Discovery and validation of novel expression signature for postcystectomy recurrence in high-risk bladder cancer

Journal of the National Cancer Institute

Volumn 106, Issue 11, 2014, Pages

  Mitra, Anirban P ^a   Lam, Lucia L ^b   Ghadessi, Mercedeh ^b   Erho, Nicholas ^b   Vergara, Ismael A ^b   Alshalalfa, Mohammed ^b   Buerki, Christine ^a   Haddad, Zaid ^b   Sierocinski, Thomas ^b   Triche, Timothy J ^a,b   Skinner, Eila C ^c   Davicioni, Elai ^b   Daneshmand, Siamak ^a   Black, Peter C ^b,d  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b GenomeDx Biosciences Inc   (Canada)

^c STANFORD CANCER INSTITUTE   (United States)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; RNA;

ADULT; AGED; ARTICLE; BLADDER CARCINOMA; CANCER PATIENT; CANCER PROGNOSIS; CANCER RECURRENCE; CANCER SURGERY; CLASSIFIER; CYSTECTOMY; FEMALE; GENE EXPRESSION PROFILING; GENOMICS; HIGH RISK PATIENT; HUMAN; MAJOR CLINICAL STUDY; MALE; MICROARRAY ANALYSIS; MUSCLE INVASIVE BLADDER CANCER; PATIENT IDENTIFICATION; POSTOPERATIVE PERIOD; PREDICTIVE VALUE; PRIORITY JOURNAL; RECURRENCE RISK; RISK ASSESSMENT; VALIDATION STUDY; AREA UNDER THE CURVE; GENE EXPRESSION REGULATION; GENETICS; KAPLAN MEIER METHOD; LYMPH NODE METASTASIS; MIDDLE AGED; NEOPLASM RECURRENCE, LOCAL; NOMOGRAM; PATHOLOGY; RECEIVER OPERATING CHARACTERISTIC; TUMOR INVASION; URINARY BLADDER NEOPLASMS;

ADULT; AGED; AREA UNDER CURVE; CYSTECTOMY; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; KAPLAN-MEIER ESTIMATE; LYMPHATIC METASTASIS; MALE; MIDDLE AGED; NEOPLASM INVASIVENESS; NEOPLASM RECURRENCE, LOCAL; NOMOGRAMS; PREDICTIVE VALUE OF TESTS; RNA, NEOPLASM; ROC CURVE; TRANSCRIPTOME; URINARY BLADDER NEOPLASMS;

EID: 84922481508     PISSN: 00278874     EISSN: 14602105     Source Type: Journal    
DOI: 10.1093/jnci/dju290     Document Type: Article

References (39)

1. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin. 2011;61(2):69-90.
2. Stein JP, Lieskovsky G, Cote R, et al. Radical cystectomy in the treatment of invasive bladder cancer: long-term results in 1, 054 patients. J Clin Oncol. 2001;19(3):666-675.
3. Shariat SF, Karakiewicz PI, Palapattu GS, et al. Outcomes of radical cystectomy for transitional cell carcinoma of the bladder: a contemporary series from the Bladder Cancer Research Consortium. J Urol. 2006;176(6):2414-2422.
4. Mitra AP, Quinn DI, Dorff TB, et al. Factors influencing post-recurrence survival in bladder cancer following radical cystectomy. BJU Int. 2012;109(6):846-854.
5. Rink M, Lee DJ, Kent M, et al. Predictors of cancer-specific mortality after disease recurrence following radical cystectomy. BJU Int. 2013;111(3 b):E30-E36.
6. Leow JJ, Martin-Doyle W, Rajagopal PS, et al. Adjuvant chemotherapy for invasive bladder cancer: a 2013 updated systematic review and metaanalysis of randomized trials. Eur Urol. 2014;66(1):42-54.
7. Calabrò F, Sternberg CN. Neoadjuvant and adjuvant chemotherapy in muscle-invasive bladder cancer. Eur Urol. 2009;55(2):348-358.
8. International Bladder Cancer Nomogram Consortium. Postoperative nomogram predicting risk of recurrence after radical cystectomy for bladder cancer. J Clin Oncol. 2006;24(24):3967-3972.
9. Karakiewicz PI, Shariat SF, Palapattu GS, et al. Nomogram for predicting disease recurrence after radical cystectomy for transitional cell carcinoma of the bladder. J Urol. 2006;176(4):1354-1362.
10. Birkhahn M, Mitra AP, Cote RJ. Molecular markers for bladder cancer: the road to a multimarker approach. Expert Rev Anticancer Ther. 2007;7(12):1717-1727.
11. Stadler WM, Lerner SP, Groshen S, et al. Phase III study of molecularly targeted adjuvant therapy in locally advanced urothelial cancer of the bladder based on p53 status. J Clin Oncol. 2011;29(25):3443-3449.
12. Mitra AP, Bartsch CC, Cote RJ. Strategies for molecular expression profiling in bladdercancer. Cancer Metastasis Rev. 2009;28(3-4):317-326.
13. Riester M, Taylor JM, Feifer A, et al. Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. Clin Cancer Res. 2012;18(5):1323-1333.
14. Sanchez-Carbayo M, Socci ND, Lozano J, et al. Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays. J Clin Oncol. 2006;24(5):778-789.
15. Blaveri E, Simko JP, Korkola JE, et al. Bladder cancer outcome and subtype classification by gene expression. Clin Cancer Res. 2005;11(11):4044-4055.
16. Mitra AP, Pagliarulo V, Yang D, et al. Generation of a concise gene panel for outcome prediction in urinary bladder cancer. J Clin Oncol. 2009;27(24):3929-3937.
17. Lindgren D, Frigyesi A, Gudjonsson S, et al. Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome. Cancer Res. 2010;70(9):3463-3472.
18. Catto JW, Abbod MF, Wild PJ, et al. The application of artificial intelligence to microarray data: identification of a novel gene signature to identify bladder cancer progression. Eur Urol. 2010;57(3):398-406.
19. Mitra AP, Castelao JE, Hawes D, et al. Combination of molecular alterations and smoking intensity predicts bladder cancer outcome: a report from the Los Angeles Cancer Surveillance Program. Cancer. 2013;119(4):756-765.
20. Urinary bladder. In: Edge SB, Byrd DR, Compton CC, Fritz AG, Greene FL, Trotti A, eds. AJCC Cancer Staging Manual. 7th ed. New York, NY: Springer; 2010:497-505.
21. Kim WJ, Kim EJ, Kim SK, et al. Predictive value of progression-related gene classifier in primary non-muscle invasive bladder cancer. Mol Cancer. 2010;9:3.
22. Kim WJ, Kim SK, Jeong P, et al. A four-gene signature predicts disease progression in muscle invasive bladder cancer. Mol Med. 2011;17(5-6):478-485.
23. Fine JP, Gray RJ. A proportional hazards model for the subdistribution of a competing risk. J Am Stat Assoc. 1999;94(446):496-509.
24. Cui Q, Ma Y, Jaramillo M, et al. A map of human cancer signaling. Mol Syst Biol. 2007;3:152.
25. Awan A, Bari H, Yan F, et al. Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network. IET Syst Biol. 2007;1(5):292-297.
26. Li L, Tibiche C, Fu C, et al. The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. Genome Res. 2012;22(7):1222-1230.
27. Newman RH, Hu J, Rho HS, et al. Construction of human activity-based phosphorylation networks. Mol Syst Biol. 2013;9:655.
28. Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One. 2010;5(11):e13984.
29. Chambers JM, Cleveland WS, Kleiner B, Tukey PA. Graphical Methods for Data Analysis. New Jersey, NJ: Wadsworth & Brooks/Cole Publishing Company; 1983.
30. The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014;507(7492):315-322.
31. Als AB, Dyrskjøt L, Von Der Maase H, et al. Emmprin and survivin predict response and survival following cisplatin-containing chemotherapy in patients with advanced bladder cancer. Clin Cancer Res. 2007;13(15):4407-4414.
32. Logothetis CJ, Johnson DE, Chong C, et al. Adjuvant cyclophosphamide, doxorubicin, and cisplatin chemotherapy for bladder cancer: an update. J Clin Oncol. 1988;6(10):1590-1596.
33. Abdueva D, Wing M, Schaub B, Triche T, Davicioni E. Quantitative expression profiling in formalin-fixed paraffin-embedded samples by Affymetrix microarrays. J Mol Diagn. 2010;12(4):409-417.
34. Okoniewski MJ, Yates T, Dibben S, Miller CJ. An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data. Genome Biol. 2007;8(5):R79.
35. Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.
36. Kapranov P, St Laurent G, Raz T, et al. The majority of total nuclearencoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol. 2010;8:149.
37. Mitra SA, Mitra AP, Triche TJ. A central role for long non-coding RNA in cancer. Front Genet. 2012;3:17.
38. Stockle M, Meyenburg W, Wellek S, et al. Adjuvant polychemotherapy of nonorgan-confined bladder cancer after radical cystectomy revisited: longterm results of a controlled prospective study and further clinical experience. J Urol. 1995;153(1):47-52.
39. Mitra AP, Cote RJ. Molecular pathogenesis and diagnostics of bladder cancer. Annu Rev Pathol. 2009;4:251-285