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

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• dc.contributor.author Earl, Julieca
• dc.contributor.author Rico, Danielca
• dc.contributor.author Carrillo, Enriqueca
• dc.contributor.author Rodríguez Santiago, Benjamínca
• dc.contributor.author Méndez Pertuz, Marinelaca
• dc.contributor.author Auer, Herbertca
• dc.contributor.author Gómez, Gonzaloca
• dc.contributor.author Barton Grossman, Herbertca
• dc.contributor.author Pisano, David G.ca
• dc.contributor.author Schulz, Wolfgangca
• dc.contributor.author Pérez Jurado, Luis Albertoca
• dc.contributor.author Carrato, Alfredoca
• dc.contributor.author Theodorescu, Danca
• dc.contributor.author Chanock, Stephen J.ca
• dc.contributor.author Valencia, Alfonsoca
• dc.contributor.author Real, Francisco X.ca
• dc.date.accessioned 2015-12-11T08:52:11Z
• dc.date.available 2015-12-11T08:52:11Z
• dc.date.issued 2015ca
• 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/pdfca
• 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/s12864-015-1450-3ca
• dc.identifier.doi http://dx.doi.org/10.1186/s12864-015-1450-3
• dc.identifier.issn 1471-2164ca
• dc.identifier.uri http://hdl.handle.net/10230/25381
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof BMC Genomics. 2015;16:403
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/201663
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SAF2011-15934
• 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.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/4.0
• 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.subject.other Càncer
• dc.subject.other Tumors -- Tractament
• dc.title The UBC-40 urothelial bladder cancer cell line index: a genomic resource for functional studiesca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca