Post genome-wide association studies functional characterization of prostate cancer risk loci

BMC Genomics

Volumn 14, Issue SUPP 8, 2013, Pages

  Jiang, Junfeng ^a   Cui, Weirong ^a   Vongsangnak, Wanwipa ^a   Hu, Guang ^a   Shen, Bairong ^a  

^a SOOCHOW UNIVERSITY   (China)

Author keywords

gene ontology; Genome wide association study; network; pathway; prostate cancer

Indexed keywords

ANDROGEN RECEPTOR; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; MYC PROTEIN; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; SOMATOMEDIN B RECEPTOR; SOMATOMEDIN C; STAT1 PROTEIN; STAT3 PROTEIN; STAT5 PROTEIN; TRANSCRIPTION FACTOR SP1;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; APOPTOSIS; ARTICLE; CANCER RISK; CELL ADHESION; CELL CYCLE; CELL CYCLE REGULATION; CELL DEATH; CELL PROLIFERATION; ENRICHMENT CULTURE; EXON; G1 PHASE CELL CYCLE CHECKPOINT; GENE CONSTRUCT; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; HUMAN; INTRON; LYMPHOBLASTOID CELL LINE; PROGNOSIS; PROSTATE CANCER; QUANTITATIVE TRAIT LOCUS; RESPIRATORY CHAIN; S PHASE CELL CYCLE CHECKPOINT; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION;

COMPUTATIONAL BIOLOGY; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROSTATIC NEOPLASMS; QUANTITATIVE TRAIT LOCI; TUMOR MARKERS, BIOLOGICAL;

EID: 84889633349     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-S8-S9     Document Type: Article

References (76)

1. Crawford ED. Epidemiology of prostate cancer. Urology 2003, 62(6 Suppl 1):3-12.
2. Chen J, Zhang D, Yan W, Yang D, Shen B. Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next-generation sequencing era. BioMed research international 2013, 2013:901578. 3727129, 23957008.
3. Tang Y, Yan W, Chen J, Luo C, Kaipia A, Shen B. Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer. BMC systems biology 2013, 7(Suppl 3):S6.
4. Wang Y, Chen J, Li Q, Wang H, Liu G, Jing Q, Shen B. Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Comput Biol Chem 2011, 35(3):151-158. 10.1016/j.compbiolchem.2011.04.003, 21704261.
5. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106(23):9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
6. Drake TA, Schadt EE, Davis RC, Lusis AJ. Integrating genetic and gene expression data to study the metabolic syndrome and diabetes in mice. Am J Ther 2005, 12(6):503-511. 10.1097/01.mjt.0000178775.39149.64, 16280644.
7. Botstein D, Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 2003, 33 Suppl:228-237.
8. Gudmundsson J, Sulem P, Steinthorsdottir V, Bergthorsson JT, Thorleifsson G, Manolescu A, Rafnar T, Gudbjartsson D, Agnarsson BA, Baker A, et al. Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet 2007, 39(8):977-983. 10.1038/ng2062, 17603485.
9. Thomas G, Jacobs KB, Yeager M, Kraft P, Wacholder S, Orr N, Yu K, Chatterjee N, Welch R, Hutchinson A, et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 2008, 40(3):310-315. 10.1038/ng.91, 18264096.
10. Gudmundsson J, Sulem P, Rafnar T, Bergthorsson JT, Manolescu A, Gudbjartsson D, Agnarsson BA, Sigurdsson A, Benediktsdottir KR, Blondal T, et al. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet 2008, 40(3):281-283. 10.1038/ng.89, 3598012, 18264098.
11. Lu Y, Zhang Z, Yu H, Zheng SL, Isaacs WB, Xu J, Sun J. Functional annotation of risk loci identified through genome-wide association studies for prostate cancer. Prostate 2011, 71:955-963. 10.1002/pros.21311, 3070182, 21541972.
12. Eeles RA, Kote-Jarai Z, Giles GG, Olama AA, Guy M, Jugurnauth SK, Mulholland S, Leongamornlert DA, Edwards SM, Morrison J, et al. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 2008, 40(3):316-321. 10.1038/ng.90, 18264097.
13. Gudmundsson J, Sulem P, Manolescu A, Amundadottir LT, Gudbjartsson D, Helgason A, Rafnar T, Bergthorsson JT, Agnarsson BA, Baker A, et al. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet 2007, 39(5):631-637. 10.1038/ng1999, 17401366.
14. Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, Wacholder S, Minichiello MJ, Fearnhead P, Yu K, Chatterjee N, et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007, 39(5):645-649. 10.1038/ng2022, 17401363.
15. Lou H, Yeager M, Li H, Bosquet JG, Hayes RB, Orr N, Yu K, Hutchinson A, Jacobs KB, Kraft P, et al. Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility. Proc Natl Acad Sci USA 2009, 106(19):7933-7938. 10.1073/pnas.0902104106, 2671324, 19383797.
16. Chang BL, Cramer SD, Wiklund F, Isaacs SD, Stevens VL, Sun J, Smith S, Pruett K, Romero LM, Wiley KE, et al. Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk. Hum Mol Genet 2009, 18(7):1368-1375. 10.1093/hmg/ddp035, 2722195, 19153072.
17. Storey JD, Madeoy J, Strout JL, Wurfel M, Ronald J, Akey JM. Gene-expression variation within and among human populations. Am J Hum Genet 2007, 80(3):502-509. 10.1086/512017, 1821107, 17273971.
18. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, et al. Population genomics of human gene expression. Nat Genet 2007, 39(10):1217-1224. 10.1038/ng2142, 2683249, 17873874.
19. Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, Wong KC, Taylor J, Burnett E, Gut I, Farrall M, et al. A genome-wide association study of global gene expression. Nat Genet 2007, 39(10):1202-1207. 10.1038/ng2109, 17873877.
20. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 2003, 422(6929):297-302. 10.1038/nature01434, 12646919.
21. Cheung VG, Spielman RS, Ewens KG, Weber TM, Morley M, Burdick JT. Mapping determinants of human gene expression by regional and genome-wide association. Nature 2005, 437(7063):1365-1369. 10.1038/nature04244, 3005311, 16251966.
22. Kwan T, Benovoy D, Dias C, Gurd S, Provencher C, Beaulieu P, Hudson TJ, Sladek R, Majewski J. Genome-wide analysis of transcript isoform variation in humans. Nat Genet 2008, 40(2):225-231. 10.1038/ng.2007.57, 18193047.
23. Petretto E, Mangion J, Dickens NJ, Cook SA, Kumaran MK, Lu H, Fischer J, Maatz H, Kren V, Pravenec M, et al. Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet 2006, 2(10):e172. 10.1371/journal.pgen.0020172, 1617131, 17054398.
24. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315(5813):848-853. 10.1126/science.1136678, 2665772, 17289997.
25. Min JL, Taylor JM, Richards JB, Watts T, Pettersson FH, Broxholme J, Ahmadi KR, Surdulescu GL, Lowy E, Gieger C, et al. The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits. PloS one 2011, 6(7):e22070. 10.1371/journal.pone.0022070, 3137612, 21789213.
26. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 2008, 4(10):e1000214. 10.1371/journal.pgen.1000214, 2556086, 18846210.
27. Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, Dolan ME, Cox NJ. SCAN: SNP and copy number annotation. Bioinformatics 2010, 26(2):259-262. 10.1093/bioinformatics/btp644, 2852202, 19933162.
28. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, et al. Genetics of gene expression and its effect on disease. Nature 2008, 452(7186):423-428. 10.1038/nature06758, 18344981.
29. Zeller T, Wild P, Szymczak S, Rotival M, Schillert A, Castagne R, Maouche S, Germain M, Lackner K, Rossmann H, et al. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. PloS one 2010, 5(5):e10693. 10.1371/journal.pone.0010693, 2872668, 20502693.
30. Goring HH, Curran JE, Johnson MP, Dyer TD, Charlesworth J, Cole SA, Jowett JB, Abraham LJ, Rainwater DL, Comuzzie AG, et al. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 2007, 39(10):1208-1216. 10.1038/ng2119, 17873875.
31. Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, et al. Variations in DNA elucidate molecular networks that cause disease. Nature 2008, 452(7186):429-435. 10.1038/nature06757, 2841398, 18344982.
32. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, et al. A survey of genetic human cortical gene expression. Nat Genet 2007, 39(12):1494-1499. 10.1038/ng.2007.16, 17982457.
33. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2008, 6(5):e107. 10.1371/journal.pbio.0060107, 2365981, 18462017.
34. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M, et al. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 2009, 325(5945):1246-1250. 10.1126/science.1174148, 2867218, 19644074.
35. Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, Gabriel WN, Welsh-Bohmer KA, Hulette CM, Denny TN, Goldstein DB. Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol 2008, 6(12):e1.
36. Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M. Mapping complex disease traits with global gene expression. Nat Rev Genet 2009, 10(3):184-194. 10.1038/nrg2537, 19223927.
37. Ding J, Gudjonsson JE, Liang L, Stuart PE, Li Y, Chen W, Weichenthal M, Ellinghaus E, Franke A, Cookson W, et al. Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals. Am J Hum Genet 2010, 87(6):779-789. 10.1016/j.ajhg.2010.10.024, 2997368, 21129726.
38. Nica AC, Parts L, Glass D, Nisbet J, Barrett A, Sekowska M, Travers M, Potter S, Grundberg E, Small K, et al. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet 2011, 7(2):e1002003. 10.1371/journal.pgen.1002003, 3033383, 21304890.
39. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG. Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 2007, 39(2):226-231. 10.1038/ng1955, 3005333, 17206142.
40. Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, Mirkov S, Ramirez J, Liu W, Lin YS, Moloney C, et al. Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet 2011, 7(5):e1002078. 10.1371/journal.pgen.1002078, 3102751, 21637794.
41. Guo AY, Sun J, Jia P, Zhao Z. A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC systems biology 2010, 4:10. 10.1186/1752-0509-4-10, 2834616, 20156358.
42. Jia P, Zheng S, Long J, Zheng W, Zhao Z. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics 2011, 27(1):95-102. 10.1093/bioinformatics/btq615, 3008643, 21045073.
43. Sun J, Jia P, Fanous AH, van den Oord E, Chen X, Riley BP, Amdur RL, Kendler KS, Zhao Z. Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. PloS one 2010, 5(6):e11351. 10.1371/journal.pone.0011351, 2894047, 20613869.
44. Jia P, Ewers JM, Zhao Z. Prioritization of epilepsy associated candidate genes by convergent analysis. PloS one 2011, 6(2):e17162. 10.1371/journal.pone.0017162, 3044734, 21390307.
45. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 2003, 34(3):267-273. 10.1038/ng1180, 12808457.
46. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102(43):15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
47. Wang K, Li M, Bucan M. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 2007, 81(6):1278-1283. 10.1086/522374, 2276352, 17966091.
48. Chen J, Wang Y, Shen B, Zhang D. Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data. Computational and mathematical methods in medicine 2013, 2013:909525. 3562646, 23401724.
49. Chen J, Zhang D, Zhang W, Tang Y, Yan W, Guo L, Shen B. Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis. Journal of translational medicine 2013, 11:169. 10.1186/1479-5876-11-169, 3740788, 23841900.
50. Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J, Chen Z, Beroukhim R, Wang H, Lupien M, et al. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell 2009, 138(2):245-256. 10.1016/j.cell.2009.04.056, 2726827, 19632176.
51. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006, 38(11):1289-1297. 10.1038/ng1901, 17013392.
52. Pavlides S, Tsirigos A, Vera I, Flomenberg N, Frank PG, Casimiro MC, Wang C, Fortina P, Addya S, Pestell RG, et al. Loss of stromal caveolin-1 leads to oxidative stress, mimics hypoxia and drives inflammation in the tumor microenvironment, conferring the "reverse Warburg effect": a transcriptional informatics analysis with validation. Cell Cycle 2010, 9(11):2201-2219. 10.4161/cc.9.11.11848, 20519932.
53. Tombal B. What is the pathophysiology of a hormone-resistant prostate tumour?. Eur J Cancer 2011, 47(Suppl 3):S179-188.
54. Vesely DL. Metabolic targets of cardiac hormones' therapeutic anti-cancer effects. Curr Pharm Des 2010, 16(9):1159-1166. 10.2174/138161210790963887, 20030620.
55. Redig AJ, Munshi HG. Metabolic syndrome after hormone-modifying therapy: risks associated with antineoplastic therapy. Oncology (Williston Park) 2010, 24(9):839-844.
56. Russell PJ, Bennett S, Stricker P. Growth factor involvement in progression of prostate cancer. Clin Chem 1998, 44(4):705-723.
57. Sankpal UT, Goodison S, Abdelrahim M, Basha R. Targeting Sp1 transcription factors in prostate cancer therapy. Med Chem 2011, 7(5):518-525. 10.2174/157340611796799203, 22022994.
58. Djavan B, Waldert M, Seitz C, Marberger M. Insulin-like growth factors and prostate cancer. World J Urol 2001, 19(4):225-233. 10.1007/s003450100220, 11550779.
59. Heinlein CA, Chang C. Androgen receptor in prostate cancer. Endocr Rev 2004, 25(2):276-308. 10.1210/er.2002-0032, 15082523.
60. Chi SG, deVere White RW, Meyers FJ, Siders DB, Lee F, Gumerlock PH. p53 in prostate cancer: frequent expressed transition mutations. J Natl Cancer Inst 1994, 86(12):926-933. 10.1093/jnci/86.12.926, 7515114.
61. Kaltz-Wittmer C, Klenk U, Glaessgen A, Aust DE, Diebold J, Lohrs U, Baretton GB. FISH analysis of gene aberrations (MYC, CCND1, ERBB2, RB, and AR) in advanced prostatic carcinomas before and after androgen deprivation therapy. Lab Invest 2000, 80(9):1455-1464. 10.1038/labinvest.3780152, 11005213.
62. Filippova GN. Genetics and epigenetics of the multifunctional protein CTCF. Curr Top Dev Biol 2008, 80:337-360.
63. Zhu JG, Dai QS, Han ZD, He HC, Mo RJ, Chen G, Chen YF, Wu YD, Yang SB, Jiang FN, et al. Expression of SOCSs in human prostate cancer and their association in prognosis. Mol Cell Biochem 2013, 381:51-59. 10.1007/s11010-013-1687-6, 23666742.
64. Sun J, Zheng SL, Wiklund F, Isaacs SD, Purcell LD, Gao Z, Hsu FC, Kim ST, Liu W, Zhu Y, et al. Evidence for two independent prostate cancer risk-associated loci in the HNF1B gene at 17q12. Nat Genet 2008, 40(10):1153-1155. 10.1038/ng.214, 3188432, 18758462.
65. Neuhausen SL, Slattery ML, Garner CP, Ding YC, Hoffman M, Brothman AR. Prostate cancer risk and IRS1, IRS2, IGF1, and INS polymorphisms: strong association of IRS1 G972R variant and cancer risk. Prostate 2005, 64(2):168-174. 10.1002/pros.20216, 15678496.
66. Xiao D, Powolny AA, Moura MB, Kelley EE, Bommareddy A, Kim SH, Hahm ER, Normolle D, Van Houten B, Singh SV. Phenethyl isothiocyanate inhibits oxidative phosphorylation to trigger reactive oxygen species-mediated death of human prostate cancer cells. J Biol Chem 2010, 285(34):26558-26569. 10.1074/jbc.M109.063255, 2924093, 20571029.
67. Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, et al. Humoral response profiling reveals pathways to prostate cancer progression. Mol Cell Proteomics 2008, 7(3):600-611.
68. Shaywitz AJ, Greenberg ME. CREB: a stimulus-induced transcription factor activated by a diverse array of extracellular signals. Annu Rev Biochem 1999, 68:821-861. 10.1146/annurev.biochem.68.1.821, 10872467.
69. Unni E, Sun S, Nan B, McPhaul MJ, Cheskis B, Mancini MA, Marcelli M. Changes in androgen receptor nongenotropic signaling correlate with transition of LNCaP cells to androgen independence. Cancer Res 2004, 64(19):7156-7168. 10.1158/0008-5472.CAN-04-1121, 15466214.
70. Mantamadiotis T, Papalexis N, Dworkin S. CREB signalling in neural stem/progenitor cells: Recent developments and the implications for brain tumour biology. Bioessays 2012,
71. Moon RT, Miller JR. The APC tumor suppressor protein in development and cancer. Trends Genet 1997, 13(7):256-258. 10.1016/S0168-9525(97)01196-7, 9242044.
72. Spink KE, Polakis P, Weis WI. Structural basis of the Axin-adenomatous polyposis coli interaction. EMBO J 2000, 19(10):2270-2279. 10.1093/emboj/19.10.2270, 384355, 10811618.
73. Kharaishvili G, Simkova D, Makharoblidze E, Trtkova K, Kolar Z, Bouchal J. Wnt signaling in prostate development and carcinogenesis. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2011, 155(1):11-18. 10.5507/bp.2011.016, 21475372.
74. Tuxhorn JA, Ayala GE, Smith MJ, Smith VC, Dang TD, Rowley DR. Reactive stroma in human prostate cancer: induction of myofibroblast phenotype and extracellular matrix remodeling. Clin Cancer Res 2002, 8(9):2912-2923.
75. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, de Bakker PI. SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 2008, 24(24):2938-2939. 10.1093/bioinformatics/btn564, 2720775, 18974171.
76. Lu Y, Zhang Z, Yu H, Zheng SL, Isaacs WB, Xu J, Sun J. Functional annotation of risk loci identified through genome-wide association studies for prostate cancer. Prostate 2011, 71(9):955-963. 10.1002/pros.21311, 3070182, 21541972.