Integrative Genomic Profiling of Human Prostate Cancer

Cancer Cell

Volumn 18, Issue 1, 2010, Pages 11-22

  Taylor, Barry S ^a   Schultz, Nikolaus ^a   Hieronymus, Haley ^a   Gopalan, Anuradha ^a   Xiao, Yonghong ^a   Carver, Brett S ^a   Arora, Vivek K ^a   Kaushik, Poorvi ^a   Cerami, Ethan ^a   Reva, Boris ^a   Antipin, Yevgeniy ^a   Mitsiades, Nicholas ^a   Landers, Thomas ^a   Dolgalev, Igor ^a   Major, John E ^a   Wilson, Manda ^a   Socci, Nicholas D ^a   Lash, Alex E ^a   Heguy, Adriana ^a   Eastham, James A ^a   Scher, Howard I ^a   Reuter, Victor E ^a   Scardino, Peter T ^a   Sander, Chris ^a   Sawyers, Charles L ^a,b   Gerald, William L ^a   more..

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANDROGEN RECEPTOR; BINDING PROTEIN; MICRORNA; NUCLEAR PROTEIN; PROTEIN SHQ; RING YY1 AND BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOXP1; UNCLASSIFIED DRUG;

ADULT; ARTICLE; CANCER CELL; CHROMOSOME 3P; CHROMOSOME DELETION; CONTROLLED STUDY; GENE CLUSTER; GENE DOSAGE; HUMAN; HUMAN TISSUE; MALE; METASTASIS; PRIMARY TUMOR; PRIORITY JOURNAL; PROSTATE CANCER; PROSTATECTOMY; RELAPSE; SIGNAL TRANSDUCTION;

EID: 77954255681     PISSN: 15356108     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ccr.2010.05.026     Document Type: Article

References (59)

1. Agoulnik I.U., Vaid A., Bingman W.E., Erdeme H., Frolov A., Smith C.L., Ayala G., Ittmann M.M., Weigel N.L. Role of SRC-1 in the promotion of prostate cancer cell growth and tumor progression. Cancer Res. 2005, 65:7959-7967.
2. Arber S. FoxP1: Conducting the Hox symphony in spinal motor neurons. Nat. Neurosci. 2008, 11:1122-1124.
3. Benjamini Y., Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Statist. Soc., B 1995, 57:289-300.
4. Beroukhim R., Mermel C.H., Porter D., Wei G., Raychaudhuri S., Donovan J., Barretina J., Boehm J.S., Dobson J., Urashima M., et al. The landscape of somatic copy-number alteration across human cancers. Nature 2010, 463:899-905.
5. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068. Cancer Genome Atlas Research Network.
6. Carver B.S., Tran J., Gopalan A., Chen Z., Shaikh S., Carracedo A., Alimonti A., Nardella C., Varmeh S., Scardino P.T., et al. Aberrant ERG expression cooperates with loss of PTEN to promote cancer progression in the prostate. Nat. Genet. 2009, 41:619-624.
7. Chen C.D., Welsbie D.S., Tran C., Baek S.H., Chen R., Vessella R., Rosenfeld M.G., Sawyers C.L. Molecular determinants of resistance to antiandrogen therapy. Nat. Med. 2004, 10:33-39.
8. Chen D., Zhang J., Li M., Rayburn E.R., Wang H., Zhang R. RYBP stabilizes p53 by modulating MDM2. EMBO Rep. 2009, 10:166-172.
9. Chitale D., Gong Y., Taylor B.S., Broderick S., Brennan C., Somwar R., Golas B., Wang L., Motoi N., Szoke J., et al. An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene 2009, 28:2773-2783.
10. Cooperberg M.R., Moul J.W., Carroll P.R. The changing face of prostate cancer. J. Clin. Oncol. 2005, 23:8146-8151.
11. Demichelis F., Setlur S.R., Beroukhim R., Perner S., Korbel J.O., Lafargue C.J., Pflueger D., Pina C., Hofer M.D., Sboner A., et al. Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer 2009, 48:366-380.
12. Ding L., Getz G., Wheeler D.A., Mardis E.R., McLellan M.D., Cibulskis K., Sougnez C., Greulich H., Muzny D.M., Morgan M.B., et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008, 455:1069-1075.
13. Dong J.T. Prevalent mutations in prostate cancer. J. Cell. Biochem. 2006, 97:433-447.
14. Febbo P.G., Sellers W.R. Use of expression analysis to predict outcome after radical prostatectomy. J. Urol. 2003, 170:S11-S19. discussion, S19-S20.
15. Gao T., Furnari F., Newton A.C. PHLPP: A phosphatase that directly dephosphorylates Akt, promotes apoptosis, and suppresses tumor growth. Mol. Cell 2005, 18:13-24.
16. Garraway L.A., Widlund H.R., Rubin M.A., Getz G., Berger A.J., Ramaswamy S., Beroukhim R., Milner D.A., Granter S.R., Du J., et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 2005, 436:117-122.
17. Gewinner C., Wang Z.C., Richardson A., Teruya-Feldstein J., Etemadmoghadam D., Bowtell D., Barretina J., Lin W.M., Rameh L., Salmena L., et al. Evidence that inositol polyphosphate 4-phosphatase type II is a tumor suppressor that inhibits PI3K signaling. Cancer Cell 2009, 16:115-125.
18. Ghosh D., Chinnaiyan A.M. Genomic outlier profile analysis: Mixture models, null hypotheses, and nonparametric estimation. Biostatistics 2009, 10:60-69.
19. Goatly A., Bacon C.M., Nakamura S., Ye H., Kim I., Brown P.J., Ruskone-Fourmestraux A., Cervera P., Streubel B., Banham A.H., Du M.Q. FOXP1 abnormalities in lymphoma: translocation breakpoint mapping reveals insights into deregulated transcriptional control. Mod. Pathol. 2008, 21:902-911.
20. Greenman C., Stephens P., Smith R., Dalgliesh G.L., Hunter C., Bignell G., Davies H., Teague J., Butler A., Stevens C., et al. Patterns of somatic mutation in human cancer genomes. Nature 2007, 446:153-158.
21. Grozdanov P.N., Roy S., Kittur N., Meier U.T. SHQ1 is required prior to NAF1 for assembly of H/ACA small nucleolar and telomerase RNPs. RNA 2009, 15:1188-1197.
22. Han B., Mehra R., Lonigro R.J., Wang L., Suleman K., Menon A., Palanisamy N., Tomlins S.A., Chinnaiyan A.M., Shah R.B. Fluorescence in situ hybridization study shows association of PTEN deletion with ERG rearrangement during prostate cancer progression. Mod. Pathol. 2009, 22:1083-1093.
23. He W.W., Sciavolino P.J., Wing J., Augustus M., Hudson P., Meissner P.S., Curtis R.T., Shell B.K., Bostwick D.G., Tindall D.J., et al. A novel human prostate-specific, androgen-regulated homeobox gene (NKX3.1) that maps to 8p21, a region frequently deleted in prostate cancer. Genomics 1997, 43:69-77.
24. Hermans K.G., van der Korput H.A., van Marion R., van de Wijngaart D.J., Ziel-van der Made A., Dits N.F., Boormans J.L., van der Kwast T.H., van Dekken H., Bangma C.H., et al. Truncated ETV1, fused to novel tissue-specific genes, and full-length ETV1 in prostate cancer. Cancer Res. 2008, 68:7541-7549.
25. Hieronymus H., Lamb J., Ross K.N., Peng X.P., Clement C., Rodina A., Nieto M., Du J., Stegmaier K., Raj S.M., et al. Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell 2006, 10:321-330.
26. Huang S.M., Cheng Y.S. Analysis of two CBP (cAMP-response-element-binding protein-binding protein) interacting sites in GRIP1 (glucocorticoid-receptor-interacting protein), and their importance for the function of GRIP1. Biochem. J. 2004, 382:111-119.
27. Jaiswal B.S., Janakiraman V., Kljavin N.M., Chaudhuri S., Stern H.M., Wang W., Kan Z., Dbouk H.A., Peters B.A., Waring P., et al. Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation. Cancer Cell 2009, 16:463-474.
28. Jones S., Zhang X., Parsons D.W., Lin J.C., Leary R.J., Angenendt P., Mankoo P., Carter H., Kamiyama H., Jimeno A., et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008, 321:1801-1806.
29. Kim J.H., Dhanasekaran S.M., Mehra R., Tomlins S.A., Gu W., Yu J., Kumar-Sinha C., Cao X., Dash A., Wang L., et al. Integrative analysis of genomic aberrations associated with prostate cancer progression. Cancer Res. 2007, 67:8229-8239.
30. King J.C., Xu J., Wongvipat J., Hieronymus H., Carver B.S., Leung D.H., Taylor B.S., Sander C., Cardiff R.D., Couto S.S., et al. Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nat. Genet. 2009, 41:524-526.
31. Klezovitch O., Risk M., Coleman I., Lucas J.M., Null M., True L.D., Nelson P.S., Vasioukhin V. A causal role for ERG in neoplastic transformation of prostate epithelium. Proc. Natl. Acad. Sci. USA 2008, 105:2105-2110.
32. Koon H.B., Ippolito G.C., Banham A.H., Tucker P.W. FOXP1: A potential therapeutic target in cancer. Expert Opin. Ther. Targets 2007, 11:955-965.
33. Lapointe J., Li C., Higgins J.P., van de Rijn M., Bair E., Montgomery K., Ferrari M., Egevad L., Rayford W., Bergerheim U., et al. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc. Natl. Acad. Sci. USA 2004, 101:811-816.
34. Lapointe J., Li C., Giacomini C.P., Salari K., Huang S., Wang P., Ferrari M., Hernandez-Boussard T., Brooks J.D., Pollack J.R. Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis. Cancer Res. 2007, 67:8504-8510.
35. Lieberfarb M.E., Lin M., Lechpammer M., Li C., Tanenbaum D.M., Febbo P.G., Wright R.L., Shim J., Kantoff P.W., Loda M., et al. Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res. 2003, 63:4781-4785.
36. Mucci L.A., Pawitan Y., Demichelis F., Fall K., Stark J.R., Adami H.O., Andersson S.O., Andren O., Eisenstein A., Holmberg L., et al. Testing a multigene signature of prostate cancer death in the Swedish Watchful Waiting Cohort. Cancer Epidemiol. Biomarkers Prev. 2008, 17:1682-1688.
37. Mucci L.A., Pawitan Y., Demichelis F., Fall K., Stark J.R., Adami H.O., Andersson S.O., Andren O., Eisenstein A.S., Holmberg L., et al. Nine-gene molecular signature is not associated with prostate cancer death in a watchful waiting cohort. Cancer Epidemiol. Biomarkers Prev. 2008, 17:249-251.
38. Paik S., Shak S., Tang G., Kim C., Baker J., Cronin M., Baehner F.L., Walker M.G., Watson D., Park T., et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N. Engl. J. Med. 2004, 351:2817-2826.
39. Parsons D.W., Jones S., Zhang X., Lin J.C., Leary R.J., Angenendt P., Mankoo P., Carter H., Siu I.M., Gallia G.L., et al. An integrated genomic analysis of human glioblastoma multiforme. Science 2008, 321:1807-1812.
40. Perner S., Demichelis F., Beroukhim R., Schmidt F.H., Mosquera J.M., Setlur S., Tchinda J., Tomlins S.A., Hofer M.D., Pienta K.G., et al. TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. Cancer Res. 2006, 66:8337-8341.
41. Pfaff S.L. Developmental neuroscience: Hox and Fox. Nature 2008, 455:295-297.
42. Pleasance E.D., Cheetham R.K., Stephens P.J., McBride D.J., Humphray S.J., Greenman C.D., Varela I., Lin M.L., Ordonez G.R., Bignell G.R., et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2010, 463:191-196.
43. Pleasance E.D., Stephens P.J., O'Meara S., McBride D.J., Meynert A., Jones D., Lin M.L., Beare D., Lau K.W., Greenman C., et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 2010, 463:184-190.
44. Pourmand G., Ziaee A.A., Abedi A.R., Mehrsai A., Alavi H.A., Ahmadi A., Saadati H.R. Role of PTEN gene in progression of prostate cancer. Urol. J. 2007, 4:95-100.
45. Reid A.H., Attard G., Ambroisine L., Fisher G., Kovacs G., Brewer D., Clark J., Flohr P., Edwards S., Berney D.M., et al. Molecular characterisation of ERG, ETV1 and PTEN gene loci identifies patients at low and high risk of death from prostate cancer. Br. J. Cancer 2010, 102:678-684.
46. Singh D., Febbo P.G., Ross K., Jackson D.G., Manola J., Ladd C., Tamayo P., Renshaw A.A., D'Amico A.V., Richie J.P., et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 2002, 1:203-209.
47. Singh M., Gonzales F.A., Cascio D., Heckmann N., Chanfreau G., Feigon J. Structure and functional studies of the CS domain of the essential H/ACA ribonucleoparticle assembly protein SHQ1. J. Biol. Chem. 2009, 284:1906-1916.
48. Sjoblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314:268-274.
49. Taylor B.S., Barretina J., Socci N.D., Decarolis P., Ladanyi M., Meyerson M., Singer S., Sander C. Functional copy-number alterations in cancer. PLoS ONE 2008, 3:e3179. 10.1371/journal.pone.0003179.
50. Tomlins S.A., Rhodes D.R., Perner S., Dhanasekaran S.M., Mehra R., Sun X.W., Varambally S., Cao X., Tchinda J., Kuefer R., et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310:644-648.
51. Tomlins S.A., Laxman B., Varambally S., Cao X., Yu J., Helgeson B.E., Cao Q., Prensner J.R., Rubin M.A., Shah R.B., et al. Role of the TMPRSS2-ERG gene fusion in prostate cancer. Neoplasia 2008, 10:177-188.
52. Tran C., Ouk S., Clegg N.J., Chen Y., Watson P.A., Arora V., Wongvipat J., Smith-Jones P.M., Yoo D., Kwon A., et al. Development of a second-generation antiandrogen for treatment of advanced prostate cancer. Science 2009, 324:787-790.
53. Ueki K., Fruman D.A., Yballe C.M., Fasshauer M., Klein J., Asano T., Cantley L.C., Kahn C.R. Positive and negative roles of p85 alpha and p85 beta regulatory subunits of phosphoinositide 3-kinase in insulin signaling. J. Biol. Chem. 2003, 278:48453-48466.
54. van de Vijver M.J., He Y.D., van't Veer L.J., Dai H., Hart A.A., Voskuil D.W., Schreiber G.J., Peterse J.L., Roberts C., Marton M.J., et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 2002, 347:1999-2009.
55. Wang L., Liu R., Li W., Chen C., Katoh H., Chen G.Y., McNally B., Lin L., Zhou P., Zuo T., et al. Somatic single hits inactivate the X-linked tumor suppressor FOXP3 in the prostate. Cancer Cell 2009, 16:336-346.
56. Wang Y., Moorhead M., Karlin-Neumann G., Falkowski M., Chen C., Siddiqui F., Davis R.W., Willis T.D., Faham M. Allele quantification using molecular inversion probes (MIP). Nucleic Acids Res. 2005, 33:e183. 10.1093/nar/gni177.
57. Weir B.A., Woo M.S., Getz G., Perner S., Ding L., Beroukhim R., Lin W.M., Province M.A., Kraja A., Johnson L.A., et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007, 450:893-898.
58. Wood L.D., Parsons D.W., Jones S., Lin J., Sjoblom T., Leary R.J., Shen D., Boca S.M., Barber T., Ptak J., et al. The genomic landscapes of human breast and colorectal cancers. Science 2007, 318:1108-1113.
59. Zong Y., Xin L., Goldstein A.S., Lawson D.A., Teitell M.A., Witte O.N. ETS family transcription factors collaborate with alternative signaling pathways to induce carcinoma from adult murine prostate cells. Proc. Natl. Acad. Sci. USA 2009, 106:12465-12470.