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A high resolution genomic portrait of bladder cancer: correlation between genomic aberrations and the DNA damage response

Oncogene volume 32, pages 3577–3586 (2013)Cite this article

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Abstract

One major challenge in cancer research is to understand the complex interplay between the DNA damage response (DDR), genomic integrity, and tumor development. To address these issues, we analyzed 43 bladder tumor genomes from 22 patients using single nucleotide polymorphism (SNP) arrays, and tissue expression of multiple DDR proteins, including Timeless and its interaction partner Tipin. The SNP profiles confirmed and extended known copy number alterations (CNAs) at high resolution, showed clustering of CNAs at nine common fragile sites, and revealed that most metachronous tumors were clonally related. The occurrence of many novel uniparental disomy regions (UPDs) was of potential functional importance in some tumors because UPDs spanned mutated FGFR3 and PIK3CA alleles, and also homozygous deletion of the CDKN2A tumor suppressor locus. The DDR signaling as evaluated by phospho-epitope-specific antibodies against Ser139-phosphorylated H2A histone family member X (γH2AX), ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR) was commonly activated in tumors with both moderate and high extent of accumulated genomic aberrations, the latter tumors showing a more frequent loss of ATM expression. Strikingly, the tumor genomes exhibiting the most complex alterations were associated with a high Ki67-proliferation index, abundant Timeless but not Tipin expression, aberrant p53 expression, and homozygous CDKN2A deletions. Of clinical relevance, evaluation of a tissue microarray (TMA; n=319) showed that abundant Timeless expression was associated with risk of progression to muscle-invasive disease (P<0.0005; hazard ratio, 2.4; 95% confidence interval, 1.6–3.8) and higher T stage (P<0.05). Univariate analysis confirmed this association (P=0.006) in an independent cohort (n=241) but statistical significance was not reached in a multivariate model. Overall, our results are consistent with DDR activation preceding the accumulation of genomic aberrations. Tumors with extensive genomic rearrangements were associated with inactivation of CDKN2A, excessive proliferation, and robust Timeless expression, the latter also correlating with the risk of disease progression. Moreover, we provide evidence to suggest that UPDs likely contribute to bladder tumorigenesis.

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References

  1. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D . Global cancer statistics. CA Cancer J Clin 2011; 61: 69–90.

    Article  PubMed  Google Scholar 

  2. Wu XR . Urothelial tumorigenesis: a tale of divergent pathways. Nat Rev Cancer 2005; 5: 713–725.

    Article  CAS  PubMed  Google Scholar 

  3. Lindgren D, Frigyesi A, Gudjonsson S, Sjodahl G, Hallden C, Chebil G 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: 3463–3472.

    Article  CAS  PubMed  Google Scholar 

  4. 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: 7012–7022.

    Article  CAS  PubMed  Google Scholar 

  5. Zieger K, Marcussen N, Borre M, Orntoft TF, Dyrskjot L . Consistent genomic alterations in carcinoma in situ of the urinary bladder confirm the presence of two major pathways in bladder cancer development. Int J Cancer 2009; 125: 2095–2103.

    Article  CAS  PubMed  Google Scholar 

  6. Zieger K, Wiuf C, Jensen KM, Orntoft TF, Dyrskjot L . Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer. BMC Cancer 2009; 9: 149.

    Article  PubMed  PubMed Central  Google Scholar 

  7. Koed K, Wiuf C, Christensen LL, Wikman FP, Zieger K, Moller K et al. High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors. Cancer Res 2005; 65: 34–45.

    CAS  PubMed  Google Scholar 

  8. Bartkova J, Horejsi Z, Koed K, Kramer A, Tort F, Zieger K et al. DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature 2005; 434: 864–870.

    Article  CAS  PubMed  Google Scholar 

  9. Bartek J, Lukas J, Bartkova J . DNA damage response as an anti-cancer barrier: damage threshold and the concept of ‘conditional haploinsufficiency’. Cell Cycle 2007; 6: 2344–2347.

    Article  CAS  PubMed  Google Scholar 

  10. Gorgoulis VG, Vassiliou LV, Karakaidos P, Zacharatos P, Kotsinas A, Liloglou T et al. Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature 2005; 434: 907–913.

    Article  CAS  PubMed  Google Scholar 

  11. Negrini S, Gorgoulis VG, Halazonetis TD . Genomic instability--an evolving hallmark of cancer. Nat Rev Mol Cell Biol 2010; 11: 220–228.

    Article  CAS  PubMed  Google Scholar 

  12. Halazonetis TD, Gorgoulis VG, Bartek J . An oncogene-induced DNA damage model for cancer development. Science 2008; 319: 1352–1355.

    Article  CAS  PubMed  Google Scholar 

  13. Jackson SP, Bartek J . The DNA-damage response in human biology and disease. Nature 2009; 461: 1071–1078.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Ciccia A, Elledge SJ . The DNA damage response: making it safe to play with knives. Mol Cell 2010; 40: 179–204.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Chou DM, Elledge SJ . Tipin and Timeless form a mutually protective complex required for genotoxic stress resistance and checkpoint function. Proc Natl Acad Sci USA 2006; 103: 18143–18147.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Yoshizawa-Sugata N, Masai H . Human Tim/Timeless-interacting protein, Tipin, is required for efficient progression of S phase and DNA replication checkpoint. J Biol Chem 2007; 282: 2729–2740.

    Article  CAS  PubMed  Google Scholar 

  17. McFarlane RJ, Mian S, Dalgaard JZ . The many facets of the Tim-Tipin protein families’ roles in chromosome biology. Cell Cycle 2010; 9: 700–705.

    Article  CAS  PubMed  Google Scholar 

  18. Wu Q, Hoffmann MJ, Hartmann FH, Schulz WA . Amplification and overexpression of the ID4 gene at 6p22.3 in bladder cancer. Mol Cancer 2005; 4: 16.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Santarius T, Bignell GR, Greenman CD, Widaa S, Chen L, Mahoney CL et al. GLO1-A novel amplified gene in human cancer. Genes Chromosomes Cancer 2010; 49: 711–725.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 2011; 144: 27–40.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Langbein S, Szakacs O, Wilhelm M, Sukosd F, Weber S, Jauch A et al. Alteration of the LRP1B gene region is associated with high grade of urothelial cancer. Lab Invest 2002; 82: 639–643.

    Article  CAS  PubMed  Google Scholar 

  22. Poulogiannis G, McIntyre RE, Dimitriadi M, Apps JR, Wilson CH, Ichimura K et al. PARK2 deletions occur frequently in sporadic colorectal cancer and accelerate adenoma development in Apc mutant mice. Proc Natl Acad Sci USA 2010; 107: 15145–15150.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Dereli-Oz A, Versini G, Halazonetis TD . Studies of genomic copy number changes in human cancers reveal signatures of DNA replication stress. Mol Oncol 2011; 5: 308–314.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Le Tallec B, Dutrillaux B, Lachages AM, Millot GA, Brison O, Debatisse M . Molecular profiling of common fragile sites in human fibroblasts. Nat Struct Mol Biol 2011; 18: 1421–1423.

    Article  CAS  PubMed  Google Scholar 

  25. Letessier A, Millot GA, Koundrioukoff S, Lachages AM, Vogt N, Hansen RS et al. Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site. Nature 2011; 470: 120–123.

    Article  CAS  PubMed  Google Scholar 

  26. Lapunzina P, Monk D . The consequences of uniparental disomy and copy number neutral loss-of-heterozygosity during human development and cancer. Biol Cell 2011; 103: 303–317.

    Article  PubMed  Google Scholar 

  27. Vetter G, Saumet A, Moes M, Vallar L, Le Bechec A, Laurini C et al. miR-661 expression in SNAI1-induced epithelial to mesenchymal transition contributes to breast cancer cell invasion by targeting Nectin-1 and StarD10 messengers. Oncogene 2010; 29: 4436–4448.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM et al. Signatures of mutation and selection in the cancer genome. Nature 2010; 463: 893–898.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Duggan BJ, Gray SB, McKnight JJ, Watson CJ, Johnston SR, Williamson KE . Oligoclonality in bladder cancer: the implication for molecular therapies. J Urol 2004; 171: 419–425.

    Article  PubMed  Google Scholar 

  30. Bartkova J, Rezaei N, Liontos M, Karakaidos P, Kletsas D, Issaeva N et al. Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints. Nature 2006; 444: 633–637.

    Article  CAS  PubMed  Google Scholar 

  31. Takacova S, Slany R, Bartkova J, Stranecky V, Dolezel P, Luzna P et al. DNA damage response and inflammatory signaling limit the MLL-ENL-induced leukemogenesis in vivo. Cancer cell 2012; 21: 517–531.

    Article  CAS  PubMed  Google Scholar 

  32. Kastan MB, Bartek J . Cell-cycle checkpoints and cancer. Nature 2004; 432: 316–323.

    Article  CAS  PubMed  Google Scholar 

  33. Lu ML, Wikman F, Orntoft TF, Charytonowicz E, Rabbani F, Zhang Z et al. Impact of alterations affecting the p53 pathway in bladder cancer on clinical outcome, assessed by conventional and array-based methods. Clin Cancer Res 2002; 8: 171–179.

    CAS  PubMed  Google Scholar 

  34. Olivier M, Hollstein M, Hainaut P . TP53 mutations in human cancers: origins, consequences, and clinical use. Cold Spring Harb Perspect Biol 2010; 2: a001008.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Gotter AL, Suppa C, Emanuel BS . Mammalian TIMELESS and Tipin are evolutionarily conserved replication fork-associated factors. J Mol Biol 2007; 366: 36–52.

    Article  CAS  PubMed  Google Scholar 

  36. Reinert T, Modin C, Castano FM, Lamy P, Wojdacz TK, Hansen LL et al. Comprehensive genome methylation analysis in bladder cancer: identification and validation of novel methylated genes and application of these as urinary tumor markers. Clin Cancer Res 2011; 17: 5582–5592.

    Article  CAS  PubMed  Google Scholar 

  37. Sylvester RJ, van der Meijden AP, Oosterlinck W, Witjes JA, Bouffioux C, Denis L et al. Predicting recurrence and progression in individual patients with stage Ta T1 bladder cancer using EORTC risk tables: a combined analysis of 2596 patients from seven EORTC trials. Eur Urol 2006; 49: 466–477.

    Article  PubMed  Google Scholar 

  38. Weaver BA, Silk AD, Montagna C, Verdier-Pinard P, Cleveland DW . Aneuploidy acts both oncogenically and as a tumor suppressor. Cancer Cell 2007; 11: 25–36.

    Article  CAS  PubMed  Google Scholar 

  39. Toledo LI, Murga M, Zur R, Soria R, Rodriguez A, Martinez S et al. A cell-based screen identifies ATR inhibitors with synthetic lethal properties for cancer-associated mutations. Nat Struct Mol Biol 2011; 18: 721–727.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Martin SA, Hewish M, Lord CJ, Ashworth A . Genomic instability and the selection of treatments for cancer. J Pathol 2010; 220: 281–289.

    CAS  PubMed  Google Scholar 

  41. Lord CJ, Ashworth A . The DNA damage response and cancer therapy. Nature 2012; 481: 287–294.

    Article  CAS  PubMed  Google Scholar 

  42. Tuna M, Knuutila S, Mills GB . Uniparental disomy in cancer. Trends Mol Med 2009; 15: 120–128.

    Article  CAS  PubMed  Google Scholar 

  43. Mullighan CG, Goorha S, Radtke I, Miller CB, Coustan-Smith E, Dalton JD et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 2007; 446: 758–764.

    Article  CAS  PubMed  Google Scholar 

  44. Mo L, Zheng X, Huang HY, Shapiro E, Lepor H, Cordon-Cardo C et al. Hyperactivation of Ha-ras oncogene, but not Ink4a/Arf deficiency, triggers bladder tumorigenesis. J Clin Invest 2007; 117: 314–325.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Hafner C, Knuechel R, Stoehr R, Hartmann A . Clonality of multifocal urothelial carcinomas: 10 years of molecular genetic studies. Int J Cancer 2002; 101: 1–6.

    Article  CAS  PubMed  Google Scholar 

  46. Dheekollu J, Wiedmer A, Hayden J, Speicher D, Gotter AL, Yen T et al. Timeless links replication termination to mitotic kinase activation. PLoS One 2011; 6: e19596.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Yang X, Wood PA, Hrushesky WJ . Mammalian TIMELESS is required for ATM-dependent CHK2 activation and G2/M checkpoint control. J Biol Chem 2010; 285: 3030–3034.

    Article  CAS  PubMed  Google Scholar 

  48. Unsal-Kacmaz K, Chastain PD, Qu PP, Minoo P, Cordeiro-Stone M, Sancar A et al. The human Tim/Tipin complex coordinates an intra-S checkpoint response to UV that slows replication fork displacement. Mol Cell Biol 2007; 27: 3131–3142.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Unsal-Kacmaz K, Mullen TE, Kaufmann WK, Sancar A . Coupling of human circadian and cell cycles by the timeless protein. Mol Cell Biol 2005; 25: 3109–3116.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Smith-Roe SL, Patel SS, Simpson DA, Zhou YC, Rao S, Ibrahim JG et al. Timeless functions independently of the Tim-Tipin complex to promote sister chromatid cohesion in normal human fibroblasts. Cell Cycle 2011; 10: 1618–1624.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Fu A, Leaderer D, Zheng T, Hoffman AE, Stevens RG, Zhu Y . Genetic and epigenetic associations of circadian gene TIMELESS and breast cancer risk. Mol Carcinog (e-pub ahead of print 17 October 2011; doi:10.1002/mc.20862).

    Article  PubMed  Google Scholar 

  52. Aly A, Ganesan S . BRCA1, PARP, and 53BP1: conditional synthetic lethality and synthetic viability. J Mol Cell Biol 2011; 3: 66–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Bouwman P, Aly A, Escandell JM, Pieterse M, Bartkova J, van der Gulden H et al. 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nat Struct Mol Biol 2010; 17: 688–695.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. 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: e13821.

    Article  PubMed  PubMed Central  Google Scholar 

  55. Schepeler T, Mansilla F, Christensen LL, Orntoft TF, Andersen CL . Clusterin expression can be modulated by changes in TCF1-mediated Wnt signaling. J Mol Signal 2007; 2: 6.

    Article  PubMed  PubMed Central  Google Scholar 

  56. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G et al. Integrative genomics viewer. Nat Biotechnol 2011; 29: 24–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank The John and Birthe Meyer Foundation, the Danish Cancer Society, the Danish National Research Foundation, the Ministry of Technology and Science, the Lundbeck Foundation, and the European Community’s Seventh Framework program (projects Infla-Care, Biomedreg, DDresponse, and Grant agreement no. 201663).

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Authors and Affiliations

  1. Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus N, Denmark,

    T Schepeler, P Lamy, V Hvidberg, J R Laurberg, N Fristrup, T Reinert, L Dyrskjøt & T F Ørntoft

  2. Danish Cancer Society Research Center, Copenhagen, Denmark

    J Bartkova & J Bartek

  3. Department of Molecular Biology, University of Geneva, Geneva, Switzerland

    L Tropia & T D Halazonetis

  4. Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic

    J Bartek

  5. Department of Biochemistry, University of Geneva, Geneva, Switzerland

    T D Halazonetis

  6. Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan

    C-C Pan

  7. Department of Urology, Aarhus University Hospital, Aarhus N, Denmark

    M Borre

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Schepeler, T., Lamy, P., Hvidberg, V. et al. A high resolution genomic portrait of bladder cancer: correlation between genomic aberrations and the DNA damage response. Oncogene 32, 3577–3586 (2013). https://doi.org/10.1038/onc.2012.381

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