Genomic characterization of three urinary bladder cancer cell lines: understanding genomic types of urinary bladder cancer

Abstract

Several genomic regions are frequently altered and associated with the type, stage and progression of urinary bladder cancer (UBC). We present the characterization of 5637, T24 and HT1376 UBC cell lines by karyotyping, fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) analysis. Some cytogenetic anomalies present in UBC were found in the three cell lines, such as chromosome 20 aneuploidy and the loss of 9p21. Some gene loci losses (e.g. CDKN2A) and gains (e.g. HRAS, BCL2L1 and PTPN1) were coincident across all cell lines. Although some significant heterogeneity and complexity were detected between them, their genomic profiles exhibited a similar pattern to UBC. We suggest that 5637 and HT1376 represent the E2F3/RB1 pathway due to amplification of 6p22.3, concomitant with loss of one copy of RB1 and mutation of the remaining copy. The HT1376 presented a 10q deletion involving PTEN region and no alteration of PIK3CA region which, in combination with the inactivation of TP53, bears more invasive and metastatic properties than 5637. The T24 belongs to the alternative pathway of FGFR3/CCND1 by presenting mutated HRAS and over-represented CCND1. These cell lines cover the more frequent subtypes of UBC and are reliable models that can be used, as a group, in preclinical studies.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  1. 1.

    Ismaili N, Amzerin M, Flechon A. Chemotherapy in advanced bladder cancer: current status and future. J Hematol Oncol. 2011;4:35.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Höglund M. The bladder cancer genome; chromosomal changes as prognostic makers, opportunities, and obstacles. Urol Oncol. 2012;30(4):533–40.

    Article  PubMed  Google Scholar 

  3. 3.

    Escudero D, Shirodkar S, Lokeshwar V. Bladder carcinogenesis and molecular pathways. In: Lokeshwar VB, Merseburger AS, Hautmann SH, editors. Bladder tumours: molecular aspects and clinical management. Totowa: Humana; 2011. p. 29–32.

    Google Scholar 

  4. 4.

    Hatina J, Huckenbeck W, Rieder H, Seifert HH, Schulz WA. Bladder carcinoma cell lines as models of the pathobiology of bladder cancer. Review of the literature and establishment of a new progression series. Urologe A. 2008;47(6):724–34.

    CAS  Article  PubMed  Google Scholar 

  5. 5.

    Strefford JC, Lillington DM, Steggall M, Lane TM, Nouri AME, Young BD, et al. Novel chromosome findings in bladder-cancer cell lines detected with multiplex fluorescence in situ hybridization. Cancer Genet Cytogenet. 2002;135(2):139–46.

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    Hurst CD, Fiegler H, Carr P, Williams S, Carter NP, Knowles MA. High-resolution analysis of genomic copy number alterations in bladder cancer by microarray-based comparative genomic hybridization. Oncogene. 2004;23(12):2250–63.

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Williams SV, Adams J, Coulter J, Summersgill BM, Shipley J, Knowles MA. Assessment by M-FISH of karyotypic complexity and cytogenetic evolution in bladder cancer in vitro. Genes Chromosomes Cancer. 2005;43(4):315–28.

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 2002;30(12):e57.

    Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Lindgren D, Liedberg F, Andersson A, Chebil G, Gudjonsson S, Borg A, et al. Molecular characterization of early-stage bladder carcinomas by expression profiles, FGFR3 mutation status, and loss of 9q. Oncogene. 2006;25(18):2685–96.

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Tanaka T, Miyazawa K, Tsukamoto T, Kuno T, Suzuki K. Pathobiology and chemoprevention of bladder cancer. J Oncol. 2011;2011:528353.

    PubMed  PubMed Central  Google Scholar 

  11. 11.

    Netto GJ. Molecular biomarkers in urothelial carcinoma of the bladder: are we there yet? Nat Rev Urol. 2011;9(1):41–51.

    Article  PubMed  Google Scholar 

  12. 12.

    Gallucci M, Guadagni F, Marzano R, Leonardo C, Merola R, Sentinelli S. Status of the p53, p16, RB1, and HER-2 genes and chromosomes 3, 7, 9, and 17 in advanced bladder cancer: correlation with adjacent mucosa and pathological parameters. J Clin Pathol. 2005;58(4):367–71.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Mitra AP, Datar RH, Cote RJ. Molecular pathways in invasive bladder cancer: new insights into mechanisms, progression, and target identification. J Clin Oncol. 2006;24(35):5552–64.

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    Kompier LC, Lurkin I, van der Aa MN, van Rhijn BW, van der Kwast TH, Zwarthoff EC. FGFR3, HRAS, KRAS, NRAS and PIK3CA mutations in bladder cancer and their potential as biomarkers for surveillance and therapy. PLoS One. 2010;5(11):e13821.

    Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Lindgren D, Sjödahl G, Lauss M, Staaf J, Chebil G, Lovgren K. Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma. PLoS One. 2012;7(6):e38863.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Fujii T, Shimada K, Anai S, Fujimoto K, Konishi N. ALKBH2, a novel AlkB homologue, contributes to human bladder cancer progression by regulating MUC1 expression. Cancer Sci. 2013;104(3):321–7.

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Ying L, Huang Y, Chen H, Wang Y, Xia L, Chen Y, et al. Downregulated MEG3 activates autophagy and increases cell proliferation in bladder cancer. Mol Biosyst. 2013;9(3):407–11.

    CAS  Article  PubMed  Google Scholar 

  18. 18.

    Ewald JA, Downs TM, Cetnar JP, Ricke WA. Expression microarray meta-analysis identifies genes associated with Ras/MAPK and related pathways in progression of muscle-invasive bladder transition cell carcinoma. PLoS One. 2013;8(2):e55414.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Qi Y, Chang L, Li H, Yu G, Xiao W, Xia D, et al. Over-expression of LRIG3 suppresses growth and invasion of bladder cancer cells. J Huazhong Univ Sci Technolog Med Sci. 2013;33(1):111–6.

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Karkoulis PK, Stravopodis DJ, Konstantakou EG, Voutsinas GE. Targeted inhibition of heat shock protein 90 disrupts multiple oncogenic signaling pathways, thus inducing cell cycle arrest and programmed cell death in human urinary bladder-cancer cell lines. Cancer Cell Int. 2013;13(1):11.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Pinto-Leite R, Arantes-Rodrigues R, Palmeira C, Gaivão I, Cardoso ML, Colaço A, et al. Everolimus enhances gemcitabine-induced cytotoxicity in bladder-cancer cell lines. J Toxicol Environ Health A. 2012;75(13–15):788–99.

    CAS  Article  PubMed  Google Scholar 

  22. 22.

    Chiong E, Dadbin A, Harris LD, Sabichi AL, Grossman HB. The use of short tandem repeat profiling to characterize human bladder-cancer cell lines. J Urol. 2009;181(6):2737–48.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Masters JR. Cell-line authentication: end the scandal of false cell lines. Nature. 2012;492(7428):186.

    CAS  Article  PubMed  Google Scholar 

  24. 24.

    Vasconcelos-Nóbrega C, Pinto-Leite R, Arantes-Rodrigues R, Ferreira R, Brochado P, Cardoso ML, et al. In vivo and in vitro effects of RAD001 on bladder cancer. Urol Oncol. 2011;31(7):1212–21.

    Article  PubMed  Google Scholar 

  25. 25.

    Arantes-Rodrigues R, Pinto-Leite R, Ferreira R, Neuparth MJ, Pires MJ, Gaivão I, et al. Meloxicam in the treatment of in vitro and in vivo models of urinary bladder cancer. Biomed Pharmacother. 2013;67(4):277–84.

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Shaffer LG, Slovak ML, Campbell LJ. ISCN: an International System for Human Cytogenetic Nomenclature: recommendations of the International Standing Committee on Human Cytogenetic Nomenclature. S. Karger. 2009.

  27. 27.

    Bruch J, Schulz WA, Häussler J, Melzner I, Brüderlein S, Moller P, et al. Delineation of the 6p22 amplification unit in urinary bladder carcinoma cell lines. Cancer Res. 2000;60(16):4526–30.

    CAS  PubMed  Google Scholar 

  28. 28.

    Padilla-Nash HM, Heselmeyer-Haddad K, Wangsa D, Zhang H, Ghadimi BM, Macville M, et al. Jumping translocations are common in solid tumour cell lines and result in recurrent fusions of whole chromosome arms. Genes Chromosomes Cancer. 2001;30(4):349–63.

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    Fadl-Elmula I, Kytölä S, Pan Y, Lui WO, Derienzo G, Forsberg L. Characterization of chromosomal abnormalities in uroepithelial carcinomas by G-banding, spectral karyotyping and FISH analysis. Int J Cancer. 2001;92(6):824–31.

    CAS  Article  PubMed  Google Scholar 

  30. 30.

    DSMZ. German collection of microorganisms and cell cultures. http://www.dsmz.de

  31. 31.

    Gildea JJ, Golden WL, Harding MA, Theodorescu D. Genetic and phenotypic changes associated with the acquisition of tumourigenicity in human bladder cancer. Genes Chromosomes Cancer. 2000;27(3):252–63.

    CAS  Article  PubMed  Google Scholar 

  32. 32.

    Makridakis M, Gagos S, Petrolekas A, Roubelakis MG, Bitsika V, Stravodimos K. Chromosomal and proteome analysis of a new T24-based cell line model for aggressive bladder cancer. Proteomics. 2009;9(2):287–98.

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–74.

    CAS  Article  PubMed  Google Scholar 

  34. 34.

    da Silva GN, Evangelista AF, Magalhães DA, Macedo C, Búfalo MC, Sakamoto-Hojo ET, et al. Expression of genes related to apoptosis, cell cycle and signaling pathways are independent of TP53 status in urinary bladder cancer cells. Mol Biol Rep. 2011;38(6):4159–70.

    Article  PubMed  Google Scholar 

  35. 35.

    Chekaluk Y, Wu CL, Rosenberg J, Riester M, Dai Q, Lin S. Identification of nine genomic regions of amplification in urothelial carcinoma, correlation with stage, and potential prognostic and therapeutic value. PLoS One. 2013;8(4):e60927.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Elder PA, Bell SM, Knowles MA. Deletion of two regions on chromosome 4 in bladder carcinoma: definition of a critical 750kB region at 4p16.3. Oncogene. 1994;9(12):3433–66.

    CAS  PubMed  Google Scholar 

  37. 37.

    Tatarano S, Chiyomaru T, Kawakami K, Enokida H, Yoshino H, Hidaka H. miR-218 on the genomic loss region of chromosome 4p15.31 functions as a tumor suppressor in bladder cancer. Int J Oncol. 2011;39(1):13–21.

    CAS  PubMed  Google Scholar 

  38. 38.

    Richter J, Beffa L, Wagner U, Schraml P, Gasser TC, Moch H, et al. Patterns of chromosomal imbalances in advanced urinary bladder cancer detected by comparative genomic hybridization. Am J Pathol. 1998;153(5):1615–21.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Perucca D, Szepetowski P, Simon MP, Gaudray P. Molecular genetics of human bladder carcinomas. Cancer Genet Cytogenet. 1990;49(2):143–56.

    CAS  Article  PubMed  Google Scholar 

  40. 40.

    Knowles MA. What we could do now: molecular pathology of bladder cancer. Mol Pathol. 2001;54(4):215–21.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Höglund M, Säll T, Heim S, Mitelman F, Mandahl N, Fadl-Elmula I. Identification of cytogenetic subgroups and karyotypic pathways in transitional cell carcinoma. Cancer Res. 2001;61(22):8241–6.

    PubMed  Google Scholar 

  42. 42.

    Mitelman F, Johansson B, Mertens F. Mitelman database of chromosome aberrations in cancer. http://cgap.nci.nih.gov/Chromosomes/Mitelman. 2008; Accessed 25 January 2013.

  43. 43.

    Baffa R, Letko J, McClung C, LeNoir J, Vecchione A, Gomella G. Molecular genetics of bladder cancer: targets for diagnosis and therapy. J Exp Clin Cancer Res. 2006;25(2):145–60.

    CAS  PubMed  Google Scholar 

  44. 44.

    Forbes SA, Tang G, Bindal N, Bamford S, Dawson E, Cole C, et al. COSMIC (the catalogue of somatic mutations in cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 2010;38:D652–7.

    CAS  Article  PubMed  Google Scholar 

  45. 45.

    Sanchez-Carbayo M, Socci ND, Charytonowicz E, Lu M, Prystowsky M, Childs G, et al. Molecular profiling of bladder cancer using cDNA microarrays: defining histogenesis and biological phenotypes. Cancer Res. 2002;62(23):6973–80.

    CAS  PubMed  Google Scholar 

  46. 46.

    Sheahan S, Bellamy CO, Dunbar DR, Harrison DJ, Prost S. Deficiency of G1 regulators P53, P21Cip1 and/or pRb decreases hepatocyte sensitivity to TGFbeta cell cycle arrest. BMC Cancer. 2007;7:215.

    Article  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Green DR, Kroemer G. Cytoplasmic functions of the tumour suppressor p53. Nature. 2009;458(7242):1127–30.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Foulkes WD, Flanders TY, Pollock PM, Hayward NK. The CDKN2A (p16) gene and human cancer. Mol Med. 1997;3(1):5–20.

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Valastyan S, Reinhardt F, Benaich N, Calogrias D, Szász AM, Wang ZC. A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. Cell. 2009;137(6):1032–46.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Ivanov SV, Goparaju CM, Lopez P, Zavadil J, Toren-Haritan G, Rosenwald S, et al. Pro-tumorigenic effects of miR-31 loss in mesothelioma. J Biol Chem. 2010;285(30):22809–17.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Di Benedetto M, Bièche I, Deshayes F, Vacher S, Nouet S, Collura V, et al. Structural organization and expression of human MTUS1, a candidate 8p22 tumor suppressor gene encoding a family of angiotensin II AT2 receptor-interacting proteins, ATIP. Gene. 2006;380(2):127–36.

    Article  PubMed  Google Scholar 

  52. 52.

    Wang T, Chen YH, Hong H, Zeng Y, Zhang J, Lu JP, et al. Increased nucleotide polymorphic changes in the 5′-untranslated region of delta-catenin (CTNND2) gene in prostate cancer. Oncogene. 2009;28(4):555–64.

    CAS  Article  PubMed  Google Scholar 

  53. 53.

    Medeiros M, Zheng X, Novak P, Wnek SM, Chyan V, Escudero-Lourdes C, et al. Global gene expression changes in human urothelial cells exposed to low-level monomethylarsonous acid. Toxicology. 2012;291(1–3):102–12.

    CAS  Article  PubMed  Google Scholar 

  54. 54.

    Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, et al. GeneCards version 3: the human gene integrator. Database (Oxford). 2010;2010:baq020.

  55. 55.

    Mo L, Zheng X, Huang HY, Shapiro E, Lepor H, Cordon-Cardo, et al. Hyperactivation of Ha-ras oncogene, but not Ink4a/Arf deficiency, triggers bladder tumourigenesis. J Clin Invest. 2007;117(2):314–25.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  56. 56.

    Blaveri E, Brewer JL, Roydasgupta R, Fridlyand J, DeVries S, Koppie T, et al. Bladder cancer stage and outcome by array-based comparative genomic hybridization. Clin Cancer Res. 2005;11(19 Pt 1):7012–22.

    CAS  Article  PubMed  Google Scholar 

  57. 57.

    Wu XR. Urothelial tumourigenesis: a tale of divergent pathways. Nat Rev Cancer. 2005;5(9):713–25.

    CAS  Article  PubMed  Google Scholar 

  58. 58.

    Staub E, Gröne J, Mennerich D, Röpcke S, Klamann I, Hinzmann B, et al. A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer. Mol Cancer. 2006;5:37.

    Article  PubMed  PubMed Central  Google Scholar 

  59. 59.

    Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2011;40:D109–14.

    Article  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Hurst CD, Tomlinson DC, Williams SV, Platt FM, Knowles MA. Inactivation of the Rb pathway and overexpression of both isoforms of E2F3 are obligate events in bladder tumours with 6p22 amplification. Oncogene. 2008;27(19):2716–27.

    CAS  Article  PubMed  Google Scholar 

  61. 61.

    Halling-Brown MD, Bulusu KC, Patel M, Tym JE, Al-Lazikani B. canSAR: an integrated cancer public translational research and drug discovery resource. Nucleic Acids Res. 2012;40:D947–56.

    CAS  Article  PubMed  Google Scholar 

  62. 62.

    Hoffmann R. A wiki for the life sciences where authorship matters. Nat Genet. 2008;40(9):1047–51.

    CAS  Article  PubMed  Google Scholar 

  63. 63.

    Song T, Zhang X, Zhang L, Dong J, Cai W, Gao J, et al. miR-708 promotes the development of bladder carcinoma via direct repression of caspase-2. J Cancer Res Clin Oncol. 2013;139(7):1189–98.

    CAS  Article  PubMed  Google Scholar 

  64. 64.

    Brait M, Munari E, Lebron C, Noordhuis MG, Begum S, Michailidi C, et al. Genome-wide methylation profiling and the PI3K-AKT pathway analysis associated with smoking in urothelial cell carcinoma. Cell Cycle. 2013;12(7):1058–70.

    Article  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Thompson PA, Brewster AM, Kim-Anh D, Baladandayuthapani V, Broom BM, Ederton E, et al. Selective genomic copy number imbalances and probability of recurrence in early-stage breast cancer. PLoS One. 2011;6(8):e23543.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  66. 66.

    Orlando C, Sestini R, Vona G, Pinzani P, Bianchi S, Giacca M, et al. Detection of c-erbB-2 amplification in transitional cell bladder carcinoma using competitive PCR technique. J Urol. 1996;156(6):2089–93.

    CAS  Article  PubMed  Google Scholar 

  67. 67.

    Hedrich CM, Crispin JC, Rauen T, Ioannidis C, Apostolidis SA, Lo MS, et al. cAMP response element modulator α controls IL2 and IL17A expression during CD4 lineage commitment and subset distribution in lupus. Proc Natl Acad Sci U S A. 2012;109(41):16606–11.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  68. 68.

    Rosenberg E, Baniel J, Spector Y, Faerman A, Meiri E. Predicting progression of bladder urothelial carcinoma using microRNA expression. BJU Int. 2013;112(7):1027–34.

    CAS  PubMed  Google Scholar 

  69. 69.

    Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, et al. The DNA sequence and biological annotation of human chromosome 1. Nature. 2006;441(7091):315–21.

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgments

The authors express their deepest appreciation to Célia Carvalho of the Instituto de Medicina Molecular, Lisboa, Portugal, for review of the manuscript.

Conflicts of interest

None

Author information

Affiliations

Authors

Corresponding author

Correspondence to Paula Oliveira.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Pinto-Leite, R., Carreira, I., Melo, J. et al. Genomic characterization of three urinary bladder cancer cell lines: understanding genomic types of urinary bladder cancer. Tumor Biol. 35, 4599–4617 (2014). https://doi.org/10.1007/s13277-013-1604-3

Download citation

Keywords

  • Urinary bladder cancer
  • Urinary bladder cancer cell lines
  • Genomic
  • Chromosome
  • aCGH
  • MLPA