Copy number variations of circulating, cell-free DNA in urothelial carcinoma of the bladder patients treated with radical cystectomy: A prospective study

Oncotarget

Volumn 8, Issue 34, 2017, Pages 56398-56407

  Soave, Armin ^a   Chun, Felix K H ^a   Hillebrand, Timo ^b   Rink, Michael ^a   Weisbach, Lars ^a   Steinbach, Bettina ^a   Fisch, Margit ^a   Pantel, Klaus ^a   Schwarzenbach, Heidi ^a  

^a UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^b AJ Innuscreen GmbH   (Germany)

Author keywords

Cell free DNA (cfDNA); Chromosomal region; Copy number variation; Multiplex ligation dependent probe amplification (MLPA); Urothelial carcinoma of the bladder

Indexed keywords

CARBOPLATIN; CIRCULATING CELL FREE DNA; CISPLATIN; DNA; KRUPPEL LIKE FACTOR 5; MICRORNA 15A; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; UNCLASSIFIED DRUG; UVOMORULIN;

ADULT; AGED; ANXA7 GENE; ARTICLE; CANCER MORTALITY; CANCER SPECIFIC MORTALITY; CANCER SPECIFIC SURVIVAL; CDH1 GENE; COHORT ANALYSIS; CONTROLLED STUDY; COPY NUMBER VARIATION; CYSTECTOMY; DNA EXTRACTION; FEMALE; GENE; GENETIC ASSOCIATION; HISTOLOGY; HUMAN; KIAA0196 GENE; KLF5 GENE; MAJOR CLINICAL STUDY; MALE; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; PROSPECTIVE STUDY; PROSTATE CANCER; PTEN GENE; RAD21 GENE; RIPK2 GENE; TMPRSS2 GENE; TRANSITIONAL CELL CARCINOMA; TSG1 GENE; ZFHX3 GENE;

EID: 85029058356     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.17657     Document Type: Article

References (45)

1. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2015. CA Cancer J Clin. 2015; 65:5-29
2. Witjes JA, Compérat E, Cowan NC, De Santis M, Gakis G, Lebret T, Ribal MJ, Van der Heijden AG, Sherif A, and European Association of Urology. EAU guidelines on muscle-invasive and metastatic bladder cancer: summary of the 2013 guidelines. Eur Urol. 2014; 65:778-92
3. Stein JP, Lieskovsky G, Cote R, Groshen S, Feng AC, Boyd S, Skinner E, Bochner B, Thangathurai D, Mikhail M, Raghavan D, Skinner DG. Radical cystectomy in the treatment of invasive bladder cancer: long-term results in 1,054 patients. J Clin Oncol. 2001; 19:666-75
4. Rink M, Lee DJ, Kent M, Xylinas E, Fritsche HM, Babjuk M, Brisuda A, Hansen J, Green DA, Aziz A, Cha EK, Novara G, Chun FK, et al, and Bladder Cancer Research Consortium. Predictors of cancer-specific mortality after disease recurrence following radical cystectomy. BJU Int. 2013 (3 Pt B); 111:E30-36
5. Rink M, Cha EK, Green D, Hansen J, Robinson BD, Lotan Y, Sagalowsky AI, Chun FK, Karakiewicz PI, Fisch M, Scherr DS, Shariat SF. Biomolecular predictors of urothelial cancer behavior and treatment outcomes. Curr Urol Rep. 2012; 13:122-35
6. Schwarzenbach H, Hoon DS, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer. 2011; 11:426-37
7. Schwarzenbach H, Chun FK, Isbarn H, Huland H, Pantel K. Genomic profiling of cell-free DNA in blood and bone marrow of prostate cancer patients. J Cancer Res Clin Oncol. 2011; 137:811-19
8. Schwarzenbach H. Circulating nucleic acids and protease activities in blood of tumor patients. Expert Opin Biol Ther. 2012 (Suppl 1); 12:S163-69
9. Birkenkamp-Demtröder K, Nordentoft I, Christensen E, Høyer S, Reinert T, Vang S, Borre M, Agerbæk M, Jensen JB, Ørntoft TF, Dyrskjøt L. Genomic Alterations in Liquid Biopsies from Patients with Bladder Cancer. Eur Urol. 2016; 70:75-82
10. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014; 507:315-22
11. Ralla B, Stephan C, Meller S, Dietrich D, Kristiansen G, Jung K. Nucleic acid-based biomarkers in body fluids of patients with urologic malignancies. Crit Rev Clin Lab Sci. 2014; 51:200-31
12. Abbosh PH, Rosenberg JE, Plimack ER. Circulating biomarkers to guide systemic therapy for urothelial carcinoma. Urol Oncol. 2016; 34:502-09
13. Bronkhorst AJ, Aucamp J, Pretorius PJ. Cell-free DNA: preanalytical variables. Clin Chim Acta. 2015; 450:243-53
14. Xue X, Teare MD, Holen I, Zhu YM, Woll PJ. Optimizing the yield and utility of circulating cell-free DNA from plasma and serum. Clin Chim Acta. 2009; 404:100-04
15. Kirsch C, Weickmann S, Schmidt B, Fleischhacker M. An improved method for the isolation of free-circulating plasma DNA and cell-free DNA from other body fluids. Ann N Y Acad Sci. 2008; 1137:135-39
16. Legler TJ, Liu Z, Mavrou A, Finning K, Hromadnikova I, Galbiati S, Meaney C, Hultén MA, Crea F, Olsson ML, Maddocks DG, Huang D, Fisher SA, et al. Workshop report on the extraction of foetal DNA from maternal plasma. Prenat Diagn. 2007; 27:824-29
17. Su YH, Wang M, Block TM, Landt O, Botezatu I, Serdyuk O, Lichtenstein A, Melkonyan H, Tomei LD, Umansky S. Transrenal DNA as a diagnostic tool: important technical notes. Ann N Y Acad Sci. 2004; 1022:81-89
18. Müller I, Beeger C, Alix-Panabières C, Rebillard X, Pantel K, Schwarzenbach H. Identification of loss of heterozygosity on circulating free DNA in peripheral blood of prostate cancer patients: potential and technical improvements. Clin Chem. 2008; 54:688-96
19. Diaz LA Jr, Bardelli A. Liquid biopsies: genotyping circulating tumor DNA. J Clin Oncol. 2014; 32:579-86
20. Kondrashova O, Love CJ, Lunke S, Hsu AL, Waring PM, Taylor GR, and Australian Ovarian Cancer Study (AOCS) Group. High-Throughput Amplicon-Based Copy Number Detection of 11 Genes in Formalin-Fixed Paraffin-Embedded Ovarian Tumour Samples by MLPA-Seq. PLoS One. 2015; 10:e0143006
21. Bryan RT, Tselepis C. Cadherin switching and bladder cancer. J Urol. 2010; 184:423-31
22. Kawaguchi M, Hara N, Bilim V, Koike H, Suzuki M, Kim TS, Gao N, Dong Y, Zhang S, Fujinawa Y, Yamamoto O, Ito H, Tomita Y, et al. A diagnostic marker for superficial urothelial bladder carcinoma: lack of nuclear ATBF1 (ZFHX3) by immunohistochemistry suggests malignant progression. BMC Cancer. 2016; 16:805
23. Guirado M, Gil H, Saenz-Lopez P, Reinboth J, Garrido F, Cozar JM, Ruiz-Cabello F, Carretero R. Association between C13ORF31, NOD2, RIPK2 and TLR10 polymorphisms and urothelial bladder cancer. Hum Immunol. 2012; 73:668-72
24. Sfakianos JP, Lin Gellert L, Maschino A, Gotto GT, Kim PH, Al-Ahmadie H, Bochner BH. The role of PTEN tumor suppressor pathway staining in carcinoma in situ of the bladder. Urol Oncol. 2014; 32:657-62
25. Bruins HM, Djaladat H, Ahmadi H, Sherrod A, Cai J, Miranda G, Skinner EC, Daneshmand S. Incidental prostate cancer in patients with bladder urothelial carcinoma: comprehensive analysis of 1,476 radical cystoprostatectomy specimens. J Urol. 2013; 190:1704-09
26. Zitzelsberger H, Engert D, Walch A, Kulka U, Aubele M, Höfler H, Bauchinger M, Werner M. Chromosomal changes during development and progression of prostate adenocarcinomas. Br J Cancer. 2001; 84:202-08
27. Zhang S, Liu Y, Liu Z, Zhang C, Cao H, Ye Y, Wang S, Zhang Y, Xiao S, Yang P, Li J, Bai Z. Transcriptome profiling of a multiple recurrent muscle-invasive urothelial carcinoma of the bladder by deep sequencing. PLoS One. 2014; 9:e91466
28. Gupta S, Li J, Kemeny G, Bitting RL, Beaver J, Somarelli J, Ware KE, Gregory S, Armstrong AJ. Whole genomic copy number alterations in circulating tumor cells from men with abiraterone or enzalutamide resistant metastatic castrationresistant prostate cancer. Clin Cancer Res. 2017; 23:1346-57
29. Porkka KP, Ogg EL, Saramäki OR, Vessella RL, Pukkila H, Lähdesmäki H, van Weerden WM, Wolf M, Kallioniemi OP, Jenster G, Visakorpi T. The miR-15a-miR-16-1 locus is homozygously deleted in a subset of prostate cancers. Genes Chromosomes Cancer. 2011; 50:499-509
30. Huang E, Liu R, Chu Y. miRNA-15a/16: as tumor suppressors and more. Future Oncol. 2015; 11:2351-63
31. Soave A, Schmidt S, Dahlem R, Minner S, Engel O, Kluth LA, John LM, Hansen J, Schmid M, Sauter G, Shariat SF, Fisch M, Rink M. Does the extent of variant histology affect oncological outcomes in patients with urothelial carcinoma of the bladder treated with radical cystectomy? Urol Oncol. 2015; 33:21.e1-21.e9
32. Xylinas E, Rink M, Robinson BD, Lotan Y, Babjuk M, Brisuda A, Green DA, Kluth LA, Pycha A, Fradet Y, Faison T, Lee RK, Karakiewicz PI, et al. Impact of histological variants on oncological outcomes of patients with urothelial carcinoma of the bladder treated with radical cystectomy. Eur J Cancer. 2013; 49:1889-97
33. Yan M, Xu H, Waddell N, Shield-Artin K, Haviv I, McKay MJ, Fox SB, and kConFab authors. Enhanced RAD21 cohesin expression confers poor prognosis in BRCA2 and BRCAX, but not BRCA1 familial breast cancers. Breast Cancer Res. 2012; 14:R69
34. Jalava SE, Porkka KP, Rauhala HE, Isotalo J, Tammela TL, Visakorpi T. TCEB1 promotes invasion of prostate cancer cells. Int J Cancer. 2009; 124:95-102
35. Leighton X, Eidelman O, Jozwik C, Pollard HB, Srivastava M. ANXA7-GTPase as Tumor Suppressor: Mechanisms and Therapeutic Opportunities. Methods Mol Biol. 2017; 1513:23-35
36. Du C, Gao Y, Xu S, Jia J, Huang Z, Fan J, Wang X, He D, Guo P. KLF5 promotes cell migration by up-regulating FYN in bladder cancer cells. FEBS Lett. 2016; 590:408-18
37. Gao Y, Wu K, Chen Y, Zhou J, Du C, Shi Q, Xu S, Jia J, Tang X, Li F, Hui K, He D, Guo P. Beyond proliferation: KLF5 promotes angiogenesis of bladder cancer through directly regulating VEGFA transcription. Oncotarget. 2015; 6:43791-805. https://doi.org/10.18632/oncotarget.6101
38. Chen C, Benjamin MS, Sun X, Otto KB, Guo P, Dong XY, Bao Y, Zhou Z, Cheng X, Simons JW, Dong JT. KLF5 promotes cell proliferation and tumorigenesis through gene regulation and the TSU-Pr1 human bladder cancer cell line. Int J Cancer. 2006; 118:1346-1355
39. Ruiz de Sabando A, Wang C, He Y, García-Barros M, Kim J, Shroyer KR, Bannister TD, Yang VW, Bialkowska AB. ML264, A Novel Small-Molecule Compound That Potently Inhibits Growth of Colorectal Cancer. Mol Cancer Ther. 2016; 15:72-83
40. Epstein JI, Amin MB, Reuter VR, Mostofi FK. The World Health Organization/International Society of Urological Pathology consensus classification of urothelial (transitional cell) neoplasms of the urinary bladder. Bladder Consensus Conference Committee. Am J Surg Pathol. 1998; 22:1435-48
41. Lotan Y, Gupta A, Shariat SF, Palapattu GS, Vazina A, Karakiewicz PI, Bastian PJ, Rogers CG, Amiel G, Perotte P, Schoenberg MP, Lerner SP, Sagalowsky AI. Lymphovascular invasion is independently associated with overall survival, cause-specific survival, and local and distant recurrence in patients with negative lymph nodes at radical cystectomy. J Clin Oncol. 2005; 23:6533-39
42. Hong SK, Kwak C, Jeon HG, Lee E, Lee SE. Do vascular, lymphatic, and perineural invasion have prognostic implications for bladder cancer after radical cystectomy? Urology. 2005; 65:697-702
43. Novara G, Svatek RS, Karakiewicz PI, Skinner E, Ficarra V, Fradet Y, Lotan Y, Isbarn H, Capitanio U, Bastian PJ, Kassouf W, Fritsche HM, Izawa JI, et al. Soft tissue surgical margin status is a powerful predictor of outcomes after radical cystectomy: a multicenter study of more than 4,400 patients. J Urol. 2010; 183:2165-70
44. Eble J, Sauter G, Epstein JI, Sesterhenn IA (editors). Pathology and Genetics of Tumours of the Urinary System and Male Genital Organs. World Health Organization Classification of Tumours. IARCPress. Lyon. 2004
45. Rink M, Fajkovic H, Cha EK, Gupta A, Karakiewicz PI, Chun FK, Lotan Y, Shariat SF. Death certificates are valid for the determination of cause of death in patients with upper and lower tract urothelial carcinoma. Eur Urol. 2012; 61:854-55