CHECKPOINT; CELL SURFACE; COMPARATIVE TOXICOLOGY; COMPUTER PROGRAM; COPY NUMBER VARIATION; DISEASE ASSOCIATION; DNA REPAIR; ENVIRONMENTAL EXPOSURE; ENVIRONMENTAL GENOME PROJECT; GENE FUNCTION; GENE IDENTIFICATION; GENE MUTATION; GENETIC DATABASE; GENETIC VARIABILITY; GENOMICS; GENOTYPE ENVIRONMENT INTERACTION; GLIOBLASTOMA; OXIDATION; PRIORITY JOURNAL; SAMPLE SIZE; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; SYNAPTIC TRANSMISSION;

ALGORITHMS; BRAIN NEOPLASMS; CARCINOGENS; CELL TRANSFORMATION, NEOPLASTIC; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, GENETIC; DNA COPY NUMBER VARIATIONS; ENVIRONMENTAL EXPOSURE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GENE-ENVIRONMENT INTERACTION; GENETIC PREDISPOSITION TO DISEASE; GLIOBLASTOMA; HUMANS; MUTATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK ASSESSMENT; RISK FACTORS;

EID: 84873180351     PISSN: 0161813X     EISSN: 18729711     Source Type: Journal    
DOI: 10.1016/j.neuro.2012.11.001     Document Type: Article

References (67)

1. Angus W.G., Contreras M.L. The effects of Aroclor 1254 on undifferentiated and NGF-stimulated differentiating PC12 cells. Neurotoxicology 1994, 15:809-817.
2. Antonov A.V., Schmidt E.E., Dietmann S., Krestyaninova M., Hermjakob H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res 2010, 38:W78-W83.
3. Arlt M.F., Ozdemir A.C., Birkeland S.R., Lyons R.H., Glover T.W., Wilson T.E. Comparison of constitutional and replication stress-induced genome structural variation by SNP array and mate-pair sequencing. Genetics 2011, 187:675-683.
4. Barnette P., Scholl R., Blandford M., Ballard L., Tsodikov A., Magee J., et al. High-throughput detection of glutathione S-transferase polymorphic alleles in a pediatric cancer population. Cancer Epidemiol Biomarkers Prev 2004, 13:304-313.
5. Bauer-Mehren A., Bundschus M., Rautschka M., Mayer M.A., Sanz F., Furlong L.I. Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases. PLoS ONE 2011, 6:e20284.
6. Bhatti P., Stewart P.A., Hutchinson A., Rothman N., Linet M.S., Inskip P.D., et al. Lead exposure, polymorphisms in genes related to oxidative stress, and risk of adult brain tumors. Cancer Epidemiol Biomarkers Prev 2009, 18:1841-1848.
7. Brown M.C., Staniszewska I., Lazarovici P., Tuszynski G.P., Del V.L., Marcinkiewicz C. Regulatory effect of nerve growth factor in alpha9beta1 integrin-dependent progression of Glioblastoma. Neuro Oncol 2008, 10:968-980.
8. Cao J., Varnell A.L., Cooper D.C. Gulf War Syndrome: a role for organophosphate induced plasticity of locus coeruleus neurons. Nature Preceedings 2011.
9. Carter H., Chen S., Isik L., Tyekucheva S., Velculescu V.E., Kinzler K.W., et al. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res 2009, 69:6660-6667.
10. Davis A.P., Murphy C.G., Saraceni-Richards C.A., Rosenstein M.C., Wiegers T.C., Mattingly C.J. Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Res 2009, 37:D786-D792.
11. de Andrade M., Barnholtz J.S., Amos C.I., Adatto P., Spencer C., Bondy M.L. Segregation analysis of cancer in families of glioma patients. Genet Epidemiol 2001, 20:258-270.
12. De Roos A.J., Rothman N., Inskip P.D., Linet M.S., Shapiro W.R., Selker R.G., et al. Genetic polymorphisms in GSTM1, -P1, -T1, and CYP2E1 and the risk of adult brain tumors. Cancer Epidemiol Biomarkers Prev 2003, 12:14-22.
13. De Roos A.J., Rothman N., Brown M., Bell D.A., Pittman G.S., Shapiro W.R., et al. Variation in genes relevant to aromatic hydrocarbon metabolism and the risk of adult brain tumors. Neuro Oncol 2006, 8:145-155.
14. Dolle L., El Yazidi-Belkoura I, Adriaenssens E., Nurcombe V., Hondermarck H. Nerve growth factor overexpression and autocrine loop in breast cancer cells. Oncogene 2003, 22:5592-5601.
15. Dolle L., Adriaenssens E., El Yazidi-Belkoura I., Le Bourhis X., Nurcombe V., Hondermarck H. Nerve growth factor receptors and signaling in breast cancer. Curr Cancer Drug Targets 2004, 4:463-470.
16. Erichsen H.C., Chanock S.J. SNPs in cancer research and treatment. Br J Cancer 2004, 90:747-751.
17. Ezer R., Alonso M., Pereira E., Kim M., Allen J.C., Miller D.C., et al. Identification of glutathione S-transferase (GST) polymorphisms in brain tumors and association with susceptibility to pediatric astrocytomas. J Neurooncol 2002, 59:123-134.
18. Forbes S.A., Bindal N., Bamford S., Cole C., Kok C.Y., Beare D., et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 2011, 39:D945-D950.
19. Freire P., Vilela M., Deus H., Kim Y.W., Koul D., Colman H., et al. Exploratory analysis of the copy number alterations in Glioblastoma multiforme. PLoS ONE 2008, 3:e4076.
20. Furnari F.B., Fenton T., Bachoo R.M., Mukasa A., Stommel J.M., Stegh A., et al. Malignant astrocytic glioma: genetics, biology, and paths to treatment. Genes Dev 2007, 21:2683-2710.
21. Giraud S., Loum E., Bessette B., Mathonnet M., Lalloue F. P75 neurotrophin receptor is sequestered in the Golgi apparatus of the U-87 MG human Glioblastoma cell line. Int J Oncol 2011, 38:391-399.
22. Guerrero-Bosagna C., Settles M., Lucker B., Skinner M.K. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome. PLoS ONE 2010, 5:e13100.
23. Herbert M.R., Russo J.P., Yang S., Roohi J., Blaxill M., Kahler S.G., et al. Autism and environmental genomics. Neurotoxicology 2006, 27:671-684.
24. Holub J.L., Qiu Y.Y., Chu F., Madonna M.B. The role of nerve growth factor in caspase-dependent apoptosis in human BE(2)C neuroblastoma. J Pediatr Surg 2011, 46:1191-1196.
25. Huang D.W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
26. Hunter D.J. Gene-environment interactions in human diseases. Nat Rev Genet 2005, 6:287-298.
27. Kafadar A.M., Ergen A., Zeybek U., Agachan B., Kuday C., Isbir T. Paraoxonase 192 gene polymorphism and serum paraoxonase activity in high grade gliomas and meningiomas. Cell Biochem Funct 2006, 24:455-460.
28. Korshunov A., Sycheva R., Golanov A. Genetically distinct and clinically relevant subtypes of Glioblastoma defined by array-based comparative genomic hybridization (array-CGH). Acta Neuropathol 2006, 111:465-474.
29. Kunkle B., Sandberg D., Jayakar P., Felty Q., Roy D. Gene-environment interaction, susceptibility to pediatric brain tumors. Environmental factors, genes, and the development of human cancers 2010, 223-252. Springer Press, New York/Dordrecht/Heidelberg/London. D. Roy, M.T. Dorak (Eds.).
30. Lachance D.H., Yang P., Johnson D.R., Decker P.A., Kollmeyer T.M., McCoy L.S., et al. Associations of high-grade glioma with glioma risk alleles and histories of allergy and smoking. Am J Epidemiol 2011, 174:574-581.
31. Lai R., Crevier L., Thabane L. Genetic polymorphisms of glutathione S-transferases and the risk of adult brain tumors: a meta-analyis. Cancer Epidemiol Biomarkers Prev 2005, 7:1784-1790.
32. Lopez-Flores I., Lacasana M., Blanco-Munoz J., Aguilar-Garduno C., Sanchez-Villegas P., Perez-Mendez O.A., et al. Relationship between human paraoxanase-1 activity and PON1 polymorphisms in Mexican workers exposed to organophosphate pesticides. Toxicol Lett 2009, 188:84-90.
33. Manolio T.A. Genomewide association studies and assessment of the risk of disease. N Engl J Med 2010, 363:166-176.
34. Marchetti D., Mrak R.E., Paulsen D.D., Sinnappah-Kang N.D. Neurotrophin receptors and heparanase: a functional axis in human medulloblastoma invasion. J Exp Clin Cancer Res 2007, 26:5-23.
35. Margareto J., Leis O., Larrarte E., Pomposo I.C., Garibi J.M., Lafuente J.V. DNA copy number variation and gene expression analyses reveal the implication of specific oncogenes and genes in GBM. Cancer Invest 2009, 27:541-548.
36. Martinez C., Molina J.A., Alonso-Navarro H., Jimenez-Jimenez F.J., Agundez J., Garcia-Martin E. Two common nonsynonymous paraoxonase 1 (PON1) gene polymorphisms and brain astrocytoma and meningioma. BMC Neurol 2010, 10:71-78.
37. McCarroll S.A., Kuruvilla F.G., Korn J.M., Cawley S., Nemesh J., Wysoker A., et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 2008, 40:1166-1174.
38. McEachin R.C., Keller B.J., Saunders E.F., McInnis M.G. Modeling gene-by-environment interaction in comorbid depression with alcohol use disorders via an integrated bioinformatics approach. BioData Min 2008, 1:2.
39. McEachin R.C., Chen H., Sartor M.A., Saccone S.F., Keller B.J., Prossin A.R., et al. A genetic network model of cellular responses to lithium treatment and cocaine abuse in bipolar disorder. BMC Syst Biol 2010, 4:158.
40. McEachin R.C., Saccone N.L., Saccone S.F., Kleyman-Smith Y.D., Kar T., Kare R.K., et al. Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder. BMC Med Genet 2010, 11:14.
41. Mimura J., Kosaka K., Maruyama A., Satoh T., Harada N., Yoshida H., et al. Nrf2 regulates NGF mRNA induction by carnosic acid in T98G Glioblastoma cells and normal human astrocytes. J Biochem 2011, 150:209-217.
42. Myllykangas S., Tikka J., Bohling T., Knuutila S., Hollmen J. Classification of human cancers based on DNA copy number amplification modeling. BMC Med Genomics 2008, 1:15.
43. Myllykangas S., Knuutila S. Manifestation, mechanisms and mysteries of gene amplifications. Cancer Lett 2006, 232:79-89.
44. National Institutes of Health. What you need to know about brain tumors. National Cancer Institute. NIH Publication No. 02-1558. 2002.
45. Parsons D.W., Jones S., Zhang X., Lin J.C., Leary R.J., Angenendt P., et al. An integrated genomic analysis of human Glioblastoma multiforme. Science 2008, 321:1807-1812.
46. Pirooznia M., Nagarajan V., Deng Y. GeneVenn - a web application for comparing gene lists using Venn diagrams. Bioinformation 2007, 1:420-422.
47. Rajaraman P., Stewart P.A., Samet J.M., Schwartz B.S., Linet M.S., Zahm S.H., et al. Lead, genetic susceptibility, and risk of adult brain tumors. Cancer Epidemiol Biomarkers Prev 2006, 15:2514-2520.
48. Rajaraman P., Hutchinson A., Rothman N., Black P.M., Fine H.A., Loeffler J.S., et al. Oxidative response gene polymorphisms and risk of adult brain tumors. Neuro Oncol 2008, 10:709-715.
49. Rasi G., Serafino A., Bellis L., Lonardo M.T., Andreola F., Zonfrillo M., et al. Nerve growth factor involvement in liver cirrhosis and hepatocellular carcinoma. World J Gastroenterol 2007, 13:4986-4995.
50. Rauh V.A., Garfinkel R., Perera F.P., Andrews H.F., Hoepner L., Barr D.B., et al. Impact of prenatal chlorpyrifos exposure on neurodevelopment in the first 3 years of life among inner-city children. Pediatrics 2006, 118:e1845-e1859.
51. Rieder M.J., Livingston R.J., Stanaway I.B., Nickerson D.A. The environmental genome project: reference polymorphisms for drug metabolism genes and genome-wide association studies. Drug Metab Rev 2008, 40:241-261.
52. Romon R., Adriaenssens E., Lagadec C., Germain E., Hondermarck H., Le Bourhis X. Nerve growth factor promotes breast cancer angiogenesis by activating multiple pathways. Mol Cancer 2010, 9:157.
53. Santarius T., Shipley J., Brewer D., Stratton M.R., Cooper C.S. A census of amplified and overexpressed human cancer genes. Nat Rev Cancer 2010, 10:59-64.
54. Schaich M., Kestel L., Pfirrmann M., Robel K., Illmer T., Kramer M., et al. A MDR1 (ABCB1) gene single nucleotide polymorphism predicts outcome of temozolomide treatment in Glioblastoma patients. Ann Oncol 2009, 20:175-181.
55. Schoemaker M.J., Robertson L., Wigerts A., Jones M.E., Hosking F.J., Feychting M., et al. Interaction between 5 genetic variants and allergy in glioma risk. Am J Epidemiol 2010, 171:1165-1173.
56. Schwartzbaum J.A., Fisher J.L., Aldape K.D., Wrensch M. Epidemiology and molecular pathology of glioma. Nat Clin Pract Neurol 2006, 2:494-503.
57. Schwartzbaum J.A., Ahlbom A., Lonn S., Warholm M., Rannug A., Auvinen A., et al. An international case-control study of glutathione transferase and functionally related polymorphisms and risk of primary adult brain tumors. Cancer Epidemiol Biomarkers Prev 2007, 16:559-565.
58. Searles Nielson S., Mueller B.A., De Roos A.J., Viernes H.M., Farin F.M., Checkoway H. Risk of brain tumors in children and susceptibility to organophosphorus insecticides: the potential role of paraoxonase (PON1). Environ Health Perspect 2005, 113:909-913.
59. Searles Nielson S., McKean-Cowdin R., Farin M., Holly E.A., Preston-Martin S., Mueller B.A. Childhood brain tumors, residential insecticide exposure, and pesticide metabolism genes. Environ Health Perspect 2010, 118:144-149.
60. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
61. Stankiewics P., Lupski J.R. Structural variation in the human genome and its role in disease. Annu Rev Med 2010, 61:437-455.
62. Stranger B.E., Forrest M.S., Dunning M., Ingle C.E., Beazley C., Thorne N., et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315:848-853.
63. The Cancer Genome Atlas (TCGA) Comprehensive genomic characterization defines human Glioblastoma genes and core pathways. Nature 2008, 455:1061-1068.
64. Vogt N., Lefevre S.H., Apiou F., Dutrillaux A.M., Cor A., Leuraud P., et al. Molecular structure of double-minute chromosomes bearing amplified copies of the epidermal growth factor receptor gene in gliomas. Proc Natl Acad Sci USA 2004, 101:11368-11373.
65. Wang X., Tomso D.J., Liu X., Bell D.A. Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes. Toxicol Appl Pharmacol 2005, 207:84-90.
66. Weiner H.L. The role of growth factor receptors in central nervous system development and neoplasia. Neurosurgery 1995, 37:179-193.
67. Ye Y., Dang D., Zhang J., Viet C.T., Lam D.K., Dolan J., et al. Nerve growth factor links oral cancer progression, pain, and cachexia. Mol Cancer Ther 2011, 10:1667-1676.