Reprint of: The prostate cancer genome: Perspectives and potential

Urologic Oncology: Seminars and Original Investigations

Volumn 33, Issue 2, 2015, Pages 95-102

  Barbieri, Christopher E ^a   Tomlins, Scott A ^b  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Classification; Genomics; Mutations; SCNA; Sequencing; Tumor profiling

Indexed keywords

ANDROGEN; CHROMODOMAIN HELICASE DNA BINDING PROTEIN 1; MITOGEN ACTIVATED PROTEIN KINASE 1; PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN; PROTEIN P53; PROTEINASE; RAF PROTEIN; RAS PROTEIN; SPECKLE TYPE POZ PROTEIN; SPINK 1 PROTEIN; TRANSCRIPTION FACTOR ETS; UNCLASSIFIED DRUG;

CARCINOGENESIS; CELL CYCLE REGULATION; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME MUTATION; GENE DELETION; GENE FUSION; GENOMICS; HUMAN; HUMAN GENOME; MALE; PRIORITY JOURNAL; PROSTATE CANCER; PROSTATE CARCINOGENESIS; PROTEIN EXPRESSION; REVIEW; SOMATIC MUTATION; UPREGULATION; GENETIC PREDISPOSITION; GENETICS; PATHOLOGY; PROCEDURES; PROGNOSIS; PROSTATE TUMOR;

GENETIC PREDISPOSITION TO DISEASE; GENOMICS; HUMANS; MALE; PROGNOSIS; PROSTATIC NEOPLASMS;

EID: 84923381388     PISSN: 10781439     EISSN: 18732496     Source Type: Journal    
DOI: 10.1016/j.urolonc.2015.01.002     Document Type: Review

References (71)

1. Siegel R., Naishadham D., Jemal A. Cancer statistics, 2013. CA Cancer J Clin 2013, 63:11-30.
2. Barbieri C.E., Baca S.C., Lawrence M.S., et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012, 44:685-689.
3. Grasso C.S., Wu Y.M., Robinson D.R., et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 2012, 487:239-243.
4. Kumar A., White T.A., MacKenzie A.P., et al. Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proc Natl Acad Sci U S A 2011, 108:17087-17092.
5. Taylor B.S., Schultz N., Hieronymus H., et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 2010, 18:11-22.
6. Berger M.F., Lawrence M.S., Demichelis F., et al. The genomic complexity of primary human prostate cancer. Nature 2011, 470:214-220.
7. Lindberg J., Klevebring D., Liu W., et al. Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins. Eur Urol 2013, 63:347-353.
8. Baca S.C., Prandi D., Lawrence M.S., et al. Punctuated evolution of prostate cancer genomes. Cell 2013, 153:666-677.
9. Weischenfeldt J., Simon R., Feuerbach L., et al. Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell 2013, 23:159-170.
10. Beltran H., Rubin M.A. New strategies in prostate cancer: translating genomics into the clinic. Clin Cancer Res 2013, 19:517-523.
11. Lapointe J., Li C., Higgins J.P., et al. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A 2004, 101:811-816.
12. Lapointe J., Li C., Giacomini C.P., et al. Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis. Cancer Res 2007, 67:8504-8510.
13. Setlur S.R., Mertz K.D., Hoshida Y., et al. Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst 2008, 100:815-825.
14. Tomlins S.A., Rhodes D.R., Perner S., et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310:644-648.
15. Rubin M.A., Maher C.A., Chinnaiyan A.M. Common gene rearrangements in prostate cancer. J Clin Oncol 2011, 29:3659-3668.
16. Tomlins S.A., Laxman B., Dhanasekaran S.M., et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 2007, 448:595-599.
17. Tomlins S.A., Bjartell A., Chinnaiyan A.M., et al. ETS gene fusions in prostate cancer: from discovery to daily clinical practice. Eur Urol 2009, 56:275-286.
18. Brenner J.C., Chinnaiyan A.M., Tomlins S.A. ETS fusion genes in prostate cancer. Prostate Cancer: Biochemistry, Molecular Biology and Genetics 2013, 139-183. Springer New York, New York. D.J. Tindall (Ed.).
19. Park K., Tomlins S.A., Mudaliar K.M., et al. Antibody-based detection of ERG rearrangement-positive prostate cancer. Neoplasia 2010, 12:590-598.
20. Paulo P., Barros-Silva J.D., Ribeiro F.R., et al. FLI1 is a novel ETS transcription factor involved in gene fusions in prostate cancer. Genes, Chromosomes Cancer 2012, 51:240-249.
21. Furusato B., Tan S.H., Young D., et al. ERG oncoprotein expression in prostate cancer: clonal progression of ERG-positive tumor cells and potential for ERG-based stratification. Prostate Cancer Prostatic Dis 2010, 13:228-237.
22. Young A., Palanisamy N., Siddiqui J., et al. Correlation of urine TMPRSS2:ERG and PCA3 to ERG+ and total prostate cancer burden. Am J Clin Pathol 2012, 138:685-696.
23. Tomlins S.A., Palanisamy N., Siddiqui J., et al. 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, 136:935-946.
24. Shah R.B., Tadros Y., Brummell B., et al. The diagnostic use of ERG in resolving an atypical glands suspicious for cancer diagnosis in prostate biopsies beyond that provided by basal cell and alpha-methylacyl-CoA-racemase markers. Hum Pathol 2012.
25. Attard G., de Bono J.S., Clark J., et al. Studies of TMPRSS2-ERG gene fusions in diagnostic trans-rectal prostate biopsies. Clin Cancer Res 2010, 16:1340. [author reply 1340].
26. Demichelis F., Fall K., Perner S., et al. TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene 2007, 26:4596-4599.
27. Lin D.W., Newcomb L.F., Brown E.C., et al. Urinary TMPRSS2:ERG and PCA3 in an active surveillance cohort: results from a baseline analysis in the Canary Prostate Active Surveillance Study. Clin Cancer Res 2013.
28. Pettersson A., Graff R.E., Bauer S.R., et al. The TMPRSS2:ERG rearrangement, ERG expression, and prostate cancer outcomes: a cohort study and meta-analysis. Cancer Epidemiol Biomarkers Prev 2012, 21:1497-1509.
29. Borno S.T., Fischer A., Kerick M., et al. Genome-wide DNA methylation events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation. Cancer Discov 2012, 2:1024-1035.
30. Demichelis F., Setlur S.R., Beroukhim R., et al. Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer 2009, 48:366-380.
31. Krohn A., Seidel A., Burkhardt L., et al. Recurrent deletion of 3p13 targets multiple tumor suppressor genes and defines a distinct subgroup of aggressive ERG fusion positive prostate cancers. J Pathol 2013, 231:130-141.
32. Tomlins S.A., Rhodes D.R., Yu J., et al. The role of SPINK1 in ETS rearrangement-negative prostate cancers. Cancer Cell 2008, 13:519-528.
33. Beltran H., Yelensky R., Frampton G.M., et al. Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity. Eur Urol 2012, 63:920-926.
34. Bhalla R., Kunju L.P., Tomlins S.A., et al. Novel dual-color immunohistochemical methods for detecting ERG-PTEN and ERG-SPINK1 status in prostate carcinoma. Mod Pathol 2013, 26:835-848.
35. Lippolis G., Edsjo A., Stenman U.H., et al. A high-density tissue microarray from patients with clinically localized prostate cancer reveals ERG and TATI exclusivity in tumor cells. Prostate Cancer Prostatic Dis 2013, 16:145-150.
36. Brenner J.C., Ateeq B., Li Y., et al. Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. Cancer Cell 2011, 19:664-678.
37. Lindberg J., Mills I.G., Klevebring D., et al. The mitochondrial and autosomal mutation landscapes of prostate cancer. Eur Urol 2012, 63:702-708.
38. Geng C., He B., Xu L., et al. Prostate cancer-associated mutations in speckle-type POZ protein (SPOP) regulate steroid receptor coactivator 3 protein turnover. Proc Natl Acad Sci U S A 2013, 110:6997-7002.
39. Burkhardt L., Fuchs S., Krohn A., et al. CHD1 is a 5q21 tumor suppressor required for ERG rearrangement in prostate cancer. Cancer Res 2013, 73:2795-2805.
40. Liu W., Lindberg J., Sui G., et al. Identification of novel CHD1-associated collaborative alterations of genomic structure and functional assessment of CHD1 in prostate cancer. Oncogene 2012, 31:3939-3948.
41. Visakorpi T., Hyytinen E., Koivisto P., et al. In vivo amplification of the androgen receptor gene and progression of human prostate cancer. Nat Genet 1995, 9:401-406.
42. Linja M.J., Visakorpi T. Alterations of androgen receptor in prostate cancer. J Steroid Biochem Mol Biol 2004, 92:255-264.
43. Koivisto P., Kononen J., Palmberg C., et al. Androgen receptor gene amplification: a possible molecular mechanism for androgen deprivation therapy failure in prostate cancer. Cancer Res 1997, 57:314-319.
44. Hu R., Lu C., Mostaghel E.A., et al. Distinct transcriptional programs mediated by the ligand-dependent full-length androgen receptor and its splice variants in castration-resistant prostate cancer. Cancer Res 2012, 72:3457-3462.
45. Hu R., Dunn T.A., Wei S., et al. Ligand-independent androgen receptor variants derived from splicing of cryptic exons signify hormone-refractory prostate cancer. Cancer Res 2009, 69:16-22.
46. Joseph J.D., Lu N., Qian J., et al. A clinically relevant androgen receptor mutation confers resistance to 2nd generation anti-androgens enzalutamide and ARN-509. Cancer Discov 2013, 3:1020-1029.
47. Balbas M.D., Evans M.J., Hosfield D.J., et al. Overcoming mutation-based resistance to antiandrogens with rational drug design. elife 2013, 2:e00499.
48. Zhang C., Wang L., Wu D., et al. Definition of a FoxA1 cistrome that is crucial for G1 to S-phase cell-cycle transit in castration-resistant prostate cancer. Cancer Res 2011, 71:6738-6748.
49. Carver B.S., Chapinski C., Wongvipat J., et al. Reciprocal feedback regulation of PI3K and androgen receptor signaling in PTEN-deficient prostate cancer. Cancer Cell 2011, 19:575-586.
50. Mani R.S., Tomlins S.A., Callahan K., et al. Induced chromosomal proximity and gene fusions in prostate cancer. Science 2009, 326:1230.
51. Haffner M.C., Aryee M.J., Toubaji A., et al. Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nat Genet 2010, 42:668-675.
52. Cairns P., Okami K., Halachmi S., et al. Frequent inactivation of PTEN/MMAC1 in primary prostate cancer. Cancer Res 1997, 57:4997-5000.
53. Carver B.S., Tran J., Gopalan A., et al. Aberrant ERG expression cooperates with loss of PTEN to promote cancer progression in the prostate. Nat Genet 2009, 41:619-624.
54. Chen M., Pratt C.P., Zeeman M.E., et al. Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell 2011, 20:173-186.
55. Trotman L.C., Niki M., Dotan Z.A., et al. PTEN dose dictates cancer progression in the prostate. PLoS Biol 2003, 1:E59.
56. Sun X., Huang J., Homma T., et al. Genetic alterations in the PI3K pathway in prostate cancer. Anticancer Res 2009, 29:1739-1743.
57. Attard G., Swennenhuis J.F., Olmos D., et al. Characterization of ERG, AR and PTEN gene status in circulating tumor cells from patients with castration-resistant prostate cancer. Cancer Res 2009, 69:2912-2918.
58. Cairns P., Evron E., Okami K., et al. Point mutation and homozygous deletion of PTEN/MMAC1 in primary bladder cancers. Oncogene 1998, 16:3215-3218.
59. Choucair K., Ejdelman J., Brimo F., et al. PTEN genomic deletion predicts prostate cancer recurrence and is associated with low AR expression and transcriptional activity. BMC Cancer 2012, 12:543.
60. McMenamin M.E., Soung P., Perera S., et al. Loss of PTEN expression in paraffin-embedded primary prostate cancer correlates with high Gleason score and advanced stage. Cancer Res 1999, 59:4291-4296.
61. Reid A.H., Attard G., Ambroisine L., 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.
62. Cairns P., Okami K., Halachmi S., et al. Frequent inactivation of PTEN/MMAC1 in primary prostate cancer. Cancer Res 1997, 57:4997-5000.
63. Krohn A., Diedler T., Burkhardt L., et al. Genomic deletion of PTEN is associated with tumor progression and early PSA recurrence in ERG fusion-positive and fusion-negative prostate cancer. Am J Pathol 2012, 181:401-412.
64. Paju A., Hotakainen K., Cao Y., et al. Increased expression of tumor-associated trypsin inhibitor, TATI, in prostate cancer and in androgen-independent 22Rv1 cells. Eur Urol 2007, 52:1670-1679.
65. Ateeq B., Tomlins S.A., Laxman B., et al. Therapeutic targeting of SPINK1-positive prostate cancer. Sci Transl Med 2011, 3. [72ra17].
66. Bakin R.E., Gioeli D., Sikes R.A., et al. Constitutive activation of the Ras/mitogen-activated protein kinase signaling pathway promotes androgen hypersensitivity in LNCaP prostate cancer cells. Cancer Res 2003, 63:1981-1989.
67. Palanisamy N., Ateeq B., Kalyana-Sundaram S., et al. Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med 2010, 16:793-798.
68. Wang X.S., Shankar S., Dhanasekaran S.M., et al. Characterization of KRAS rearrangements in metastatic prostate cancer. Cancer Discov 2011, 1:35-43.
69. Varambally S., Dhanasekaran S.M., Zhou M., et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 2002, 419:624-629.
70. Xu K., Wu Z.J., Groner A.C., et al. EZH2 oncogenic activity in castration-resistant prostate cancer cells is polycomb-independent. Science 2012, 338:1465-1469.
71. Bhalla R., Kunju L.P., Tomlins S.A., et al. Novel dual-color immunohistochemical methods for detecting ERG-PTEN and ERG-SPINK1 status in prostate carcinoma. Mod Pathol 2013, 26:835-848.