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Abstract

Urothelial bladder cancer (UBC) is heterogeneous at the clinical, pathological and genetic levels. Tumor invasiveness (T) and grade (G) are the main factors associated with outcome and determine patient management1. A discovery exome sequencing screen (n = 17), followed by a prevalence screen (n = 60), identified new genes mutated in this tumor coding for proteins involved in chromatin modification (MLL2, ASXL2 and BPTF), cell division (STAG2, SMC1A and SMC1B) and DNA repair (ATM, ERCC2 and FANCA). STAG2, a subunit of cohesin, was significantly and commonly mutated or lost in UBC, mainly in tumors of low stage or grade, and its loss was associated with improved outcome. Loss of expression was often observed in chromosomally stable tumors, and STAG2 knockdown in bladder cancer cells did not increase aneuploidy. STAG2 reintroduction in non-expressing cells led to reduced colony formation. Our findings indicate that STAG2 is a new UBC tumor suppressor acting through mechanisms that are different from its role in preventing aneuploidy.

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Acknowledgements

We thank F. Algaba, Y. Allory, A. Cuadrado, C. González, E. López, P. Lapunzina, T. Lobato, M. Malumbres, S. Remeseiro, V.J. Sánchez-Arévalo, F. Waldman and the CNIO core facilities for valuable contributions. We also thank TCGA investigators for providing unpublished information for analysis. This work was supported, in part, by grants from Ministerio de Economia y Competitividad, Madrid (grants Consolíder ONCOBIO, Consolider INESGEN, SAF-2010-21517 and SAF2011-15934-E), Instituto de Salud Carlos III (grants G03/174, 00/0745, PI051436, PI061614, G03/174, PI080440, PI120425 and Red Temática de Investigación Cooperativa en Cáncer (RTICC)), Asociación Española Contra el Cáncer, EU-FP7-201663 and US National Institutes of Health grant RO1 CA089715. C.B.-M. is the recipient of a La Caixa International PhD Fellowship. E.L. is supported by a grant from the Fundación Banco Santander Postdoctoral Programme.

Author information

Author notes

    • Ana Sagrera
    •  & Enrique Carrillo-de-Santa-Pau

    These authors contributed equally to this work.

Affiliations

  1. Epithelial Carcinogenesis Group, Molecular Pathology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.

    • Cristina Balbás-Martínez
    • , Ana Sagrera
    • , Enrique Carrillo-de-Santa-Pau
    • , Julie Earl
    • , Eleonora Lapi
    • , Xavier Langa
    • , Laia Richart
    •  & Francisco X Real
  2. Servicio de Oncología Médica, Hospital Ramón y Cajal, Madrid, Spain.

    • Julie Earl
    •  & Alfredo Carrato
  3. Genetic and Molecular Epidemiology Group, Human Cancer Genetics Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.

    • Mirari Márquez
    • , Jesús Herranz
    •  & Núria Malats
  4. Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.

    • Miguel Vazquez
    • , Daniel Rico
    •  & Alfonso Valencia
  5. Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.

    • Francesc Castro-Giner
    • , Sergi Beltran
    • , Mònica Bayés
    • , Marta Gut
    • , Simon Heath
    •  & Ivo Gut
  6. Molecular Cytogenetics Group, Human Cancer Genetics Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.

    • Juan C Cigudosa
    •  & Rocío N Salgado
  7. Biotechnology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.

    • Orlando Domínguez
  8. Department of Pathology, Hospital del Mar–Parc de Salut Mar, Barcelona, Spain.

    • Núria Juanpere
    •  & Josep Lloreta
  9. Centre de Recerca d'Epidemiologia Ambiental, Barcelona, Spain.

    • Manolis Kogevinas
  10. Institut Municipal d'Investigació Médica (IMIM)–Institut de Recerca Hospital del Mar, Barcelona, Spain.

    • Manolis Kogevinas
    •  & Elena López-Knowles
  11. Centro de Investigación Biomédica en Red (CIBER) Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.

    • Manolis Kogevinas
  12. National School of Public Health, Athens, Greece.

    • Manolis Kogevinas
  13. Urology Service, Hospital del Mar–Parc de Salut Mar, Barcelona, Spain.

    • José A Lorente
  14. Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.

    • Josep Lloreta
    •  & Francisco X Real
  15. Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.

    • David G Pisano
  16. Departamento de Medicina, Departamento de Medicina, Universidad de Oviedo, Oviedo, Spain.

    • Adonina Tardón
  17. Translational Genomics Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA.

    • Stephen Chanock
  18. Chromosome Dynamics Group, Molecular Oncology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.

    • Ana Losada

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Contributions

C.B.-M., E.L. and L.R. designed and performed in vitro functional studies. C.B.-M. performed immunohistochemical analysis of tumor samples. A.S. and C.B.-M. designed and performed mutation validation analyses. A.S. designed and prepared HaloPlex libraries for sequencing. E.C.-d.-S.-P., M.V., F.C.-G., S.B. and D.G.P. processed and analyzed exome sequencing and targeted resequencing data. J.E., E.L.-K., D.R. and S.C. performed gene copy number analyses of tumors. M.M. coordinated subject and sample data management. A.C., M.K., J.A.L. and A.T. contributed to subject recruitment and data collection. J.H. performed statistical analyses. X.L. provided technical support with subject samples. M.B. and M.G. coordinated library preparation and sequencing. O.D. contributed to library preparation and sequencing. J.C.C. and R.N.S. contributed to the in vitro analysis of the effects of STAG2 knockdown on aneuploidy. N.J. and J.L. performed pathological review of samples. I.G. coordinated exome sequencing and targeted resequencing. I.G., S.H. and A.V. supervised bioinformatics analyses. A.L. provided scientific insight and contributed with reagents. N.M. coordinated subject recruitment and the collection of clinical and pathological data and supervised clinical-pathological-molecular association and outcome analyses. F.X.R. and N.M. conceived the study. F.X.R. supervised the overall way in which the study was conducted. F.X.R. wrote the manuscript with N.M., C.B.-M., A.S., E.C.-d.-S.-P., A.V., A.L. and I.G. contributed to manuscript writing.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Francisco X Real.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–13 and Supplementary Tables 1, 2, 5 and 7–20

Excel files

  1. 1.

    Supplementary Table 3

    Relevant mutations identified in the discovery screen (exome sequencing) (n = 17)

  2. 2.

    Supplementary Table 4

    Pathway analyses of genes mutated in UBC

  3. 3.

    Supplementary Table 6

    Design of the prevalence screen and genes included therein, depth of coverage and relevant mutations detected (total and in each individual tumor)

About this article

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DOI

https://doi.org/10.1038/ng.2799

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