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Bellmunt J, Selvarajah S, Rodig S, Salido M, de Muga S, Costa I, Bellosillo B, Werner L, Mullane S, Fay AP, O'Brien R, Barretina J, Minoche AE, Signoretti S, Montagut C, Himmelbauer H, Berman DM, Kantoff P, Choueiri TK, Rosenberg JE. Identification of ALK gene alterations in urothelial carcinoma. PLoS One 2014; 9:e103325. [PMID: 25083769 PMCID: PMC4118868 DOI: 10.1371/journal.pone.0103325] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/26/2014] [Indexed: 12/18/2022] Open
Abstract
Background Anaplastic lymphoma kinase (ALK) genomic alterations have emerged as a potent predictor of benefit from treatment with ALK inhibitors in several cancers. Currently, there is no information about ALK gene alterations in urothelial carcinoma (UC) and its correlation with clinical or pathologic features and outcome. Methods Samples from patients with advanced UC and correlative clinical data were collected. Genomic imbalances were investigated by array comparative genomic hybridization (aCGH). ALK gene status was evaluated by fluorescence in situ hybridization (FISH). ALK expression was assessed by immunohistochemistry (IHC) and high-throughput mutation analysis with Oncomap 3 platform. Next generation sequencing was performed using Illumina Genome Analyzer IIx, and Illumina HiSeq 2000 in the FISH positive case. Results 70 of 96 patients had tissue available for all the tests performed. Arm level copy number gains at chromosome 2 were identified in 17 (24%) patients. Minor copy number alterations (CNAs) in the proximity of ALK locus were found in 3 patients by aCGH. By FISH analysis, one of these samples had a deletion of the 5′ALK. Whole genome next generation sequencing was inconclusive to confirm the deletion at the level of the ALK gene at the coverage level used. We did not observe an association between ALK CNA and overall survival, ECOG PS, or development of visceral disease. Conclusions ALK genomic alterations are rare and probably without prognostic implications in UC. The potential for testing ALK inhibitors in UC merits further investigation but might be restricted to the identification of an enriched population.
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Affiliation(s)
- Joaquim Bellmunt
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
- Hospital del Mar Research Institute-IMIM, Barcelona, Spain
- * E-mail:
| | - Shamini Selvarajah
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Scott Rodig
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marta Salido
- Department of Pathology, Hospital del Mar Research Institute-IMIM, Barcelona, Spain
| | - Silvia de Muga
- Department of Pathology, Hospital del Mar Research Institute-IMIM, Barcelona, Spain
| | | | - Beatriz Bellosillo
- Department of Pathology, Hospital del Mar Research Institute-IMIM, Barcelona, Spain
| | - Lillian Werner
- Biostatistics and Computational Biology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Stephanie Mullane
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - André P. Fay
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert O'Brien
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jordi Barretina
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - André E. Minoche
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Sabina Signoretti
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Clara Montagut
- Hospital del Mar Research Institute-IMIM, Barcelona, Spain
| | - Heinz Himmelbauer
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - David M. Berman
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Philip Kantoff
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Toni K. Choueiri
- Bladder Cancer Center, Dana-Farber Cancer Institute/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan E. Rosenberg
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
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