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Keywords {🔍}

lines, cell, cancer, ubc, number, copy, article, pubmed, bladder, table, google, scholar, gene, expression, tumor, tumors, additional, upd, file, figure, data, cas, genomic, analysis, genes, fgfr, mutations, genome, chromosome, alterations, umuc, regions, information, altered, urothelial, mutation, identified, lost, line, status, size, chr, frequency, provided, losses, probes, loh, carcinoma, central, showed,

Topics {✒️}

enrique carrillo-de-santa-pau gonzalo gómez plain view carrillo-de-santa-pau carrillo-de santa pau oncogene/tumor suppressor status global expression profiles tumor suppressor-driven pathways author information authors web-based search benjamín rodríguez-santiago fgfr3-driven pathway showed genetic/epigenetic alterations inactivate bmc genomics 16 fgfr3-driven tumor pathway article download pdf genomically unstable-high group author correspondence anticancer drug sensitivity article earl full size image marinela méndez-pertuz & francisco high-grade lines tended urothelial bladder carcinoma main oncogene involved bladder cancer subtypes papillary/luminal tumor phenotypes copy number calls open access license tumor suppressor genes copy number neutral 0 = copy number neutral urothelial cell carcinoma copy number alterations chromosome/chromosome arm gain/loss high-resolution analysis specific tumor subtypes understanding urothelial carcinoma de la salut gene copy number privacy choices/manage cookies pérez-jurado & francisco urothelial bladder tumors literature search managing bladder cancer urinary bladder cancer cell line dataset complete copy number copy number data large structural variants

Questions {❓}

• P53: it has it all, but will it make it to the clinic as a marker in bladder cancer?

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WebPage:
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         headline:The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies
         description:Urothelial bladder cancer is a highly heterogeneous disease. Cancer cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression. Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events. Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing.
         datePublished:2015-05-22T00:00:00Z
         dateModified:2015-05-22T00:00:00Z
         pageStart:1
         pageEnd:16
         license:https://creativecommons.org/publicdomain/zero/1.0/
         sameAs:https://doi.org/10.1186/s12864-015-1450-3
         keywords:
            Urothelial bladder cancer
            Cell line
            Genomics
            Mutation
            Oncogene
            Tumor suppressor
            Life Sciences
            general
            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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               1471-2164
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                     address:
                        name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
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                     address:
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                     address:
                        name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
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                     address:
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                     name:Universitat Pompeu Fabra
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                        name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
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                     address:
                        name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                        type:PostalAddress
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               name:Herbert Barton Grossman
               affiliation:
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                     address:
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               name:Luis A Pérez-Jurado
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               name:Dan Theodorescu
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                     address:
                        name:University of Colorado Comprehensive Cancer Center, Aurora, USA
                        type:PostalAddress
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                     address:
                        name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                        type:PostalAddress
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                     name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre)
                     address:
                        name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                        type:PostalAddress
                     type:Organization
                     name:Universitat Pompeu Fabra
                     address:
                        name:Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
                        type:PostalAddress
                     type:Organization
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      headline:The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies
      description:Urothelial bladder cancer is a highly heterogeneous disease. Cancer cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression. Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events. Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing.
      datePublished:2015-05-22T00:00:00Z
      dateModified:2015-05-22T00:00:00Z
      pageStart:1
      pageEnd:16
      license:https://creativecommons.org/publicdomain/zero/1.0/
      sameAs:https://doi.org/10.1186/s12864-015-1450-3
      keywords:
         Urothelial bladder cancer
         Cell line
         Genomics
         Mutation
         Oncogene
         Tumor suppressor
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
      image:
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      isPartOf:
         name:BMC Genomics
         issn:
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         volumeNumber:16
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      publisher:
         name:BioMed Central
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Julie Earl
            affiliation:
                  name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
                  name:Servicio de Oncología Médica, Hospital Ramón y Cajal
                  address:
                     name:Servicio de Oncología Médica, Hospital Ramón y Cajal, Madrid, Spain
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Daniel Rico
            affiliation:
                  name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Enrique Carrillo-de-Santa-Pau
            affiliation:
                  name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Benjamín Rodríguez-Santiago
            affiliation:
                  name:Quantitative Genomic Medicine Laboratory, qGenomics
                  address:
                     name:Quantitative Genomic Medicine Laboratory, qGenomics, Barcelona, Spain
                     type:PostalAddress
                  type:Organization
                  name:Universitat Pompeu Fabra
                  address:
                     name:Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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                  type:Organization
                  name:Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)
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                     type:PostalAddress
                  type:Organization
            type:Person
            name:Marinela Méndez-Pertuz
            affiliation:
                  name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
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            name:Herbert Auer
            affiliation:
                  name:Institut de Recerca Biomèdica de Barcelona, Parc Científic de Barcelona
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                     name:Institut de Recerca Biomèdica de Barcelona, Parc Científic de Barcelona, Barcelona, Spain
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            name:Gonzalo Gómez
            affiliation:
                  name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Herbert Barton Grossman
            affiliation:
                  name:Department of Urology, MD Anderson Cancer Center
                  address:
                     name:Department of Urology, MD Anderson Cancer Center, Houston, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:David G Pisano
            affiliation:
                  name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Wolfgang A Schulz
            affiliation:
                  name:Heinrich-Heine-University
                  address:
                     name:Department of Urology, Heinrich-Heine-University, Düsseldorf, Germany
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Luis A Pérez-Jurado
            affiliation:
                  name:Universitat Pompeu Fabra
                  address:
                     name:Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
                     type:PostalAddress
                  type:Organization
                  name:Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)
                  address:
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                     type:PostalAddress
                  type:Organization
            type:Person
            name:Alfredo Carrato
            affiliation:
                  name:Servicio de Oncología Médica, Hospital Ramón y Cajal
                  address:
                     name:Servicio de Oncología Médica, Hospital Ramón y Cajal, Madrid, Spain
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Dan Theodorescu
            affiliation:
                  name:University of Colorado Comprehensive Cancer Center
                  address:
                     name:University of Colorado Comprehensive Cancer Center, Aurora, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Stephen Chanock
            affiliation:
                  name:Translational Genomics Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute
                  address:
                     name:Translational Genomics Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Alfonso Valencia
            affiliation:
                  name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Francisco X Real
            affiliation:
                  name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
                  name:Universitat Pompeu Fabra
                  address:
                     name:Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
                     type:PostalAddress
                  type:Organization
                  name:Cancer Cell Biology Programme, Centro Nacional de Investigaciones Oncológicas
                  address:
                     name:Cancer Cell Biology Programme, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
                     type:PostalAddress
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               name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
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            address:
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      affiliation:
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               type:PostalAddress
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      affiliation:
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            address:
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               type:PostalAddress
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            name:Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)
            address:
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               type:PostalAddress
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      affiliation:
            name:Servicio de Oncología Médica, Hospital Ramón y Cajal
            address:
               name:Servicio de Oncología Médica, Hospital Ramón y Cajal, Madrid, Spain
               type:PostalAddress
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      name:Dan Theodorescu
      affiliation:
            name:University of Colorado Comprehensive Cancer Center
            address:
               name:University of Colorado Comprehensive Cancer Center, Aurora, USA
               type:PostalAddress
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      affiliation:
            name:Translational Genomics Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute
            address:
               name:Translational Genomics Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
               type:PostalAddress
            type:Organization
      name:Alfonso Valencia
      affiliation:
            name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre)
            address:
               name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
               type:PostalAddress
            type:Organization
      name:Francisco X Real
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            name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre)
            address:
               name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
               type:PostalAddress
            type:Organization
            name:Universitat Pompeu Fabra
            address:
               name:Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
               type:PostalAddress
            type:Organization
            name:Cancer Cell Biology Programme, Centro Nacional de Investigaciones Oncológicas
            address:
               name:Cancer Cell Biology Programme, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
      name:Servicio de Oncología Médica, Hospital Ramón y Cajal, Madrid, Spain
      name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
      name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
      name:Quantitative Genomic Medicine Laboratory, qGenomics, Barcelona, Spain
      name:Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
      name:Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
      name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
      name:Institut de Recerca Biomèdica de Barcelona, Parc Científic de Barcelona, Barcelona, Spain
      name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
      name:Department of Urology, MD Anderson Cancer Center, Houston, USA
      name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
      name:Department of Urology, Heinrich-Heine-University, Düsseldorf, Germany
      name:Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
      name:Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
      name:Servicio de Oncología Médica, Hospital Ramón y Cajal, Madrid, Spain
      name:University of Colorado Comprehensive Cancer Center, Aurora, USA
      name:Translational Genomics Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
      name:Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
      name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
      name:Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
      name:Cancer Cell Biology Programme, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain

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