REFERENCES

1. Zhou CK, Check DP, Lortet-Tieulent J, Laversanne M, Jemal A, et al. Prostate cancer incidence in 43 populations worldwide: an analysis of time trends overall and by age group. Int J Cancer 2016;138:1388-400.

2. D’Amico AV, Whittington R, Malkowicz SB, Schultz D, Blank K, et al. Biochemical outcome after radical prostatectomy, external beam radiation therapy, or interstitial radiation therapy for clinically localized prostate cancer. JAMA 1998;280:969-74.

3. Litwin MS, Tan HJ. The diagnosis and treatment of prostate cancer: a review. JAMA 2017;317:2532-42.

4. Perlis N, Klotz L. Contemporary active surveillance: candidate selection, follow-up tools, and expected outcomes. Urol Clin North Am 2017;44:565-74.

5. Jackson WC, Suresh K, Tumati V, Allen SG, Dess RT, et al. Intermediate endpoints after postprostatectomy radiotherapy: 5-year distant metastasis to predict overall survival. Eur Urol 2018;74:413-9.

6. Ellwood-Yen K, Wongvipat J, Sawyers C. Transgenic mouse model for rapid pharmacodynamic evaluation of antiandrogens. Cancer Res 2006;66:10513-6.

7. Hsieh AC, Small EJ, Ryan CJ. Androgen-response elements in hormone-refractory prostate cancer: implications for treatment development. Lancet Oncol 2007;8:933-9.

8. Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, et al. Emerging landscape of oncogenic signatures across human cancers. Nat Genet 2013;45:1127-33.

9. Espiritu SMG, Liu LY, Rubanova Y, Bhandari V, Holgersen EM, et al. The evolutionary landscape of localized prostate cancers drives clinical aggression. Cell 2018;173:1003-13.

10. Fraser M, Sabelnykova VY, Yamaguchi TN, Heisler LE, Livingstone J, et al. Genomic hallmarks of localized, non-indolent prostate cancer. Nature 2017;541:359-64.

11. Cooperberg MR, Erho N, Chan JM, Feng FY, Fishbane N, et al. The diverse genomic landscape of clinically low-risk prostate cancer. Eur Urol 2018;74:444-52.

12. Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, et al. Integrative clinical genomics of advanced prostate cancer. Cell 2015;161:1215-28.

13. Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, et al. The long tail of oncogenic drivers in prostate cancer. Nat Genet 2018;50:645-51.

14. Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, et al. Genomic hallmarks and structural variation in metastatic prostate cancer. Cell 2018;174:758-69.

15. Taylor RA, Fraser M, Livingstone J, Espiritu SM, Thorne H, et al. Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories. Nat Commun 2017;8:13671.

16. Amin Al Olama A, Benlloch S, Antoniou AC, Giles GG, Severi G, et al. Risk analysis of prostate cancer in PRACTICAL, a multinational consortium, using 25 known prostate cancer susceptibility loci. Cancer Epidemiol Biomarkers Prev 2015;24:1121-9.

17. Eeles RA, Olama AA, Benlloch S, Saunders EJ, Leongamornlert DA, et al. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. Nat Genet 2013;45:385-91.

18. Amin Al Olama A, Kote-Jarai Z, Schumacher FR, Wiklund F, Berndt SI, et al. A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease. Hum Mol Genet 2013;22:408-15.

19. Mijuskovic M, Saunders EJ, Leongamornlert DA, Wakerell S, Whitmore I, et al. Rare germline variants in DNA repair genes and the angiogenesis pathway predispose prostate cancer patients to develop metastatic disease. Br J Cancer 2018;119:96-104.

20. Dadaev T, Saunders EJ, Newcombe PJ, Anokian E, Leongamornlert DA, et al. Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants. Nat Commun 2018;9:2256.

21. Schumacher FR, Al Olama AA, Berndt SI, Benlloch S, Ahmed M, et al. Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci. Nat Genet 2018;50:928-36.

22. Muller H. Androgen-control therapy in carcinoma of prostate. Arch Chir Neerl 1949;1:77-88.

23. van der Kwast TH, Schalken J, Ruizeveld de Winter JA, van Vroonhoven CC, Mulder E, et al. Androgen receptors in endocrine-therapy-resistant human prostate cancer. Int J Cancer 1991;48:189-93.

24. Taplin ME, Bubley GJ, Shuster TD, Frantz ME, Spooner AE, et al. Mutation of the androgen-receptor gene in metastatic androgen-independent prostate cancer. N Engl J Med 1995;332:1393-8.

25. Gaddipati JP, McLeod DG, Heidenberg HB, Sesterhenn IA, Finger MJ, et al. Frequent detection of codon 877 mutation in the androgen receptor gene in advanced prostate cancers. Cancer Res 1994;54:2861-4.

26. Petrovics G, Liu A, Shaheduzzaman S, Furusato B, Sun C, et al. Frequent overexpression of ETS-related gene-1 (ERG1) in prostate cancer transcriptome. Oncogene 2005;24:3847-52.

27. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005;310:644-8.

28. Yoshimoto M, Joshua AM, Chilton-Macneill S, Bayani J, Selvarajah S, et al. Three-color FISH analysis of TMPRSS2/ERG fusions in prostate cancer indicates that genomic microdeletion of chromosome 21 is associated with rearrangement. Neoplasia 2006;8:465-9.

29. Cancer Genome Atlas Research Network. The molecular taxonomy of primary prostate cancer. Cell 2015;163:1011-25.

30. Tomlins SA, Palanisamy N, Siddiqui J, Chinnaiyan AM, Kunju LP. Antibody-based detection of ERG rearrangements in prostate core biopsies, including diagnostically challenging cases: ERG staining in prostate core biopsies. Arch Pathol Lab Med 2012;136:935-46.

31. Park K, Tomlins SA, Mudaliar KM, Chiu YL, Esgueva R, et al. Antibody-based detection of ERG rearrangement-positive prostate cancer. Neoplasia 2010;12:590-8.

32. Mertz KD, Setlur SR, Dhanasekaran SM, Demichelis F, Perner S, et al. Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old model. Neoplasia 2007;9:200-6.

33. Baker SJ, Reddy EP. Understanding the temporal sequence of genetic events that lead to prostate cancer progression and metastasis. Proc Natl Acad Sci U S A 2013;110:14819-20.

34. Dal Pra A, Lalonde E, Sykes J, Warde F, Ishkanian A, et al. TMPRSS2-ERG status is not prognostic following prostate cancer radiotherapy: implications for fusion status and DSB repair. Clin Cancer Res 2013;19:5202-9.

35. Minner S, Enodien M, Sirma H, Luebke AM, Krohn A, et al. ERG status is unrelated to PSA recurrence in radically operated prostate cancer in the absence of antihormonal therapy. Clin Cancer Res 2011;17:5878-88.

36. Kron KJ, Murison A, Zhou S, Huang V, Yamaguchi TN, et al. TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer. Nat Genet 2017;49:1336-45.

37. Boysen G, Rodrigues DN, Rescigno P, Seed G, Dolling D, et al. SPOP mutated/CHD1-deleted lethal prostate cancer and abiraterone sensitivity. Clin Cancer Res 2018;24:5585-93.

38. Barbieri CE, Baca SC, Lawrence MS, Demichelis F, Blattner M, et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012;44:685-9.

39. Grasso CS, Wu YM, Robinson DR, Cao X, Dhanasekaran SM, et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 2012;487:239-43.

40. Trotman LC, Niki M, Dotan ZA, Koutcher JA, Di Cristofano A, et al. Pten dose dictates cancer progression in the prostate. PLoS Biol 2003;1:E59.

41. Ren S, Peng Z, Mao JH, Yu Y, Yin C, et al. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Res 2012;22:806-21.

42. Mendes-Pereira AM, Martin SA, Brough R, McCarthy A, Taylor JR, et al. Synthetic lethal targeting of PTEN mutant cells with PARP inhibitors. EMBO Mol Med 2009;1:315-22.

43. Forster MD, Dedes KJ, Sandhu S, Frentzas S, Kristeleit R, et al. Treatment with olaparib in a patient with PTEN-deficient endometrioid endometrial cancer. Nat Rev Clin Oncol 2011;8:302-6.

44. Dedes KJ, Wetterskog D, Mendes-Pereira AM, Natrajan R, Lambros MB, et al. PTEN deficiency in endometrioid endometrial adenocarcinomas predicts sensitivity to PARP inhibitors. Sci Transl Med 2010;2:53ra75.

45. McEllin B, Camacho CV, Mukherjee B, Hahm B, Tomimatsu N, et al. PTEN loss compromises homologous recombination repair in astrocytes: implications for glioblastoma therapy with temozolomide or poly(ADP-ribose) polymerase inhibitors. Cancer Res 2010;70:5457-64.

46. Gupta A, Yang Q, Pandita RK, Hunt CR, Xiang T, et al. Cell cycle checkpoint defects contribute to genomic instability in PTEN deficient cells independent of DNA DSB repair. Cell Cycle 2009;8:2198-210.

47. Fraser M, Zhao H, Luoto KR, Lundin C, Coackley C, et al. PTEN deletion in prostate cancer cells does not associate with loss of RAD51 function: implications for radiotherapy and chemotherapy. Clin Cancer Res 2012;18:1015-27.

48. Zimmermann M, Murina O, Reijns MAM, Agathanggelou A, Challis R, et al. CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions. Nature 2018;559:285-9.

49. Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, et al. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet 2015;47:736-45.

50. Zafarana G, Ishkanian AS, Malloff CA, Locke JA, Sykes J, et al. Copy number alterations of c-MYC and PTEN are prognostic factors for relapse after prostate cancer radiotherapy. Cancer 2012;118:4053-62.

51. Locke JA, Zafarana G, Ishkanian AS, Milosevic M, Thoms J, et al. NKX3.1 haploinsufficiency is prognostic for prostate cancer relapse following surgery or image-guided radiotherapy. Clin Cancer Res 2012;18:308-16.

52. Ishkanian AS, Zafarana G, Thoms J, Bristow RG. Array CGH as a potential predictor of radiocurability in intermediate risk prostate cancer. Acta Oncol 2010;49:888-94.

53. Castro E, Jugurnauth-Little S, Karlsson Q, Al-Shahrour F, Piñeiro-Yañez E, et al. High burden of copy number alterations and c-MYC amplification in prostate cancer from BRCA2 germline mutation carriers. Ann Oncol 2015;26:2293-300.

54. Risbridger GP, Taylor RA, Clouston D, Sliwinski A, Thorne H, et al. Patient-derived xenografts reveal that intraductal carcinoma of the prostate is a prominent pathology in BRCA2 mutation carriers with prostate cancer and correlates with poor prognosis. Eur Urol 2015;67:496-503.

55. Berlin A, Lalonde E, Sykes J, Zafarana G, Chu KC, et al. NBN gain is predictive for adverse outcome following image-guided radiotherapy for localized prostate cancer. Oncotarget 2014;5:11081-90.

56. Guo H, Ahmed M, Zhang F, Yao CQ, Li S, et al. Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer. Nat Genet 2016;48:1142-50.

57. Le Tallec B, Millot GA, Blin ME, Brison O, Dutrillaux B, et al. Common fragile site profiling in epithelial and erythroid cells reveals that most recurrent cancer deletions lie in fragile sites hosting large genes. Cell Rep 2013;4:420-8.

58. Lalonde E, Ishkanian AS, Sykes J, Fraser M, Ross-Adams H, et al. Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study. Lancet Oncol 2014;15:1521-32.

59. Hieronymus H, Schultz N, Gopalan A, Carver BS, Chang MT, et al. Copy number alteration burden predicts prostate cancer relapse. Proc Natl Acad Sci U S A 2014;111:11139-44.

60. Lalonde E, Alkallas R, Chua MLK, Fraser M, Haider S, et al. Translating a prognostic DNA genomic classifier into the clinic: retrospective validation in 563 localized prostate tumors. Eur Urol 2017;72:22-31.

61. Blattner M, Liu D, Robinson BD, Huang D, Poliakov A, et al. SPOP mutation drives prostate tumorigenesis in vivo through coordinate regulation of PI3K/mTOR and AR signaling. Cancer Cell 2017;31:436-51.

62. Hjorth-Jensen K, Maya-Mendoza A, Dalgaard N, SigurÐsson JO, Bartek J, et al. SPOP promotes transcriptional expression of DNA repair and replication factors to prevent replication stress and genomic instability. Nucleic Acids Res 2018;46:9484-95.

63. Burkhardt L, Fuchs S, Krohn A, Masser S, Mader M, et al. CHD1 is a 5q21 tumor suppressor required for ERG rearrangement in prostate cancer. Cancer Res 2013;73:2795-805.

64. Geng C, Rajapakshe K, Shah SS, Shou J, Eedunuri VK, et al. Androgen receptor is the key transcriptional mediator of the tumor suppressor SPOP in prostate cancer. Cancer Res 2014;74:5631-43.

65. Mateo J, Boysen G, Barbieri CE, Bryant HE, Castro E, et al. DNA repair in prostate cancer: biology and clinical implications. Eur Urol 2017;71:417-25.

66. Pritchard CC, Mateo J, Walsh MF, De Sarkar N, Abida W, et al. Inherited DNA-repair gene mutations in men with metastatic prostate cancer. N Engl J Med 2016;375:443-53.

67. Mateo J, Carreira S, Sandhu S, Miranda S, Mossop H, et al. DNA-repair defects and olaparib in metastatic prostate cancer. N Engl J Med 2015;373:1697-708.

68. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 2012;481:389-93.

69. Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, et al. The genomic complexity of primary human prostate cancer. Nature 2011;470:214-20.

70. Shen MM, Abate-Shen C. Molecular genetics of prostate cancer: new prospects for old challenges. Genes Dev 2010;24:1967-2000.

71. Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, et al. Punctuated evolution of prostate cancer genomes. Cell 2013;153:666-77.

72. Weischenfeldt J, Simon R, Feuerbach L, Schlangen K, Weichenhan D, et al. Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell 2013;23:159-70.

73. Buyyounouski MK, Pickles T, Kestin LL, Allison R, Williams SG. Validating the interval to biochemical failure for the identification of potentially lethal prostate cancer. J Clin Oncol 2012;30:1857-63.

74. Noguchi M, Stamey TA, McNeal JE, Nolley R. Prognostic factors for multifocal prostate cancer in radical prostatectomy specimens: lack of significance of secondary cancers. J Urol 2003;170:459-63.

75. Wise AM, Stamey TA, McNeal JE, Clayton JL. Morphologic and clinical significance of multifocal prostate cancers in radical prostatectomy specimens. Urology 2002;60:264-9.

76. Haffner MC, Mosbruger T, Esopi DM, Fedor H, Heaphy CM, et al. Tracking the clonal origin of lethal prostate cancer. J Clin Invest 2013;123:4918-22.

77. Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, et al. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet 2015;47:367-72.

78. Løvf M, Zhao S, Axcrona U, Johannessen B, Bakken AC, et al. Multifocal primary prostate cancer exhibits high degree of genomic heterogeneity. Eur Urol 2018; doi: 10.1016/j.eururo.2018.08.009.

79. Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, et al. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet 2018;50:682-92.

80. Wang X, Qiao Y, Asangani IA, Ateeq B, Poliakov A, et al. Development of peptidomimetic inhibitors of the ERG gene fusion product in prostate cancer. Cancer Cell 2017;31:532-48.

81. Hamdy FC, Donovan JL, Lane JA, Mason M, Metcalfe C, et al. 10-year outcomes after monitoring, surgery, or radiotherapy for localized prostate cancer. N Engl J Med 2016;375:1415-24.

82. Albertsen PC, Hanley JA, Fine J. 20-year outcomes following conservative management of clinically localized prostate cancer. JAMA 2005;293:2095-101.

83. Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, et al. Integration of copy number and transcriptomics provides risk stratification in prostate cancer: a discovery and validation cohort study. EBioMedicine 2015;2:1133-44.

84. Su F, Zhang W, Zhang D, Zhang Y, Pang C, et al. Spatial intratumor genomic heterogeneity within localized prostate cancer revealed by single-nucleus sequencing. Eur Urol 2018;74:551-9.

85. Kim Y, Ignatchenko V, Yao CQ, Kalatskaya I, Nyalwidhe JO, et al. Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics 2012;11:1870-84.

86. Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, et al. Structural alterations driving castration-resistant prostate cancer revealed by linked-read genome sequencing. Cell 2018;174:433-47.

87. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 2010;18:11-22.

88. Camacho N, Van Loo P, Edwards S, Kay JD Matthews L, et al. Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. PLoS Genet 2017;13:e1007001.

89. Ren S, Wei GH, Liu D, Wang L, Hou Y, et al. Whole-genome and transcriptome sequencing of prostate cancer identify new genetic alterations driving disease progression. Eur Urol 2017; doi: 10.1016/j.eururo.2017.08.027.

Journal of Translational Genetics and Genomics
ISSN 2578-5281 (Online)
Follow Us

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/