SNP-SNP Interaction Network in Angiogenesis Genes Associated with Prostate Cancer Aggressiveness

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Lin, Hui Yi ^a   Amankwah, Ernest K ^a   Tseng, Tung Sung ^b   Qu, Xiaotao ^a   Chen, Dung Tsa ^a   Park, Jong Y ^a  

^a H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^b LOUISIANA STATE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; FIBULIN; PROTEOHEPARAN SULFATE;

ADULT; AGED; ANGIOGENESIS; ARTICLE; CANCER PATIENT; CANCER RISK; CARCINOGENESIS; CONTROLLED STUDY; CSF1 GENE; GENE; GENE INTERACTION; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; MMP16 GENE; PROSTATE CANCER; RANDOM FOREST; REGRESSION ANALYSIS; ROBO1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SNP SNP INTERACTION;

DISEASE PROGRESSION; EPISTASIS, GENETIC; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MALE; NEOVASCULARIZATION, PATHOLOGIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PROSTATIC NEOPLASMS;

EID: 84875704374     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059688     Document Type: Article

References (69)

1. Siegel R, Naishadham D, Jemal A, (2012) Cancer statistics, 2012. CA: A Cancer Journal for Clinicians 62: 10-29.
2. Damber JE, Aus G, (2008) Prostate cancer. Lancet 371: 1710-1721.
3. Albertsen PC, (2006) PSA and the conservative treatment of early prostate cancer. Arch Ital Urol Androl 78: 152-153.
4. Weis SM, Cheresh DA, (2011) Tumor angiogenesis: molecular pathways and therapeutic targets. Nat Med 17: 1359-1370.
5. Carmeliet P, Jain RK, (2011) Molecular mechanisms and clinical applications of angiogenesis. Nature 473: 298-307.
6. Carmeliet P, (2005) Angiogenesis in life, disease and medicine. Nature 438: 932-936.
7. Potente M, Gerhardt H, Carmeliet P, (2011) Basic and therapeutic aspects of angiogenesis. Cell 146: 873-887.
8. Folkman J, (2007) Angiogenesis: an organizing principle for drug discovery? Nat Rev Drug Discov 6: 273-286.
9. De Bock K, Mazzone M, Carmeliet P, (2011) Antiangiogenic therapy, hypoxia, and metastasis: risky liaisons, or not? Nat Rev Clin Oncol 8: 393-404.
10. Hanahan D, Christofori G, Naik P, Arbeit J, (1996) Transgenic mouse models of tumour angiogenesis: the angiogenic switch, its molecular controls, and prospects for preclinical therapeutic models. Eur J Cancer 32A: 2386-2393.
11. Nicholson B, Theodorescu D, (2004) Angiogenesis and prostate cancer tumor growth. J Cell Biochem 91: 125-150.
12. Hrouda D, Nicol DL, Gardiner RA, (2003) The role of angiogenesis in prostate development and the pathogenesis of prostate cancer. Urol Res 30: 347-355.
13. Jain L, Vargo CA, Danesi R, Sissung TM, Price DK, et al. (2009) The role of vascular endothelial growth factor SNPs as predictive and prognostic markers for major solid tumors. Mol Cancer Ther 8: 2496-2508.
14. Crawford ED, (2003) Epidemiology of prostate cancer. Urology 62: 3-12.
15. Hull GW, Rabbani F, Abbas F, Wheeler TM, Kattan MW, et al. (2002) Cancer control with radical prostatectomy alone in 1,000 consecutive patients. J Urol 167: 528-534.
16. Sfar S, Hassen E, Saad H, Mosbah F, Chouchane L, (2006) Association of VEGF genetic polymorphisms with prostate carcinoma risk and clinical outcome. Cytokine 35: 21-28.
17. Jacobs EJ, Hsing AW, Bain EB, Stevens VL, Wang Y, et al. (2008) Polymorphisms in angiogenesis-related genes and prostate cancer. Cancer Epidemiol Biomarkers Prev 17: 972-977.
18. Faupel-Badger JM, Kidd LC, Albanes D, Virtamo J, Woodson K, et al. (2008) Association of IL-10 polymorphisms with prostate cancer risk and grade of disease. Cancer Causes Control 19: 119-124.
19. Thomas G, Jacobs KB, Yeager M, Kraft P, Wacholder S, et al. (2008) Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 40: 310-315.
20. Nam RK, Zhang W, Siminovitch K, Shlien A, Kattan MW, et al. (2011) New variants at 10q26 and 15q21 are associated with aggressive prostate cancer in a genome-wide association study from a prostate biopsy screening cohort. Cancer Biol Ther 12: 997-1004.
21. Penney KL, Pyne S, Schumacher FR, Sinnott JA, Mucci LA, et al. (2010) Genome-wide association study of prostate cancer mortality. Cancer Epidemiol Biomarkers Prev 19: 2869-2876.
22. Cordell HJ, (2009) Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10: 392-404.
23. Moore JH, Williams SM, (2002) New strategies for identifying gene-gene interactions in hypertension. Ann Med 34: 88-95.
24. Moore JH, (2003) The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 56: 73-82.
25. Onay VU, Briollais L, Knight JA, Shi E, Wang Y, et al. (2006) SNP-SNP interactions in breast cancer susceptibility. BMC Cancer 6: 114.
26. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, et al. (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. American Journal of Human Genetics 69: 138-147.
27. Van Emburgh BO, Hu JJ, Levine EA, Mosley LJ, Case LD, et al. (2008) Polymorphisms in drug metabolism genes, smoking, and p53 mutations in breast cancer. Molecular Carcinogenesis 47: 88-99.
28. Lin HY, Wang W, Liu YH, Soong SJ, York TP, et al. (2008) Comparison of multivariate adaptive regression splines and logistic regression in detecting SNP-SNP interactions and their application in prostate cancer. J Hum Genet 53: 802-811.
29. Lin HY, Desmond R, Bridges SL Jr, Soong SJ, (2008) Variable selection in logistic regression for detecting SNP-SNP interactions: the rheumatoid arthritis example. Eur J Hum Genet 16: 735-741.
30. Ioannidis JP, Castaldi P, Evangelou E, (2010) A compendium of genome-wide associations for cancer: critical synopsis and reappraisal. Journal of the National Cancer Institute 102: 846-858.
31. Lin HY, Chen AY, Tsai YY, Qu X, Tseng TS, et al. (2012) TRM: A Powerful Two-Stage Machine Learning Approach for Identifying SNP-SNP Interactions. Ann Hum Genet 76: 53-62.
32. Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, et al. (2007) Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nature Genetics 39: 645-649.
33. de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, et al. (2005) Efficiency and power in genetic association studies. Nat Genet 37: 1217-1223.
34. Storey JD, (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society: Series B 64: 479-498.
35. Bedard PL, Krzyzanowska MK, Pintilie M, Tannock IF, (2007) Statistical power of negative randomized controlled trials presented at American Society for Clinical Oncology annual meetings. Journal of Clinical Oncology 25: 3482-3487.
36. Migliaccio A, Castoria G, Di Domenico M, Ciociola A, Lombardi M, et al. (2006) Crosstalk between EGFR and extranuclear steroid receptors. Ann N Y Acad Sci 1089: 194-200.
37. Bonaccorsi L, Nosi D, Muratori M, Formigli L, Forti G, et al. (2007) Altered endocytosis of epidermal growth factor receptor in androgen receptor positive prostate cancer cell lines. J Mol Endocrinol 38: 51-66.
38. Leotoing L, Manin M, Monte D, Baron S, Communal Y, et al. (2007) Crosstalk between androgen receptor and epidermal growth factor receptor-signalling pathways: a molecular switch for epithelial cell differentiation. J Mol Endocrinol 39: 151-162.
39. Wang Y, Chen J, Li Q, Wang H, Liu G, et al. (2011) Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Comput Biol Chem 35: 151-158.
40. Seki M, Watanabe A, Enomoto S, Kawamura T, Ito H, et al. (2010) Human ROBO1 is cleaved by metalloproteinases and gamma-secretase and migrates to the nucleus in cancer cells. FEBS Lett 584: 2909-2915.
41. Rundhaug JE, (2005) Matrix metalloproteinases and angiogenesis. J Cell Mol Med 9: 267-285.
42. Jung M, Romer A, Keyszer G, Lein M, Kristiansen G, et al. (2003) mRNA expression of the five membrane-type matrix metalloproteinases MT1-MT5 in human prostatic cell lines and their down-regulation in human malignant prostatic tissue. Prostate 55: 89-98.
43. Lin F, Wang X, Jie Z, Hong X, Li X, et al. (2011) Inhibitory effects of miR-146b-5p on cell migration and invasion of pancreatic cancer by targeting MMP16. J Huazhong Univ Sci Technolog Med Sci 31: 509-514.
44. Hadchouel A, Decobert F, Franco-Montoya ML, Halphen I, Jarreau PH, et al. (2008) Matrix metalloproteinase gene polymorphisms and bronchopulmonary dysplasia: identification of MMP16 as a new player in lung development. PLoS One 3: e3188.
45. Legg JA, Herbert JM, Clissold P, Bicknell R, (2008) Slits and Roundabouts in cancer, tumour angiogenesis and endothelial cell migration. Angiogenesis 11: 13-21.
46. Latil A, Chene L, Cochant-Priollet B, Mangin P, Fournier G, et al. (2003) Quantification of expression of netrins, slits and their receptors in human prostate tumors. Int J Cancer 103: 306-315.
47. Ito H, Funahashi S, Yamauchi N, Shibahara J, Midorikawa Y, et al. (2006) Identification of ROBO1 as a novel hepatocellular carcinoma antigen and a potential therapeutic and diagnostic target. Clin Cancer Res 12: 3257-3264.
48. Enjuanes A, Fernandez V, Hernandez L, Navarro A, Bea S, et al. (2011) Identification of methylated genes associated with aggressive clinicopathological features in mantle cell lymphoma. PLoS One 6: e19736.
49. Espinosa I, Edris B, Lee CH, Cheng HW, Gilks CB, et al. (2011) CSF1 expression in nongynecological leiomyosarcoma is associated with increased tumor angiogenesis. Am J Pathol 179: 2100-2107.
50. Lin EY, Nguyen AV, Russell RG, Pollard JW, (2001) Colony-stimulating factor 1 promotes progression of mammary tumors to malignancy. J Exp Med 193: 727-740.
51. Kacinski BM, (1997) CSF-1 and its receptor in breast carcinomas and neoplasms of the female reproductive tract. Mol Reprod Dev 46: 71-74.
52. Chambers SK, Kacinski BM, Ivins CM, Carcangiu ML, (1997) Overexpression of epithelial macrophage colony-stimulating factor (CSF-1) and CSF-1 receptor: a poor prognostic factor in epithelial ovarian cancer, contrasted with a protective effect of stromal CSF-1. Clin Cancer Res 3: 999-1007.
53. Pyonteck SM, Gadea BB, Wang HW, Gocheva V, Hunter KE, et al. (2012) Deficiency of the macrophage growth factor CSF-1 disrupts pancreatic neuroendocrine tumor development. Oncogene 31: 1459-1467.
54. Albig AR, Neil JR, Schiemann WP, (2006) Fibulins 3 and 5 antagonize tumor angiogenesis in vivo. Cancer Res 66: 2621-2629.
55. Albig AR, Schiemann WP, (2004) Fibulin-5 antagonizes vascular endothelial growth factor (VEGF) signaling and angiogenic sprouting by endothelial cells. DNA Cell Biol 23: 367-379.
56. Albig AR, Schiemann WP, (2005) Fibulin-5 function during tumorigenesis. Future Oncol 1: 23-35.
57. Xie L, Palmsten K, MacDonald B, Kieran MW, Potenta S, et al. (2008) Basement membrane derived fibulin-1 and fibulin-5 function as angiogenesis inhibitors and suppress tumor growth. Exp Biol Med (Maywood) 233: 155-162.
58. Wlazlinski A, Engers R, Hoffmann MJ, Hader C, Jung V, et al. (2007) Downregulation of several fibulin genes in prostate cancer. Prostate 67: 1770-1780.
59. Schiemann WP, Blobe GC, Kalume DE, Pandey A, Lodish HF, (2002) Context-specific effects of fibulin-5 (DANCE/EVEC) on cell proliferation, motility, and invasion. Fibulin-5 is induced by transforming growth factor-beta and affects protein kinase cascades. J Biol Chem 277: 27367-27377.
60. Lee YH, Albig AR, Regner M, Schiemann BJ, Schiemann WP, (2008) Fibulin-5 initiates epithelial-mesenchymal transition (EMT) and enhances EMT induced by TGF-beta in mammary epithelial cells via a MMP-dependent mechanism. Carcinogenesis 29: 2243-2251.
61. Zhou Z, Wang J, Cao R, Morita H, Soininen R, et al. (2004) Impaired angiogenesis, delayed wound healing and retarded tumor growth in perlecan heparan sulfate-deficient mice. Cancer Res 64: 4699-4702.
62. Mauri P, Scarpa A, Nascimbeni AC, Benazzi L, Parmagnani E, et al. (2005) Identification of proteins released by pancreatic cancer cells by multidimensional protein identification technology: a strategy for identification of novel cancer markers. FASEB J 19: 1125-1127.
63. Gronborg M, Kristiansen TZ, Iwahori A, Chang R, Reddy R, et al. (2006) Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics 5: 157-171.
64. Datta MW, Hernandez AM, Schlicht MJ, Kahler AJ, DeGueme AM, et al. (2006) Perlecan, a candidate gene for the CAPB locus, regulates prostate cancer cell growth via the Sonic Hedgehog pathway. Mol Cancer 5: 9.
65. Savore C, Zhang C, Muir C, Liu R, Wyrwa J, et al. (2005) Perlecan knockdown in metastatic prostate cancer cells reduces heparin-binding growth factor responses in vitro and tumor growth in vivo. Clin Exp Metastasis 22: 377-390.
66. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K, (2002) A comprehensive review of genetic association studies. Genet Med 4: 45-61.
67. Garcia-Magarinos M, Lopez-de-Ullibarri I, Cao R, Salas A, (2009) Evaluating the ability of tree-based methods and logistic regression for the detection of SNP-SNP interaction. Annals of Human Genetics 73: 360-369.
68. Hua L, Lin H, Li D, Li L, Liu Z, (2012) Mining Functional Gene Modules Linked with Rheumatoid Arthritis Using a SNP-SNP Network. Genomics, Proteomics and Bioinformatics 10: 23-34.
69. Li H, Lee Y, Chen JL, Rebman E, Li J, et al. (2012) Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. Journal of the American Medical Informatics Association 19: 295-305.