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The UBC-40 urothelial bladder cancer cell line index: a genomic resource for functional studies

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dc.contributor.author Earl, Julie
dc.contributor.author Rico, Daniel
dc.contributor.author Carrillo, Enrique
dc.contributor.author Rodríguez Santiago, Benjamín
dc.contributor.author Méndez Pertuz, Marinela
dc.contributor.author Auer, Herbert
dc.contributor.author Gómez, Gonzalo
dc.contributor.author Barton Grossman, Herbert
dc.contributor.author Pisano, David G.
dc.contributor.author Schulz, Wolfgang
dc.contributor.author Pérez Jurado, Luis Alberto
dc.contributor.author Carrato, Alfredo
dc.contributor.author Theodorescu, Dan
dc.contributor.author Chanock, Stephen J.
dc.contributor.author Valencia, Alfonso
dc.contributor.author Real, Francisco X.
dc.date.accessioned 2015-12-11T08:52:11Z
dc.date.available 2015-12-11T08:52:11Z
dc.date.issued 2015
dc.identifier.citation Earl J, Rico D, Carrillo E, Rodríguez-Santiago B, Méndez-Pertuz M, Auer H et al. The UBC-40 urothelial bladder cancer cell line index: a genomic resource for functional studies. BMC Genomics. 2015;16:403. DOI: 10.1186/s12864-015-1450-3
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/25381
dc.description.abstract Background. 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./nResults. 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./nConclusions. 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.
dc.description.sponsorship This work was supported, in part, by grants Consolider ONCOBIO, SAF2011-15934-E, Red Temática de Investigación Cooperativa en Cáncer (RTICC)]; Asociación Española Contra el Cáncer, EU-FP7-201663, and NIH RO-1 (CA089715); and National Institutes of Health grants CA075115 and CA104106 (to D.T.).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2015;16:403
dc.rights © 2015 Earl et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0
dc.subject.other Càncer
dc.subject.other Tumors -- Tractament
dc.title The UBC-40 urothelial bladder cancer cell line index: a genomic resource for functional studies
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/s12864-015-1450-3
dc.subject.keyword Urothelial bladder cancer
dc.subject.keyword Cell line
dc.subject.keyword Genomics
dc.subject.keyword Mutation
dc.subject.keyword Oncogene
dc.subject.keyword Tumor suppressor
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/201663
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SAF2011-15934
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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