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Sanchez Calle A, Kawamura Y, Yamamoto Y, Takeshita F, Ochiya T. Emerging roles of long non-coding RNA in cancer. Cancer Sci 2018; 109:2093-2100. [PMID: 29774630 PMCID: PMC6029823 DOI: 10.1111/cas.13642] [Citation(s) in RCA: 438] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/14/2018] [Indexed: 12/11/2022] Open
Abstract
Since comprehensive analysis of the mammalian genome revealed that the majority of genomic products are transcribed in long non‐coding RNA (lncRNA), increasing attention has been paid to these transcripts. The applied next‐generation sequencing technologies have provided accumulating evidence of dysregulated lncRNA in cancer. The implication of this finding can be seen in many forms and at multiple levels. With impacts ranging from integrating chromatin remodeling complexes to regulating transcription and post‐transcriptional processes, aberrant expression of lncRNA may have repercussions in cell proliferation, tumor progression or metastasis. lncRNA may act as enhancers, scaffolds or decoys by physically interacting with other RNA species or proteins, resulting in a direct impact on cell signaling cascades. Even though their functional classification is well‐established in the context of cancer, clearer characterization in terms of their phenotypic outputs is needed to optimize and identify suitable candidates that enable the development of new therapeutic strategies and the design of novel diagnostic approaches. The present article aims to outline different cancer‐associated lncRNA according to their contribution to tumor suppression or tumor promotion based on their most current functional annotations.
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Affiliation(s)
- Anna Sanchez Calle
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
| | - Yumi Kawamura
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
- Ph.D. Program in Human Biology; School of Integrative and Global Majors; University of Tsukuba; Tsukuba Japan
| | - Yusuke Yamamoto
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
| | - Fumitaka Takeshita
- Department of Functional Analysis; FIOC; National Cancer Center Research Institute; Tokyo Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine; National Cancer Center Research Institute; Tokyo Japan
- Institute of Medical Science; Tokyo Medical University; Tokyo Japan
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Earl J, Rico D, Carrillo-de-Santa-Pau E, Rodríguez-Santiago B, Méndez-Pertuz M, Auer H, Gómez G, Grossman HB, Pisano DG, Schulz WA, Pérez-Jurado LA, Carrato A, Theodorescu D, Chanock S, Valencia A, Real FX. The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies. BMC Genomics 2015; 16:403. [PMID: 25997541 PMCID: PMC4470036 DOI: 10.1186/s12864-015-1450-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 03/09/2015] [Indexed: 12/11/2022] Open
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. RESULTS 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. CONCLUSIONS 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.
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Affiliation(s)
- Julie Earl
- Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain. .,Servicio de Oncología Médica, Hospital Ramón y Cajal, Madrid, Spain.
| | - Daniel Rico
- Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.
| | - Enrique Carrillo-de-Santa-Pau
- Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.
| | - Benjamín Rodríguez-Santiago
- Quantitative Genomic Medicine Laboratory, qGenomics, Barcelona, Spain. .,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain.
| | - Marinela Méndez-Pertuz
- Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.
| | - Herbert Auer
- Institut de Recerca Biomèdica de Barcelona, Parc Científic de Barcelona, Barcelona, Spain.
| | - Gonzalo Gómez
- Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.
| | | | - David G Pisano
- Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.
| | - Wolfgang A Schulz
- Department of Urology, Heinrich-Heine-University, Düsseldorf, Germany.
| | - Luis A Pérez-Jurado
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain.
| | - Alfredo Carrato
- Servicio de Oncología Médica, Hospital Ramón y Cajal, Madrid, Spain.
| | - Dan Theodorescu
- University of Colorado Comprehensive Cancer Center, 80045, Aurora, CO, USA.
| | - Stephen Chanock
- Translational Genomics Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA.
| | - Alfonso Valencia
- Structural Computational Biology Group, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain.
| | - Francisco X Real
- Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain. .,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain. .,Cancer Cell Biology Programme, Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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Balbás-Martínez C, Sagrera A, Carrillo-de-Santa-Pau E, Earl J, Márquez M, Vazquez M, Lapi E, Castro-Giner F, Beltran S, Bayés M, Carrato A, Cigudosa JC, Domínguez O, Gut M, Herranz J, Juanpere N, Kogevinas M, Langa X, López-Knowles E, Lorente JA, Lloreta J, Pisano DG, Richart L, Rico D, Salgado RN, Tardón A, Chanock S, Heath S, Valencia A, Losada A, Gut I, Malats N, Real FX. Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nat Genet 2013; 45:1464-9. [PMID: 24121791 PMCID: PMC3840052 DOI: 10.1038/ng.2799] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 09/16/2013] [Indexed: 12/11/2022]
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 management (1). 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, BPTF), cell division (STAG2, SMC1A, SMC1B), and DNA repair (ATM, ERCC2, FANCA). STAG2, a subunit of cohesin, was significantly and commonly mutated/lost in UBC, mainly in tumors of low stage/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 novel UBC tumor suppressor acting through mechanisms that are different from its role to prevent aneuploidy.
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Affiliation(s)
- Cristina Balbás-Martínez
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
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Balbás-Martínez C, Rodríguez-Pinilla M, Casanova A, Domínguez O, Pisano DG, Gómez G, Lloreta J, Lorente JA, Malats N, Real FX. ARID1A alterations are associated with FGFR3-wild type, poor-prognosis, urothelial bladder tumors. PLoS One 2013; 8:e62483. [PMID: 23650517 PMCID: PMC3641081 DOI: 10.1371/journal.pone.0062483] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 03/20/2013] [Indexed: 02/06/2023] Open
Abstract
Urothelial bladder cancer (UBC) is heterogeneous at the clinical, pathological, genetic, and epigenetic levels. Exome sequencing has identified ARID1A as a novel tumor suppressor gene coding for a chromatin remodeling protein that is mutated in UBC. Here, we assess ARID1A alterations in two series of patients with UBC. In the first tumor series, we analyze exons 2–20 in 52 primary UBC and find that all mutant tumors belong to the aggressive UBC phenotype (high grade non-muscle invasive and muscle invasive tumors) (P = 0.05). In a second series (n = 84), we assess ARID1A expression using immunohistochemistry, a surrogate for mutation analysis, and find that loss of expression increases with higher stage/grade, it is inversely associated with FGFR3 overexpression (P = 0.03) but it is not correlated with p53 overexpression (P = 0.30). We also analyzed the expression of cytokeratins in the same set of tumor and find, using unsupervised clustering, that tumors with ARID1A loss of expression are generally KRT5/6-low. In this patient series, loss of ARID1A expression is also associated with worse prognosis, likely reflecting the higher prevalence of losses found in tumors of higher stage and grade. The independent findings in these two sets of patients strongly support the notion that ARID1A inactivation is a key player in bladder carcinogenesis occurring predominantly in FGFR3 wild type tumors.
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MESH Headings
- Aged
- Aged, 80 and over
- Base Sequence
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/mortality
- Carcinoma, Transitional Cell/pathology
- Cell Line, Tumor
- DNA Mutational Analysis
- DNA-Binding Proteins
- Female
- HEK293 Cells
- Humans
- Kaplan-Meier Estimate
- Male
- Middle Aged
- Mutation, Missense
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Prognosis
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/mortality
- Urinary Bladder Neoplasms/pathology
- Urothelium/pathology
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Affiliation(s)
- Cristina Balbás-Martínez
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - María Rodríguez-Pinilla
- Lymphoma Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Ariel Casanova
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Orlando Domínguez
- Genomics Unit, Biotechnology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - David G. Pisano
- Bioinformatics Unit, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Gonzalo Gómez
- Bioinformatics Unit, Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Josep Lloreta
- Department of Pathology, Hospital del Mar, Barcelona, Spain
- Departament de Ciències Experimentals de i la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Núria Malats
- Genetic and Molecular Epidemiology Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Francisco X. Real
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Departament de Ciències Experimentals de i la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail:
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Abstract
Detailed molecular insights into bladder cancer biology might allow more detailed prognostication and optimization of treatment with the objective of improving patient outcome and quality of life. However, in bladder cancer research the search for biomarkers has been called into question and has even obtained notoriety. It is unlikely that any single marker will be able to improve prognostication for patients with bladder cancer above and beyond grade and stage, but a combination of multiple independent markers might more precisely predict the outcome. From a previous review, we identified seven biomarkers to study within the setting of the Bladder Cancer Prognosis Programme (BCPP), a 5-year multicentre programme of research based at the University of Birmingham and funded by Cancer Research UK, investigating their effectiveness in predicting recurrence and progression. As part of the ongoing quality-assurance process for BCPP we present an updated review of our selected biomarkers, as well as highlighting other recent important developments in bladder cancer research.
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Affiliation(s)
- Richard T Bryan
- Department of Public Health Epidemiology and Biostatistics, School of Population Sciences, University of Birmingham, Birmingham, UK.
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