Somatic copy number alterations by whole-exome sequencing implicates YWHAZ and PTK2 in castration-resistant prostate cancer

Journal of Pathology

Volumn 231, Issue 4, 2013, Pages 505-516

  Menon, Roopika ^a   Deng, Mario ^a   Rüenauver, Kerstin ^a   Queisser, Angela ^a   Pfeifer, Martin ^d   Offermann, Anne ^a   Boehm, Diana ^a   Vogel, Wenzel ^a   Scheble, Veit ^b   Fend, Falko ^c   Kristiansen, Glen ^a   Wernert, Nicolas ^a   Oberbeckmann, Nicole ^b   Biskup, Saskia ^b   Rubin, Mark A ^c   Adler, David ^a   Perner, Sven ^a  

^a UNIVERSITY HOSPITAL BONN   (Germany)

^b CEGAT GMBH   (Germany)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

^d UNIVERSITY OF COLOGNE   (Germany)

Author keywords

castration resistant prostate cancer; therapeutic targets: whole exome sequencing

Indexed keywords

2 [5 CHLORO 2 (2 METHOXY 4 MORPHOLINOANILINO) 4 PYRIMIDINYLAMINO] N METHYLBENZAMIDE; FOCAL ADHESION KINASE 1; FORMALDEHYDE; MEMBRANE PROTEIN; MESSENGER RNA; PARAFFIN; UNCLASSIFIED DRUG; YWHAZ PROTEIN;

APOPTOSIS; ARTICLE; CANCER CELL CULTURE; CANCER GROWTH; CANCER PATIENT; CASTRATION RESISTANT PROSTATE CANCER; CELL ASSAY; CELL CYCLE ARREST; CELL INVASION; CELL MIGRATION; CELL PROLIFERATION; CLINICAL ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; DNA EXTRACTION; EXOME; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; GENE DOSAGE; GENE FREQUENCY; GENE SEQUENCE; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; IN VITRO STUDY; MALE; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; SEQUENCE ANALYSIS; SOMATIC COPY NUMBER; VALIDATION PROCESS;

CASTRATION-RESISTANT PROSTATE CANCER; THERAPEUTIC TARGETS: WHOLE-EXOME SEQUENCING;

14-3-3 PROTEINS; CELL PROLIFERATION; DNA COPY NUMBER VARIATIONS; DNA MUTATIONAL ANALYSIS; EXOME; FOCAL ADHESION KINASE 1; GENE KNOCKDOWN TECHNIQUES; GENETIC ASSOCIATION STUDIES; HUMANS; MALE; MOLECULAR TARGETED THERAPY; MORPHOLINES; NEOPLASM INVASIVENESS; NEOPLASM PROTEINS; ORCHIECTOMY; PARAFFIN EMBEDDING; PROSTATIC NEOPLASMS; SEQUENCE ANALYSIS, DNA; TREATMENT FAILURE; TUMOR CELLS, CULTURED;

EID: 84887516476     PISSN: 00223417     EISSN: 10969896     Source Type: Journal    
DOI: 10.1002/path.4274     Document Type: Article

References (52)

1. Jemal A, Siegel R, Xu J, et al., Cancer statistics, 2010. CA Cancer J Clin 2010; 60: 277-300.
2. Rubin MA, Maher CA, Chinnaiyan AM,. Common gene rearrangements in prostate cancer. J Clin Oncol 2011; 29: 3659-3668.
3. Chi KN, Bjartell A, Dearnaley D, et al., Castration-resistant prostate cancer: from new pathophysiology to new treatment targets. Eur Urol 2009; 56: 594-605.
4. Amaral TM, Macedo D, Fernandes I, et al., Castration-resistant prostate cancer: mechanisms, targets, and treatment. Prostate Cancer 2012; 2012: 327253.
5. Omlin A, de Bono JS,. Therapeutic options for advanced prostate cancer: 2011 update. Curr Urol Rep 2012; 13: 170-178.
6. Pezaro CJ, Mukherji D, De Bono JS,. Abiraterone acetate: redefining hormone treatment for advanced prostate cancer. Drug Discov Today 2012; 17: 221-226.
7. Richards J, Lim AC, Hay CW, et al., Interactions of abiraterone, eplerenone, and prednisolone with wild-type and mutant androgen receptor: a rationale for increasing abiraterone exposure or combining with MDV3100. Cancer Res 2012; 72: 2176-2182.
8. Tomlins SA, Laxman B, Varambally S, et al., Role of the TMPRSS2-ERG gene fusion in prostate cancer. Neoplasia 2008; 10: 177-188.
9. Tomlins SA, Rhodes DR, Perner S, et al., Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005; 310: 644-648.
10. Tomlins SA, Aubin SM, Siddiqui J, et al., Urine TMPRSS2:ERG fusion transcript stratifies prostate cancer risk in men with elevated serum PSA. Sci Transl Med 2011; 3: 94ra72.
11. Kristiansen G., Diagnostic and prognostic molecular biomarkers for prostate cancer. Histopathology 2012; 60: 125-141.
12. Esgueva R, Perner S, C JL, et al., Prevalence of TMPRSS2-ERG and SLC45A3-ERG gene fusions in a large prostatectomy cohort. Mod Pathol 2010; 23: 539-546.
13. 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.
14. Danila DC, Anand A, Sung CC, et al., TMPRSS2-ERG status in circulating tumor cells as a predictive biomarker of sensitivity in castration-resistant prostate cancer patients treated with abiraterone acetate. Eur Urol 2011; 60: 897-904.
15. Meyerson M, Gabriel S, Getz G,. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010; 11: 685-696.
16. Beltran H, Rickman DS, Park K, et al., Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discov 2011; 1: 487-495.
17. Friedlander TW, Roy R, Tomlins SA, et al., Common structural and epigenetic changes in the genome of castration-resistant prostate cancer. Cancer Res 2012; 72: 616-625.
18. Berger MF, Lawrence MS, Demichelis F, et al., The genomic complexity of primary human prostate cancer. Nature 2011; 470: 214-220.
19. Grasso CS, Wu YM, Robinson DR, et al., The mutational landscape of lethal castration-resistant prostate cancer. Nature 2012; 487: 239-243.
20. Menon R, Deng M, Boehm M, et al., Exome enrichment and SOLiD sequencing of formalin-fixed paraffin-embedded (FFPE) prostate cancer tissue. Int J Mol Sci 2012; 13: 8933-8942.
21. Schweiger MR, Kerick M, Timmermann B, et al., Genome-wide massively parallel sequencing of formaldehyde-fixed paraffin-embedded (FFPE) tumor tissues for copy number and mutation analysis. PLoS One 2009; 4: e5548.
22. Kerick M, Isau M, Timmermann B, et al., Targeted high throughput sequencing in clinical cancer settings: formaldehyde-fixed paraffin-embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genom 2011; 4: 68.
23. Scheble VJ, Scharf G, Braun M, et al., ERG rearrangement in local recurrences compared to distant metastases of castration-resistant prostate cancer. Virchows Arch 2012; 461: 157-162.
24. Scheble VJ, Braun M, Wilbertz T, et al., ERG rearrangement in small cell prostatic and lung cancer. Histopathology 2010; 56: 937-943.
25. Homer N, Merriman B, Nelson SF,. BFAST: an alignment tool for large scale genome resequencing. PLoS One 2009; 4: e7767.
26. Li H, Handsaker B, Wysoker A, et al., The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25: 2078-2079.
27. McKenna A, Hanna M, Banks E, et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: 1297-1303.
28. Koboldt DC, Zhang Q, Larson DE, et al., VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012; 22: 568-576.
29. Weiss J, Sos ML, Seidel D, et al., Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer. Sci Transl Med 2010; 2: 62ra93.
30. Perner S, Demichelis F, Beroukhim R, et al., TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. Cancer Res 2006; 66: 8337-8341.
31. Wilbertz T, Wagner P, Petersen K, et al., SOX2 gene amplification and protein overexpression are associated with better outcome in squamous cell lung cancer. Mod Pathol 2011; 24: 944-953.
32. Braun M, Kirsten R, Rupp NJ, et al., Quantification of protein expression in cells and cellular subcompartments on immunohistochemical sections using a computer supported image analysis system. Histol Histopathol 2013; 28: 605-610.
33. Barbieri CE, Baca SC, Lawrence MS, et al., Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012; 44: 685-689.
34. Neal CL, Yao J, Yang W, et al., 14-3-3ζ overexpression defines high risk for breast cancer recurrence and promotes cancer cell survival. Cancer Res 2009; 69: 3425-3432.
35. Danes CG, Wyszomierski SL, Lu J, et al., 14-3-3 ζ down-regulates p53 in mammary epithelial cells and confers luminal filling. Cancer Res 2008; 68: 1760-1767.
36. Squire JA,. TMPRSS2-ERG and PTEN loss in prostate cancer. Nat Genet 2009; 41: 509-510.
37. Bubendorf L, Kononen J, Koivisto P, et al., Survey of gene amplifications during prostate cancer progression by high-throughout fluorescence in situ hybridization on tissue microarrays. Cancer Res 1999; 59: 803-806.
38. Supino R, Favini E, Cuccuru G, et al., Effect of paclitaxel on intracellular localization of c-Myc and P-c-Myc in prostate carcinoma cell lines. Ann N Y Acad Sci 2007; 1095: 175-181.
39. Beroukhim R, Mermel CH, Porter D, et al., The landscape of somatic copy-number alteration across human cancers. Nature 2010; 463: 899-905.
40. Jenkins RB, Qian J, Lieber MM, et al., Detection of c-myc oncogene amplification and chromosomal anomalies in metastatic prostatic carcinoma by fluorescence in situ hybridization. Cancer Res 1997; 57: 524-531.
41. Forbes SA, Bindal N, Bamford S, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Cell Lines Project. Nucleic Acids Res 2011; 39: D945-D950.
42. Taylor BS, Schultz N, Hieronymus H, et al., Integrative genomic profiling of human prostate cancer. Cancer Cell 2010; 18: 11-22.
43. Neal CL, Yu D,. 14-3-3 ζ as a prognostic marker and therapeutic target for cancer. Expert Opin Ther Targets 2010; 14: 1343-1354.
44. Macha MA, Matta A, Chauhan S, et al., 14-3-3 ζ is a molecular target in guggulsterone induced apoptosis in head and neck cancer cells. BMC Cancer 2010; 10: 655.
45. Murata T, Takayama K, Urano T, et al., 14-3-3 ζ, a novel androgen-responsive gene, is upregulated in prostate cancer and promotes prostate cancer cell proliferation and survival. Clin Cancer Res 2012; 18: 5617-5627.
46. Sood AK, Coffin JE, Schneider GB, et al., Biological significance of focal adhesion kinase in ovarian cancer: role in migration and invasion. Am J Pathol 2004; 165: 1087-1095.
47. Halder J, Lin YG, Merritt WM, et al., Therapeutic efficacy of a novel focal adhesion kinase inhibitor, TAE226, in ovarian carcinoma. Cancer Res 2007; 67: 10976-10983.
48. Recher C, Ysebaert L, Beyne-Rauzy O, et al., Expression of focal adhesion kinase in acute myeloid leukemia is associated with enhanced blast migration, increased cellularity, and poor prognosis. Cancer Res 2004; 64: 3191-3197.
49. Aronsohn MS, Brown HM, Hauptman G, et al., Expression of focal adhesion kinase and phosphorylated focal adhesion kinase in squamous cell carcinoma of the larynx. Laryngoscope 2003; 113: 1944-1948.
50. Liu TJ, LaFortune T, Honda T, et al., Inhibition of both focal adhesion kinase and insulin-like growth factor-I receptor kinase suppresses glioma proliferation in vitro and in vivo. Mol Cancer Ther 2007; 6: 1357-1367.
51. Kurio N, Shimo T, Fukazawa T, et al., Anti-tumor effect in human breast cancer by TAE226, a dual inhibitor for FAK and IGF-IR in vitro and in vivo. Exp Cell Res 2011; 317: 1134-1146.
52. Johnson TR, Khandrika L, Kumar B, et al., Focal adhesion kinase controls aggressive phenotype of androgen-independent prostate cancer. Mol Cancer Res 2008; 6: 1639-1648.