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Mau B, Johnson B, Hansel DE, McConkey DJ. The Many Faces of Muscle-Invasive Bladder Cancer: Histopathological and Molecular Characterization. Semin Radiat Oncol 2023; 33:1-11. [PMID: 36517188 DOI: 10.1016/j.semradonc.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Brian Mau
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR
| | - Burles Johnson
- Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD
| | - Donna E Hansel
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR; Present address: Division Head, Pathology and Laboratory Medicine, U.T. M.D. Anderson Cancer Center, Houston, Texas 77030 USA
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD.
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2
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Multiparametric Classification of Non-Muscle Invasive Papillary Urothelial Neoplasms: Combining Morphological, Phenotypical, and Molecular Features for Improved Risk Stratification. Int J Mol Sci 2022; 23:ijms23158133. [PMID: 35897708 PMCID: PMC9330009 DOI: 10.3390/ijms23158133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 02/05/2023] Open
Abstract
Diagnosis and grading of non-invasive papillary urothelial tumors according to the current WHO classification poses some challenges for pathologists. The diagnostic reproducibility of separating low-grade and high-grade lesions is low, which impacts their clinical management. Whereas papillary urothelial neoplasms with low malignant potential (PUN-LMP) and low-grade papillary non-invasive carcinoma (LG-PUC) are comparable and show frequent local recurrence but rarely metastasize, high-grade papillary non-invasive carcinoma (HG-PUC) has a poor prognosis. The main objective of this work is to develop a multiparametric classification to unambiguously distinguish low-grade and high-grade tumors, considering immunohistochemical stains for p53, FGFR3, CK20, MIB-1, p16, p21 and p-HH3, and pathogenic mutations in TP53, FGFR3, TP53, ERCC2, PIK3CA, PTEN and STAG2. We reviewed and analyzed the clinical and histological data of 45 patients with a consensus diagnosis of PUN-LMP (n = 8), non-invasive LG-PUC (n = 23), and HG-PUC (n = 14). The proliferation index and mitotic count assessed with MIB-1 and P-HH3 staining, respectively correlated with grading and clinical behavior. Targeted sequencing confirmed frequent FGFR3 mutations in non-invasive papillary tumors and identified mutations in TP53 as high-risk. Cluster analysis of the different immunohistochemical and molecular parameters allowed a clear separation in two different clusters: cluster 1 corresponding to PUN-LMP and LG-PUC (low MIB-1 and mitotic count/FGFR3 and STAG2 mutations) and cluster 2, HG-PUC (high MIB-1 and mitosis count/CK20 +++ expression, FGFR3 WT and TP53 mutation). Further analysis is required to validate and analyze the reproducibility of these clusters and their biological and clinical implication.
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Animal Models in Bladder Cancer. Biomedicines 2021; 9:biomedicines9121762. [PMID: 34944577 PMCID: PMC8698361 DOI: 10.3390/biomedicines9121762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Bladder cancer (urothelial cancer of the bladder) is the most common malignancy affecting the urinary system with an increasing incidence and mortality. Mouse models of bladder cancer should possess a high value of reproducibility, predictability, and translatability to allow mechanistic, chemo-preventive, and therapeutic studies that can be furthered into human clinical trials. OBJECTIVES To provide an overview and resources on the origin, molecular and pathological characteristics of commonly used animal models in bladder cancer. METHODS A PubMed and Web of Science search was performed for relevant articles published between 1980 and 2021 using words such as: "bladder" and/or "urothelial carcinoma" and animal models. Animal models of bladder cancer can be categorized as autochthonous (spontaneous) and non-autochthonous (transplantable). The first are either chemically induced models or genetically engineered models. The transplantable models can be further subclassified as syngeneic (murine bladder cancer cells implanted into immunocompetent or transgenic mice) and xenografts (human bladder cancer cells implanted into immune-deficient mice). These models can be further divided-based on the site of the tumor-as orthotopic (tumor growth occurs within the bladder) and heterotopic (tumor growth occurs outside of the bladder).
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Bejrananda T, Kanjanapradit K, Saetang J, Sangkhathat S. Impact of immunohistochemistry-based subtyping of GATA3, CK20, CK5/6, and CK14 expression on survival after radical cystectomy for muscle-invasive bladder cancer. Sci Rep 2021; 11:21186. [PMID: 34707176 PMCID: PMC8551252 DOI: 10.1038/s41598-021-00628-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/13/2021] [Indexed: 12/27/2022] Open
Abstract
Molecular subtyping of muscle-invasive bladder cancer (MIBC) predicts disease progression and treatment response. However, standard subtyping based on transcriptomic analysis is relatively expensive. This study tried to use immunohistochemistry (IHC) to subtype MIBC based on GATA3, CK20, CK5/6, and CK14 protein expression. The IHC-based subtypes in MIBC subtypes were classified as luminal (GATA3+ CK5/6−, 38.6%), basal (GATA3−CK5/6+, 12.9%), mixed (GATA3+ CK5/6+, 37.9%), and double-negative (GATA3−CK5/6−, 10.6%) in 132 MIBC patients. All individual markers and clinicopathological parameters were analyzed against treatment outcomes after radical cystectomy. The mean patient age was 65.6 years, and the male to female ratio was 6.8:1. Positive IHC expression of GATA3, CK20, CK5/6, and CK14 were 80.3%, 50.8%, 42.4%, and 28.0%, respectively. Only GATA3 and CK5/6 were significantly associated with survival outcome (p values = 0.004 and 0.02). The mixed subtype was significantly better in 5-year OS at 42.8%, whereas the double-negative subtype had the worst prognosis (5-year OS 7.14%). The double-negative subtype had a hazard ratio of 3.29 (95% CI 1.71–6.32). Subtyping using GATA3 and CK5/6 was applicable in MIBCs, and patients with the double-negative subtype were at the highest risk and may require more intensive therapy.
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Affiliation(s)
- Tanan Bejrananda
- Urology Unit, Division of Surgery, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand.
| | - Kanet Kanjanapradit
- Division of Pathology, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
| | - Jirakrit Saetang
- EZ-Mol-Design Laboratory, Faculty of Medicine, Prince of Songkhla University, Hat Yai, Songkhla, 90110, Thailand.,Division of Surgery, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
| | - Surasak Sangkhathat
- Division of Surgery, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand.,Translational Medicine Research Center, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
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5
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Uysal D, Kowalewski KF, Kriegmair MC, Wirtz R, Popovic ZV, Erben P. A comprehensive molecular characterization of the 8q22.2 region reveals the prognostic relevance of OSR2 mRNA in muscle invasive bladder cancer. PLoS One 2021; 16:e0248342. [PMID: 33711044 PMCID: PMC7954304 DOI: 10.1371/journal.pone.0248342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/25/2021] [Indexed: 12/27/2022] Open
Abstract
Technological advances in molecular profiling have enabled the comprehensive identification of common regions of gene amplification on chromosomes (amplicons) in muscle invasive bladder cancer (MIBC). One such region is 8q22.2, which is largely unexplored in MIBC and could harbor genes with potential for outcome prediction or targeted therapy. To investigate the prognostic role of 8q22.2 and to compare different amplicon definitions, an in-silico analysis of 357 patients from The Cancer Genome Atlas, who underwent radical cystectomy for MIBC, was performed. Amplicons were generated using the GISTIC2.0 algorithm for copy number alterations (DNA_Amplicon) and z-score normalization for mRNA gene overexpression (RNA_Amplicon). Kaplan-Meier survival analysis, univariable, and multivariable Cox proportional hazard ratios were used to relate amplicons, genes, and clinical parameters to overall (OS) and disease-free survival (DFS). Analyses of the biological functions of 8q22.2 genes and genomic events in MIBC were performed to identify potential targets. Genes with prognostic significance from the in silico analysis were validated using RT-qPCR of MIBC tumor samples (n = 46). High 8q22.2 mRNA expression (RNA-AMP) was associated with lymph node metastases. Furthermore, 8q22.2 DNA and RNA amplified patients were more likely to show a luminal subtype (DNA_Amplicon_core: p = 0.029; RNA_Amplicon_core: p = 0.01). Overexpression of the 8q22.2 gene OSR2 predicted shortened DFS in univariable (HR [CI] 1.97 [1.2; 3.22]; p = 0.01) and multivariable in silico analysis (HR [CI] 1.91 [1.15; 3.16]; p = 0.01) and decreased OS (HR [CI] 6.25 [1.37; 28.38]; p = 0.0177) in RT-qPCR data analysis. Alterations in different levels of the 8q22.2 region are associated with manifestation of different clinical characteristics in MIBC. An in-depth comprehensive molecular characterization of genomic regions involved in cancer should include multiple genetic levels, such as DNA copy number alterations and mRNA gene expression, and could lead to a better molecular understanding. In this study, OSR2 is identified as a potential biomarker for survival prognosis.
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Affiliation(s)
- Daniel Uysal
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Karl-Friedrich Kowalewski
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | | | - Ralph Wirtz
- STRATIFYER Molecular Pathology GmbH, Köln, Germany
| | - Zoran V. Popovic
- Institute of Pathology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Philipp Erben
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- * E-mail:
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6
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Lin CL, Tan X, Chen M, Kusi M, Hung CN, Chou CW, Hsu YT, Wang CM, Kirma N, Chen CL, Lin CH, Lathrop KI, Elledge R, Kaklamani VG, Mitsuya K, Huang THM. ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer. BMC Med Genomics 2020; 13:69. [PMID: 32408897 PMCID: PMC7222439 DOI: 10.1186/s12920-020-0729-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Chromothripsis is an event of genomic instability leading to complex chromosomal alterations in cancer. Frequent long-range chromatin interactions between transcription factors (TFs) and targets may promote extensive translocations and copy-number alterations in proximal contact regions through inappropriate DNA stitching. Although studies have proposed models to explain the initiation of chromothripsis, few discussed how TFs influence this process for tumor progression. METHODS This study focused on genomic alterations in amplification associated regions within chromosome 17. Inter-/intra-chromosomal rearrangements were analyzed using whole genome sequencing data of breast tumors in the Cancer Genome Atlas (TCGA) cohort. Common ERα binding sites were defined based on MCF-7, T47D, and MDA-MB-134 breast cancer cell lines using univariate K-means clustering methods. Nanopore sequencing technology was applied to validate frequent rearrangements detected between ATC loci on 17q23 and an ERα hub on 20q13. The efficacy of pharmacological inhibition of a potentially druggable target gene on 17q23 was evaluated using breast cancer cell lines and patient-derived circulating breast tumor cells. RESULTS There are five adjoining regions from 17q11.1 to 17q24.1 being hotspots of chromothripsis. Inter-/intra-chromosomal rearrangements of these regions occurred more frequently in ERα-positive tumors than in ERα-negative tumors. In addition, the locations of the rearrangements were often mapped within or close to dense ERα binding sites localized on these five 17q regions or other chromosomes. This chromothriptic event was linked to concordant upregulation of 96 loci that predominantly regulate cell-cycle machineries in advanced luminal tumors. Genome-editing analysis confirmed that an ERα hub localized on 20q13 coordinately regulates a subset of these loci localized on 17q23 through long-range chromosome interactions. One of these loci, Tousled Like Kinase 2 (TLK2) known to participate in DNA damage checkpoint control, is an actionable target using phenothiazine antipsychotics (PTZs). The antiproliferative effect of PTZs was prominent in high TLK2-expressing cells, compared to low expressing cells. CONCLUSION This study demonstrates a new approach for identifying tumorigenic drivers from genomic regions highly susceptible to ERα-related chromothripsis. We found a group of luminal breast tumors displaying 17q-related chromothripsis for which antipsychotics can be repurposed as treatment adjuncts.
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Affiliation(s)
- Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Xi Tan
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chia-Nung Hung
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chih-Wei Chou
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Ya-Ting Hsu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Nameer Kirma
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Kate I Lathrop
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Richard Elledge
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Virginia G Kaklamani
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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Cooley LF, McLaughlin KA, Meeks JJ. Genomic and Therapeutic Landscape of Non-muscle-invasive Bladder Cancer. Urol Clin North Am 2019; 47:35-46. [PMID: 31757298 DOI: 10.1016/j.ucl.2019.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Non-muscle-invasive bladder cancer (NMIBC) is heterogeneous, but current diagnostic and treatment strategies rely primarily on clinical parameters, lacking individualization to tumor and host genetics and biology. The heterogeneity of NMIBCs is derived from mutations, mutation signatures, chromosomal loss, and disruption of molecular pathways, which ultimately affects tumor progression, recurrence, and responsiveness to intravesical and systemic chemotherapy. Although research is still underway, advances in sequencing technology, insight into differential bacillus Calmette-Guérin responses, and new investigational treatment targets will soon offer clinicians new, precision-based tools to risk stratify and determine treatment regimens for future patients with bladder cancer.
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Affiliation(s)
- Lauren Folgosa Cooley
- Department of Urology, Feinberg School of Medicine, Northwestern University, 300 East Superior Street, Tarry 16-703, Chicago, IL 60611, USA
| | - Kimberly A McLaughlin
- Department of Urology, Feinberg School of Medicine, Northwestern University, 300 East Superior Street, Tarry 16-703, Chicago, IL 60611, USA; Department of Biochemistry, Northwestern University, Feinberg School of Medicine, Polsky Urologic Cancer Institute, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Joshua J Meeks
- Department of Urology, Feinberg School of Medicine, Northwestern University, 300 East Superior Street, Tarry 16-703, Chicago, IL 60611, USA; Department of Biochemistry, Northwestern University, Feinberg School of Medicine, Polsky Urologic Cancer Institute, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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8
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Hurst CD, Knowles MA. Mutational landscape of non-muscle-invasive bladder cancer. Urol Oncol 2018; 40:295-303. [PMID: 30446444 DOI: 10.1016/j.urolonc.2018.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 09/11/2018] [Accepted: 10/10/2018] [Indexed: 12/16/2022]
Abstract
Non-muscle-invasive bladder cancer (NMIBC) includes stage Ta and stage T1 tumors and carcinoma in situ (CIS). Grading of Ta tumors subdivides these lesions into papillary urothelial neoplasms of low malignant potential and low- and high-grade noninvasive papillary urothelial carcinoma. CIS is by definition high-grade and the majority of stage T1 tumors are of high-grade. This pathologic heterogeneity is associated with divergent clinical outcome, with significantly worse prognosis for patients with T1 tumors or CIS. A wealth of molecular information has accumulated on NMIBC including mutational data that ranges from the whole chromosome level to next generation sequence data at nucleotide level. This has not only identified key genes that are mutated in NMIBC, but also provides insight into the processes that shape their mutational landscape. Although molecular analyses cannot yet provide definitive personal prognostic information, many differences between these entities promise improved disease management in the future. Most information is available for Ta and T1 samples and this is the focus of this review.
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Affiliation(s)
- Carolyn D Hurst
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, United Kingdom
| | - Margaret A Knowles
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, United Kingdom.
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9
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Wang X, Steensma JT, Bailey MH, Feng Q, Padda H, Johnson KJ. Characteristics of The Cancer Genome Atlas cases relative to U.S. general population cancer cases. Br J Cancer 2018; 119:885-892. [PMID: 30131556 PMCID: PMC6189215 DOI: 10.1038/s41416-018-0140-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Background Despite anecdotal reports of differences in clinical and demographic
characteristics of The Cancer Genome Atlas (TCGA) relative to general population
cancer cases, differences have not been systematically evaluated. Methods Data from 11,160 cases with 33 cancer types were ascertained from
TCGA data portal. Corresponding data from the Surveillance, Epidemiology, and End
Results (SEER) 18 and North American Association of Central Cancer Registries
databases were obtained. Differences in characteristics were compared using
Student’s t, Chi-square, and Fisher’s exact
tests. Differences in mean survival months were assessed using restricted mean
survival time analysis and generalised linear model. Results TCGA cases were 3.9 years (95% CI 1.7–6.2) younger on average than
SEER cases, with a significantly younger mean age for 20/33 cancer types. Although
most cancer types had a similar sex distribution, race and stage at diagnosis
distributions were disproportional for 13/18 and 25/26 assessed cancer types,
respectively. Using 12 months as an end point, the observed mean survival months
were longer for 27 of 33 TCGA cancer types. Conclusions Differences exist in the characteristics of TCGA vs. general
population cancer cases. Our study highlights population subgroups where increased
sample collection is warranted to increase the applicability of cancer
genomic research results to all individuals.
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Affiliation(s)
- Xiaoyan Wang
- Brown School, Washington University in St. Louis, St. Louis MO, USA
| | | | - Matthew H Bailey
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis MO, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis MO, USA
| | - Qianxi Feng
- Brown School, Washington University in St. Louis, St. Louis MO, USA
| | - Hannah Padda
- Brown School, Washington University in St. Louis, St. Louis MO, USA
| | - Kimberly J Johnson
- Brown School, Washington University in St. Louis, St. Louis MO, USA. .,Siteman Cancer Center, Washington University in St. Louis, St. Louis MO, USA.
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10
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Magbanua MJM, Rugo HS, Wolf DM, Hauranieh L, Roy R, Pendyala P, Sosa EV, Scott JH, Lee JS, Pitcher B, Hyslop T, Barry WT, Isakoff SJ, Dickler M, Van't Veer L, Park JW. Expanded Genomic Profiling of Circulating Tumor Cells in Metastatic Breast Cancer Patients to Assess Biomarker Status and Biology Over Time (CALGB 40502 and CALGB 40503, Alliance). Clin Cancer Res 2018; 24:1486-1499. [PMID: 29311117 PMCID: PMC5856614 DOI: 10.1158/1078-0432.ccr-17-2312] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/18/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022]
Abstract
Purpose: We profiled circulating tumor cells (CTCs) to study the biology of blood-borne metastasis and to monitor biomarker status in metastatic breast cancer (MBC).Methods: CTCs were isolated from 105 patients with MBC using EPCAM-based immunomagnetic enrichment and fluorescence-activated cells sorting (IE/FACS), 28 of whom had serial CTC analysis (74 samples, 2-5 time points). CTCs were subjected to microfluidic-based multiplex QPCR array of 64 cancer-related genes (n = 151) and genome-wide copy-number analysis by array comparative genomic hybridization (aCGH; n = 49).Results: Combined transcriptional and genomic profiling showed that CTCs were 26% ESR1-ERBB2-, 48% ESR1+ERBB2-, and 27% ERBB2+ Serial testing showed that ERBB2 status was more stable over time compared with ESR1 and proliferation (MKI67) status. While cell-to-cell heterogeneity was observed at the single-cell level, with increasingly stable expression in larger pools, patient-specific CTC expression "fingerprints" were also observed. CTC copy-number profiles clustered into three groups based on the extent of genomic aberrations and the presence of large chromosomal imbalances. Comparative analysis showed discordance in ESR1/ER (27%) and ERBB2/HER2 (23%) status between CTCs and matched primary tumors. CTCs in 65% of the patients were considered to have low proliferation potential. Patients who harbored CTCs with high proliferation (MKI67) status had significantly reduced progression-free survival (P = 0.0011) and overall survival (P = 0.0095) compared with patients with low proliferative CTCs.Conclusions: We demonstrate an approach for complete isolation of EPCAM-positive CTCs and downstream comprehensive transcriptional/genomic characterization to examine the biology and assess breast cancer biomarkers in these cells over time. Clin Cancer Res; 24(6); 1486-99. ©2018 AACR.
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Affiliation(s)
- Mark Jesus M Magbanua
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California.
| | - Hope S Rugo
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Denise M Wolf
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Louai Hauranieh
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center and Computational Biology and Informatics, University of California at San Francisco, San Francisco, California
| | - Praveen Pendyala
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Eduardo V Sosa
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Janet H Scott
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Jin Sun Lee
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Brandelyn Pitcher
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina
| | - Terry Hyslop
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina
| | - William T Barry
- Alliance Statistics and Data Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Steven J Isakoff
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Maura Dickler
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Van't Veer
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - John W Park
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California.
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Abstract
Here, we describe the use of complementary techniques applicable to different types of samples to analyze chromosomal alterations in urothelial carcinoma. By a conventional chromosome analysis on fresh biopsies, it is possible to delineate the status of ploidy and rough chromosomal aberrations. The multi-target fluorescence in situ hybridization (FISH) UroVysion test, for the rapid detection of chromosomal aneusomy of chromosomes 3, 7, and 17 and/or deletion of 9p21 locus, is applicable to urine specimens as well as to formalin-fixed paraffin-embedded (FFPE) specimens and fresh biopsies. Finally, array comparative genomic hybridization (array-CGH) gives the possibility of analyzing the DNA in a single experiment from a biopsy of the tumor but also from FFPE specimens; this technique is able to detect alterations at the genome level not excluding any chromosome.
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12
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Lee JY, Kim K, Sung HH, Jeon HG, Jeong BC, Seo SI, Jeon SS, Lee HM, Choi HY, Kwon GY, Kim KM, Lee J, Lim HY, Park SH. Molecular Characterization of Urothelial Carcinoma of the Bladder and Upper Urinary Tract. Transl Oncol 2017; 11:37-42. [PMID: 29161613 PMCID: PMC5699894 DOI: 10.1016/j.tranon.2017.10.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/13/2017] [Accepted: 10/23/2017] [Indexed: 01/12/2023] Open
Abstract
PURPOSE A better understanding of the molecular basis of urothelial carcinoma (UC) is needed to refine the clinical decision-making process. METHODS AND MATERIALS We performed next-generation sequencing to investigate the mutational and transcriptional profiles of commonly mutated genes in UC using Ampliseq v2. Copy number variations (CNVs) were detected with nCounter assay. Genetic alterations between upper tract UC (UTUC) and urinary bladder UC (UBUC) were compared. RESULTS Tumor samples from 31 UTUC and 61 UBUC patients were included in analysis. The two groups showed similar clinicopathologic features including tumor grade and stage. Median survival was longer in UTUC than UBUC patients, though this was statistically nonsignificant (59 vs 41 months, P=.137). In total, we found 982 genetic alterations from 92 samples: single nucleotide variants were the most common type of somatic mutation (479/508, 94.3%). Frequently detected somatic mutations included TP53 (68.5%), KDR (41.3%), and PIK3CA (17.4%). Notably, RB1 mutations were the only mutations significantly different between the UBUC and UTUC groups (19.7% vs. 0%, P=.020). The most common types of CNVs included amplifications (56/62, 90.3%): 17.7% of patients identified amplifications in NOTCH1. We also identified five translocations in the entire study population, including one case with FGFR3-TACC3 (Chr4) fusion. CONCLUSION Within a small study population, we identified similar genetic alterations in both UTUC and UBUC patients, indicating a basis for similar management strategies.
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Affiliation(s)
- Ji Yun Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kyung Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun Hwan Sung
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hwang Gyun Jeon
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byong Chang Jeong
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seong Il Seo
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seong Soo Jeon
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun Moo Lee
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Han-Yong Choi
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ghee-Young Kwon
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ho Yeong Lim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Hoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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13
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Kamal M, Holliday DL, Morrison EE, Speirs V, Toomes C, Bell SM. Loss of CSMD1 expression disrupts mammary duct formation while enhancing proliferation, migration and invasion. Oncol Rep 2017; 38:283-292. [PMID: 28534981 DOI: 10.3892/or.2017.5656] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 05/11/2017] [Indexed: 11/06/2022] Open
Abstract
The CUB and sushi multiple domains 1 (CSMD1) gene maps to chromosome 8p23, a region deleted in many cancers. Loss of CSMD1 expression is associated with poor prognosis in breast cancer suggesting that it acts as a tumour suppressor in this cancer. However, the function of CSMD1 is largely unknown. Herein, we investigated CSMD1 functions in cell line models. CSMD1 expression was suppressed in MCF10A and LNCaP cells using short hairpin RNA. Functional assays were performed focusing on the 'normal' MCF10A cell line. Suppression of CSMD1 significantly increased the proliferation, cell migration and invasiveness of MCF10A cells compared to shcontrols. shCSMD1 cells also showed significantly reduced adhesion to Matrigel and fibronectin. In a three-dimensional Matrigel model of MCF10A cells, reduced CSMD1 expression resulted in the development of larger and more poorly differentiated breast acini-like structures that displayed impaired lumen formation. Loss of CSMD1 expression disrupts a model of mammary duct formation while enhancing proliferation, migration and invasion. Our data suggest that CSMD1 is involved in the suppression of a transformed phenotype.
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Affiliation(s)
- Mohamed Kamal
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Deborah L Holliday
- Leeds Institute of Cancer and Pathology, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Ewan E Morrison
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Valerie Speirs
- Leeds Institute of Cancer and Pathology, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Carmel Toomes
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Sandra M Bell
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
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14
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Abstract
Bladder cancer is a highly prevalent disease and is associated with substantial morbidity, mortality and cost. Environmental or occupational exposures to carcinogens, especially tobacco, are the main risk factors for bladder cancer. Most bladder cancers are diagnosed after patients present with macroscopic haematuria, and cases are confirmed after transurethral resection of bladder tumour (TURBT), which also serves as the first stage of treatment. Bladder cancer develops via two distinct pathways, giving rise to non-muscle-invasive papillary tumours and non-papillary (solid) muscle-invasive tumours. The two subtypes have unique pathological features and different molecular characteristics. Indeed, The Cancer Genome Atlas project identified genetic drivers of muscle-invasive bladder cancer (MIBC) as well as subtypes of MIBC with distinct characteristics and therapeutic responses. For non-muscle-invasive bladder cancer (NMIBC), intravesical therapies (primarily Bacillus Calmette-Guérin (BCG)) with maintenance are the main treatments to prevent recurrence and progression after initial TURBT; additional therapies are needed for those who do not respond to BCG. For localized MIBC, optimizing care and reducing morbidity following cystectomy are important goals. In metastatic disease, advances in our genetic understanding of bladder cancer and in immunotherapy are being translated into new therapies.
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15
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Glaser AP, Fantini D, Shilatifard A, Schaeffer EM, Meeks JJ. The evolving genomic landscape of urothelial carcinoma. Nat Rev Urol 2017; 14:215-229. [PMID: 28169993 DOI: 10.1038/nrurol.2017.11] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Survival of patients with urothelial carcinoma (including bladder cancer and upper tract urothelial carcinoma) is limited by our current approaches to staging, surgery, and chemotherapy. Large-scale, next-generation sequencing collaborations, such as The Cancer Genome Atlas, have already identified drivers and vulnerabilities of urothelial carcinoma. This disease has a high degree of mutational heterogeneity and a high frequency of somatic mutations compared with other solid tumours, potentially resulting in an increased neoantigen burden. Mutational heterogeneity is mediated by multiple factors including the apolipoprotein B mRNA editing enzyme catalytic polypeptide family of enzymes, smoking exposure, viral integrations, and intragene and intergene fusion proteins. The mutational landscape of urothelial carcinoma, including specific mutations in pathways and driver genes, such as FGFR3, ERBB2, PIK3CA, TP53, and STAG2, affects tumour aggressiveness and response to therapy. The next generation of therapies for urothelial carcinoma will be based on patient-specific targetable mutations found in individual tumours. This personalized-medicine approach to urothelial carcinoma has already resulted in unique clinical trial design and has the potential to improve patient outcomes and survival.
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Affiliation(s)
- Alexander P Glaser
- Northwestern University, Department of Urology, 303 E. Chicago Avenue, Tarry 16-703, Chicago, Illinois 60611, USA
| | - Damiano Fantini
- Northwestern University, Department of Urology, 303 E. Chicago Avenue, Tarry 16-703, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Northwestern University, Department of Urology, 303 E. Chicago Avenue, Tarry 16-703, Chicago, Illinois 60611, USA
| | - Edward M Schaeffer
- Northwestern University, Department of Urology, 303 E. Chicago Avenue, Tarry 16-703, Chicago, Illinois 60611, USA
| | - Joshua J Meeks
- Northwestern University, Department of Urology, 303 E. Chicago Avenue, Tarry 16-703, Chicago, Illinois 60611, USA
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16
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Kanemoto K, Fukuta K, Kawai N, Tozawa K, Ochiai M, Okamoto K, Ohnami S, Sakamoto H, Yoshida T, Kanai Y, Katoh M, Yasui T, Kohri K, Kakizoe T, Nakagama H. Genomic Landscape of Experimental Bladder Cancer in Rodents and Its Application to Human Bladder Cancer: Gene Amplification and Potential Overexpression of Cyp2a5/CYP2A6 Are Associated with the Invasive Phenotype. PLoS One 2016; 11:e0167374. [PMID: 27902773 PMCID: PMC5130269 DOI: 10.1371/journal.pone.0167374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/30/2016] [Indexed: 11/23/2022] Open
Abstract
Non-muscle invasive (superficial) bladder cancer is a low-grade malignancy with good prognosis, while muscle invasive (invasive) bladder cancer is a high-grade malignancy with poor prognosis. N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) induces superficial bladder cancers with papillary morphology in rats and invasive bladder cancers with infiltrating phenotype in mice. In this study, we analyzed genomic landscapes of rodent BBN-induced bladder cancers using array-based comparative genomic hybridization (array CGH). While no significant copy number alterations were detected in superficial bladder tumors in rats, copy number gains in chromosomal regions 2D-E1, 7qA3, 9F2, and 11C-D were detected in invasive bladder tumors in mice. Amplification of representative genes located on 2D-E1 and 7qA3 chromosomal regions was confirmed by quantitative PCR. Cyp2a22 and Cyp2a5 genes but not Cyp2g1, Cyp2a12, and Rab4b genes on mouse chromosome 7qA3 were amplified in invasive bladder cancers. Although the human ortholog gene of Cyp2a22 has not been confirmed, the mouse Cyp2a5 gene is the ortholog of the human CYP2A6 gene located in chromosomal region 19q13.2, and CYP2A6 was identified by database search as one of the closest human homolog to mouse Cyp2a22. Considering a possibility that this region may be related to mouse 7qA3, we analyzed CYP2A6 copy number and expression in human bladder cancer using cell lines and resected tumor specimens. Although only one of eight cell lines showed more than one copy increase of the CYP2A6 gene, CYP2A6 amplification was detected in six out of 18 primary bladder tumors where it was associated with the invasive phenotype. Immunohistochemical analyses of 118 primary bladder tumors revealed that CYP2A6 protein expression was also higher in invasive tumors, especially in those of the scattered type. Together, these findings indicate that the amplification and overexpression of the CYP2A6 gene are characteristic of human bladder cancers with increased malignancy and that CYP2A6 can be a candidate prognostic biomarker in this type of cancer.
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Affiliation(s)
- Kazuhiro Kanemoto
- Division of Cancer Development System, National Cancer Center Research Institute, Tokyo, Japan
- Department of Nephro-Urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Katsuhiro Fukuta
- Department of Nephro-Urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Noriyasu Kawai
- Department of Nephro-Urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Keiichi Tozawa
- Department of Nephro-Urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Masako Ochiai
- Division of Cancer Development System, National Cancer Center Research Institute, Tokyo, Japan
| | - Koji Okamoto
- Division of Cancer Differentiation, National Cancer Center Research Institute, Tokyo, Japan
| | - Sumiko Ohnami
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yae Kanai
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Masaru Katoh
- Department of Omics Network, National Cancer Center Research Institute, Tokyo, Japan
| | - Takahiro Yasui
- Department of Nephro-Urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kenjiro Kohri
- Department of Nephro-Urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Tadao Kakizoe
- National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Nakagama
- Division of Cancer Development System, National Cancer Center Research Institute, Tokyo, Japan
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17
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Ruan P, Shen J, Santella RM, Zhou S, Wang S. NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals. Nucleic Acids Res 2016; 44:e134. [PMID: 27302130 PMCID: PMC5027497 DOI: 10.1093/nar/gkw546] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/04/2016] [Indexed: 12/13/2022] Open
Abstract
DNA methylation plays an important role in many biological processes. Existing epigenome-wide association studies (EWAS) have successfully identified aberrantly methylated genes in many diseases and disorders with most studies focusing on analysing methylation sites one at a time. Incorporating prior biological information such as biological networks has been proven to be powerful in identifying disease-associated genes in both gene expression studies and genome-wide association studies (GWAS) but has been under studied in EWAS. Although recent studies have noticed that there are differences in methylation variation in different groups, only a few existing methods consider variance signals in DNA methylation studies. Here, we present a network-assisted algorithm, NEpiC, that combines both mean and variance signals in searching for differentially methylated sub-networks using the protein–protein interaction (PPI) network. In simulation studies, we demonstrate the power gain from using both the prior biological information and variance signals compared to using either of the two or neither information. Applications to several DNA methylation datasets from the Cancer Genome Atlas (TCGA) project and DNA methylation data on hepatocellular carcinoma (HCC) from the Columbia University Medical Center (CUMC) suggest that the proposed NEpiC algorithm identifies more cancer-related genes and generates better replication results.
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Affiliation(s)
- Peifeng Ruan
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China
| | - Jing Shen
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Regina M Santella
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Shuigeng Zhou
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
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18
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Admoni-Elisha L, Nakdimon I, Shteinfer A, Prezma T, Arif T, Arbel N, Melkov A, Zelichov O, Levi I, Shoshan-Barmatz V. Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment. PLoS One 2016; 11:e0148500. [PMID: 27078856 PMCID: PMC4831809 DOI: 10.1371/journal.pone.0148500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 01/19/2016] [Indexed: 12/31/2022] Open
Abstract
In many cancers, cells undergo re-programming of metabolism, cell survival and anti-apoptotic defense strategies, with the proteins mediating this reprogramming representing potential biomarkers. Here, we searched for novel biomarker proteins in chronic lymphocytic leukemia (CLL) that can impact diagnosis, treatment and prognosis by comparing the protein expression profiles of peripheral blood mononuclear cells from CLL patients and healthy donors using specific antibodies, mass spectrometry and binary logistic regression analyses and other bioinformatics tools. Mass spectrometry (LC-HR-MS/MS) analysis identified 1,360 proteins whose expression levels were modified in CLL-derived lymphocytes. Some of these proteins were previously connected to different cancer types, including CLL, while four other highly expressed proteins were not previously reported to be associated with cancer, and here, for the first time, DDX46 and AK3 are linked to CLL. Down-regulation expression of two of these proteins resulted in cell growth inhibition. High DDX46 expression levels were associated with shorter survival of CLL patients and thus can serve as a prognosis marker. The proteins with modified expression include proteins involved in RNA splicing and translation and particularly mitochondrial proteins involved in apoptosis and metabolism. Thus, we focused on several metabolism- and apoptosis-modulating proteins, particularly on the voltage-dependent anion channel 1 (VDAC1), regulating both metabolism and apoptosis. Expression levels of Bcl-2, VDAC1, MAVS, AIF and SMAC/Diablo were markedly increased in CLL-derived lymphocytes. VDAC1 levels were highly correlated with the amount of CLL-cancerous CD19+/CD5+ cells and with the levels of all other apoptosis-modulating proteins tested. Binary logistic regression analysis demonstrated the ability to predict probability of disease with over 90% accuracy. Finally, based on the changes in the levels of several proteins in CLL patients, as revealed from LC-HR-MS/MS, we could distinguish between patients in a stable disease state and those who would be later transferred to anti-cancer treatments. The over-expressed proteins can thus serve as potential biomarkers for early diagnosis, prognosis, new targets for CLL therapy, and treatment guidance of CLL, forming the basis for personalized therapy.
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MESH Headings
- Aged
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Blotting, Western
- Chromatography, Liquid
- Female
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukocytes, Mononuclear/metabolism
- Male
- Prognosis
- Proteome/analysis
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Tandem Mass Spectrometry/methods
- Tumor Cells, Cultured
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Affiliation(s)
- Lee Admoni-Elisha
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Itay Nakdimon
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anna Shteinfer
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tal Prezma
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tasleem Arif
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Nir Arbel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anna Melkov
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ori Zelichov
- Department of Hematology, Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Itai Levi
- Department of Hematology, Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Varda Shoshan-Barmatz
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
- * E-mail:
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19
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Sanford T, Porten S, Meng MV. Molecular Analysis of Upper Tract and Bladder Urothelial Carcinoma: Results from a Microarray Comparison. PLoS One 2015; 10:e0137141. [PMID: 26317352 PMCID: PMC4552875 DOI: 10.1371/journal.pone.0137141] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/12/2015] [Indexed: 11/18/2022] Open
Abstract
Introduction Prior studies have shown genetic similarities between upper tract and bladder urothelial carcinoma. However, upper tract urothelial carcinoma tends to be higher grade than bladder urothelial carcinoma and tends to form in patients with certain familial conditions (e.g. Lynch Syndrome), indicating there may be unique biologic processes in these tumors. The purpose of this study was to evaluate the differences in gene expression between upper tract and bladder urothelial carcinoma using microarray data. Design, Setting, Participants A search of publicly available microarray datasets identified a clinically annotated dataset of 12 upper tract and 20 bladder urothelial carcinoma specimens. Gene expression analysis of data derived from the Affymetrix HGU133Plus2 chip was performed. Bioconductor packages were used to evaluate clustering, differential gene expression, pathways relevant to oncology, and a basal/luminal signature in upper tract versus bladder urothelial carcinoma. Results When separated by pathologic T stage, there was evidence of differential clustering among pT3 tumors and significant gene expression differences in 81 genes. Pathway analysis revealed differences in HGF and TNF signaling pathways. Upper tract tumors tended to have high expression of genes associated with a luminal subtype. One of the genes most highly expressed in upper tract tumors, SLITRK6, is the target of an antibody drug conjugate (AGS15E) currently in phase I clinical trials. Conclusions This study provides evidence for molecular differences between upper tract and bladder urothelial carcinoma, some of which contribute to oncologic-relevant pathways. Upper tract tumors tended to express genes consistent with a luminal subtype. We also identify a marker, SLITRK6, as a potential target for patients with advanced upper tract urothelial carcinoma.
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Affiliation(s)
- Thomas Sanford
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Sima Porten
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
| | - Maxwell V Meng
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
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20
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Molecular events in muscle-invasive bladder cancer development. Bladder Cancer 2015. [DOI: 10.1002/9781118674826.ch29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Gene expression patterns combined with network analysis identify hub genes associated with bladder cancer. Comput Biol Chem 2015; 56:71-83. [DOI: 10.1016/j.compbiolchem.2015.04.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 04/03/2015] [Accepted: 04/03/2015] [Indexed: 02/06/2023]
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22
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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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Abstract
Classic as well as more recent large-scale genomic analyses have uncovered multiple genes and pathways important for bladder cancer development. Genes involved in cell-cycle control, chromatin regulation, and receptor tyrosine and PI3 kinase-mammalian target of rapamycin signaling pathways are commonly mutated in muscle-invasive bladder cancer. Expression-based analyses have identified distinct types of bladder cancer that are similar to subsets of breast cancer, and have prognostic and therapeutic significance. These observations are leading to novel therapeutic approaches in bladder cancer, providing optimism for therapeutic progress.
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Affiliation(s)
- William Martin-Doyle
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02115, USA.
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Kobayashi T, Owczarek TB, McKiernan JM, Abate-Shen C. Modelling bladder cancer in mice: opportunities and challenges. Nat Rev Cancer 2015; 15:42-54. [PMID: 25533675 PMCID: PMC4386904 DOI: 10.1038/nrc3858] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The prognosis and treatment of bladder cancer have improved little in the past 20 years. Bladder cancer remains a debilitating and often fatal disease, and is among the most costly cancers to treat. The generation of informative mouse models has the potential to improve our understanding of bladder cancer progression, as well as to affect its diagnosis and treatment. However, relatively few mouse models of bladder cancer have been described, and in particular, few that develop invasive cancer phenotypes. This Review focuses on opportunities for improving the landscape of mouse models of bladder cancer.
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Affiliation(s)
- Takashi Kobayashi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Tomasz B Owczarek
- 1] Department of Urology, Columbia University Medical Center. [2] Institute of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York 10032, USA
| | | | - Cory Abate-Shen
- 1] Department of Urology, Columbia University Medical Center. [2] Institute of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York 10032, USA. [3] Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA. [4] Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, USA
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Greife A, Knievel J, Ribarska T, Niegisch G, Schulz WA. Concomitant downregulation of the imprinted genes DLK1 and MEG3 at 14q32.2 by epigenetic mechanisms in urothelial carcinoma. Clin Epigenetics 2014; 6:29. [PMID: 25741387 PMCID: PMC4348104 DOI: 10.1186/1868-7083-6-29] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/07/2014] [Indexed: 01/01/2023] Open
Abstract
Background The two oppositely imprinted and expressed genes, DLK1 and MEG3, are located in the same gene cluster at 14q32. Previous studies in bladder cancer have suggested that tumor suppressor genes are located in this region, but these have not been identified. Results We observed that both DLK1 and MEG3 are frequently silenced in urothelial cancer tissues and cell lines. The concomitant downregulation of the two genes is difficult to explain by known mechanisms for inactivating imprinted genes, namely deletion of active alleles or epitype switching. Indeed, quantitative PCR revealed more frequent copy number gains than losses in the gene cluster that were, moreover, consistent within each sample, excluding gene losses as the cause of downregulation. Instead, we observed distinctive epigenetic alterations at the three regions controlling DLK1 and MEG3 expression, namely the DLK1 promoter; the intergenic (IG) and MEG3 differentially methylated regions (DMRs). Bisulfite sequencing and pyrosequencing revealed novel patterns of DNA methylation in tumor cells, which were distinct from that of either paternal allele. Furthermore, chromatin immunoprecipitation demonstrated loss of active and gain of repressive histone modifications at all regulatory sequences. Conclusions Our data support the idea that the main cause of the prevalent downregulation of DLK1 and MEG3 in urothelial carcinoma is epigenetic silencing across the 14q32 imprinted gene cluster, resulting in the unusual concomitant inactivation of oppositely expressed and imprinted genes. Electronic supplementary material The online version of this article (doi:10.1186/1868-7083-6-29) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Annemarie Greife
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Judith Knievel
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Teodora Ribarska
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
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26
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Conconi D, Panzeri E, Redaelli S, Bovo G, Viganò P, Strada G, Dalprà L, Bentivegna A. Chromosomal imbalances in human bladder urothelial carcinoma: similarities and differences between biopsy samples and cancer stem-like cells. BMC Cancer 2014; 14:646. [PMID: 25178926 PMCID: PMC4162911 DOI: 10.1186/1471-2407-14-646] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The existence of two distinct groups of tumors with different clinical characteristic is a remarkable feature of transitional cell carcinomas (TCCs) of the bladder. More than 70% are low-grade (LG) non-infiltrating (NI) cancers at diagnosis, but 60-80% of them recur at least one time and 10-20% progress in stage and grade. On the other hand, about 20% of tumors show muscle invasion (IN) and have a poor prognosis with <50% survival after 5 years. This study focuses on the complexity of the bladder cancer genome, and for the first time to our knowledge, on the possibility to compare genomic alterations of in vitro selected cancer stem-like cells (CSCs), and their original biopsy in order to identify different genomic signature already present in the early stages of tumorigenesis of LG and HG tumors. METHODS We initially used conventional chromosome analysis on TCC biopsies with different histotypes (LG vs HG) in order to detect rough differences between them. Then, we performed array comparative genomic hybridization (aCGH) on 10 HG and 10 LG tumors providing an overview of copy number alterations (CNAs). Finally, we made a comparison of the overall CNAs in 16 biopsies and their respective CSCs isolated from them. RESULTS Our findings indicate that LG and HG bladder cancer differ with regard to their genomic profile even in the early stage of tumorigenesis; moreover, we identified a subgroup of LG samples with a higher tendency to lose genomic regions which could represent a more aggressive phenotype. CONCLUSIONS The outcomes not only provide valuable information to deeper studying TCC carcinogenesis, but also could help in the clinic for diagnosis and prognosis of patients who will benefit from a more aggressive therapy.
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Affiliation(s)
| | | | | | | | | | | | | | - Angela Bentivegna
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, via Cadore 48, 20052 Monza, Italy.
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27
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Scaravilli M, Asero P, Tammela TLJ, Visakorpi T, Saramäki OR. Mapping of the chromosomal amplification 1p21-22 in bladder cancer. BMC Res Notes 2014; 7:547. [PMID: 25135188 PMCID: PMC4143550 DOI: 10.1186/1756-0500-7-547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 07/25/2014] [Indexed: 11/24/2022] Open
Abstract
Background The aim of the study was to characterize a recurrent amplification at chromosomal region 1p21-22 in bladder cancer. Methods ArrayCGH (aCGH) was performed to identify DNA copy number variations in 7 clinical samples and 6 bladder cancer cell lines. FISH was used to map the amplicon at 1p21-22 in the cell lines. Gene expression microarrays and qRT-PCR were used to study the expression of putative target genes in the region. Results aCGH identified an amplification at 1p21-22 in 10/13 (77%) samples. The minimal region of the amplification was mapped to a region of about 1 Mb in size, containing a total of 11 known genes. The highest amplification was found in SCaBER squamous cell carcinoma cell line. Four genes, TMED5, DR1, RPL5 and EVI5, showed significant overexpression in the SCaBER cell line compared to all the other samples tested. Oncomine database analysis revealed upregulation of DR1 in superficial and infiltrating bladder cancer samples, compared to normal bladder. Conclusions In conclusions, we have identified and mapped chromosomal amplification at 1p21-22 in bladder cancer as well as studied the expression of the genes in the region. DR1 was found to be significantly overexpressed in the SCaBER, which is a model of squamous cell carcinoma. However, the overexpression was found also in a published clinical sample cohort of superficial and infiltrating bladder cancers. Further studies with more clinical material are needed to investigate the role of the amplification at 1p21-22.
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Affiliation(s)
| | | | | | | | - Outi R Saramäki
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology - BioMediTech, University of Tampere and Tampere University Hospital, Tampere, Finland.
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28
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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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Gurung PMS, Veerakumarasivam A, Williamson M, Counsell N, Douglas J, Tan WS, Feber A, Crabb SJ, Short SC, Freeman A, Powles T, Hoskin PJ, West CM, Kelly JD. Loss of expression of the tumour suppressor gene AIMP3 predicts survival following radiotherapy in muscle-invasive bladder cancer. Int J Cancer 2014; 136:709-20. [PMID: 24917520 DOI: 10.1002/ijc.29022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 05/05/2014] [Accepted: 05/08/2014] [Indexed: 11/10/2022]
Abstract
The aim of this study was to test the utility of AIMP3, an upstream regulator of DNA damage response following genotoxic stress, as a clinical biomarker in muscle-invasive bladder cancer (MIBC). AIMP3 was identified from a meta-analysis of a global gene-expression dataset. AIMP3 protein expression was determined by immunohistochemistry on a customised bladder cancer tissue-microarray (TMA). The mechanism of gene silencing was probed using methylation-specific PCR. The association between AIMP3 expression, Tp53 transactivity and genomic stability was analysed. In vitro AIMP3 translocation to the nucleus in response to ionising radiation was demonstrated using immunofluorescence. Radiosensitisation effects of siRNA-mediated AIMP3-knockdown were measured using colony forming assays. TMAs derived from patients enrolled in BCON, a Phase III multicentre radiotherapy trial in bladder cancer (ISRCTN45938399) were used to evaluate the association between AIMP3 expression and survival. The prognostic value of AIMP3 expression was determined in a TMA derived from patients treated by radical cystectomy. Loss of AIMP3 expression was frequent in MIBC and associated with impaired Tp53 transactivity and genomic instability. AIMP3-knockdown was associated with an increase in radioresistance. Loss of AIMP3 expression was associated with survival in MIBC patients following radiotherapy (HR = 0.53; 95% CI: 0.36 to 0.78, p = 0.002) but was not prognostic in the cystectomy set. In conclusion, AIMP3 expression is lost in a subset of bladder cancers and is significantly predictive of survival following radiotherapy in MIBC patients.
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Affiliation(s)
- Pratik M S Gurung
- Division of Surgery and Interventional Science, University College London (UCL), London, United Kingdom
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30
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Magbanua MJM, Roy R, Sosa EV, Hauranieh L, Kablanian A, Eisenbud LE, Ryazantsev A, Au A, Scott JH, Melisko M, Park JW. Genome-wide copy number analysis of cerebrospinal fluid tumor cells and their corresponding archival primary tumors. GENOMICS DATA 2014; 2:60-2. [PMID: 26484071 PMCID: PMC4535622 DOI: 10.1016/j.gdata.2014.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/02/2014] [Indexed: 11/10/2022]
Abstract
A debilitating complication of breast cancer is the metastatic spread of tumor cells to the leptomeninges or cerebrospinal fluid (CSF). Patients diagnosed with this aggressive clinical syndrome, known as leptomeningeal carcinomatosis, have very poor prognosis. Despite improvements in detecting cerebrospinal fluid tumor cells (CSFTCs), information regarding their molecular biology is extremely limited. In our recent work, we utilized a protocol previously used for circulating tumor cell isolation to purify tumor cells from the CSF. We then performed genomic characterization of CSFTCs as well as archival tumors from the same patient. Here, we describe the microarray data and quality controls associated with our study published in the Cancer Research journal in 2013 [1]. We also provide an R script containing code for quality control of microarray data and assessment of copy number calls. The microarray data has been deposited into Gene Expression Omnibus under accession # GSE46068.
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Affiliation(s)
- Mark Jesus M Magbanua
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA ; Helen Diller Family Comprehensive Cancer Center Computational Biology Core, University of California San Francisco, San Francisco, California, USA
| | - Eduardo V Sosa
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Louai Hauranieh
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Andrea Kablanian
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Lauren E Eisenbud
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Artem Ryazantsev
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Alfred Au
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Janet H Scott
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Michelle Melisko
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - John W Park
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
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Chaturvedi N, de Menezes RX, Goeman JJ. Fused lasso algorithm for Cox' proportional hazards and binomial logit models with application to copy number profiles. Biom J 2014; 56:477-92. [PMID: 24496763 DOI: 10.1002/bimj.201200241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 10/15/2013] [Accepted: 10/19/2013] [Indexed: 11/09/2022]
Abstract
This paper presents an efficient algorithm based on the combination of Newton Raphson and Gradient Ascent, for using the fused lasso regression method to construct a genome-based classifier. The characteristic structure of copy number data suggests that feature selection should take genomic location into account for producing more interpretable results for genome-based classifiers. The fused lasso penalty, an extension of the lasso penalty, encourages sparsity of the coefficients and their differences by penalizing the L1-norm for both of them at the same time, thus using genomic location. The major advantage of the algorithm over other existing fused lasso optimization techniques is its ability to predict binomial as well as survival response efficiently. We apply our algorithm to two publicly available datasets in order to predict survival and binary outcomes.
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Affiliation(s)
- Nimisha Chaturvedi
- Epidemiology and Biostatistics, Vrije Universiteit Medical Center, Amsterdam, The Netherlands; Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
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Riester M, Werner L, Bellmunt J, Selvarajah S, Guancial EA, Weir BA, Stack EC, Park RS, O'Brien R, Schutz FAB, Choueiri TK, Signoretti S, Lloreta J, Marchionni L, Gallardo E, Rojo F, Garcia DI, Chekaluk Y, Kwiatkowski DJ, Bochner BH, Hahn WC, Ligon AH, Barletta JA, Loda M, Berman DM, Kantoff PW, Michor F, Rosenberg JE. Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma. Clin Cancer Res 2014; 20:1873-83. [PMID: 24486590 DOI: 10.1158/1078-0432.ccr-13-0759] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE Metastatic urothelial carcinoma of the bladder is associated with multiple somatic copy-number alterations (SCNAs). We evaluated SCNAs to identify predictors of poor survival in patients with metastatic urothelial carcinoma treated with platinum-based chemotherapy. EXPERIMENTAL DESIGN We obtained overall survival (OS) and array DNA copy-number data from patients with metastatic urothelial carcinoma in two cohorts. Associations between recurrent SCNAs and OS were determined by a Cox proportional hazard model adjusting for performance status and visceral disease. mRNA expression was evaluated for potential candidate genes by NanoString nCounter to identify transcripts from the region that are associated with copy-number gain. In addition, expression data from an independent cohort were used to identify candidate genes. RESULTS Multiple areas of recurrent significant gains and losses were identified. Gain of 1q23.3 was independently associated with a shortened OS in both cohorts [adjusted HR, 2.96; 95% confidence interval (CI), 1.35-6.48; P = 0.01 and adjusted HR, 5.03; 95% CI, 1.43-17.73; P < 0.001]. The F11R, PFDN2, PPOX, USP21, and DEDD genes, all located on 1q23.3, were closely associated with poor outcome. CONCLUSIONS 1q23.3 copy-number gain displayed association with poor survival in two cohorts of metastatic urothelial carcinoma. The identification of the target of this copy-number gain is ongoing, and exploration of this finding in other disease states may be useful for the early identification of patients with poor-risk urothelial carcinoma. Prospective validation of the survival association is necessary to demonstrate clinical relevance.
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Affiliation(s)
- Markus Riester
- Authors' Affiliations: Departments of Biostatistics and Computational Biology, and Medical Oncology; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute; Department of Biostatistics, Harvard School of Public Health; Department of Pathology; Translational Medicine Division, Brigham and Women's Hospital, Boston; Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Sidney Kimmel Cancer Center; Department of Pathology, Johns Hopkins University, Baltimore, Maryland; Department of Urology, Memorial Sloan-Kettering Cancer Center, New York, New York; and Hospital del Mar Research Institute-IMIM, Barcelona; and Hospital Parc Tauli, Sabadell, Spain
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Pinto-Leite R, Carreira I, Melo J, Ferreira SI, Ribeiro I, Ferreira J, Filipe M, Bernardo C, Arantes-Rodrigues R, Oliveira P, Santos L. Genomic characterization of three urinary bladder cancer cell lines: understanding genomic types of urinary bladder cancer. Tumour Biol 2014; 35:4599-617. [PMID: 24459064 DOI: 10.1007/s13277-013-1604-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 12/30/2013] [Indexed: 11/25/2022] Open
Abstract
Several genomic regions are frequently altered and associated with the type, stage and progression of urinary bladder cancer (UBC). We present the characterization of 5637, T24 and HT1376 UBC cell lines by karyotyping, fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) analysis. Some cytogenetic anomalies present in UBC were found in the three cell lines, such as chromosome 20 aneuploidy and the loss of 9p21. Some gene loci losses (e.g. CDKN2A) and gains (e.g. HRAS, BCL2L1 and PTPN1) were coincident across all cell lines. Although some significant heterogeneity and complexity were detected between them, their genomic profiles exhibited a similar pattern to UBC. We suggest that 5637 and HT1376 represent the E2F3/RB1 pathway due to amplification of 6p22.3, concomitant with loss of one copy of RB1 and mutation of the remaining copy. The HT1376 presented a 10q deletion involving PTEN region and no alteration of PIK3CA region which, in combination with the inactivation of TP53, bears more invasive and metastatic properties than 5637. The T24 belongs to the alternative pathway of FGFR3/CCND1 by presenting mutated HRAS and over-represented CCND1. These cell lines cover the more frequent subtypes of UBC and are reliable models that can be used, as a group, in preclinical studies.
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Affiliation(s)
- Rosário Pinto-Leite
- Cytogenetic Laboratory, Department of Human Genetics, Hospital Center of Trás-os-Montes and Alto Douro, Vila Real, Portugal
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Brito I, Hupé P, Neuvial P, Barillot E. Stability-based comparison of class discovery methods for DNA copy number profiles. PLoS One 2013; 8:e81458. [PMID: 24339933 PMCID: PMC3855312 DOI: 10.1371/journal.pone.0081458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 10/22/2013] [Indexed: 11/19/2022] Open
Abstract
MOTIVATION Array-CGH can be used to determine DNA copy number, imbalances in which are a fundamental factor in the genesis and progression of tumors. The discovery of classes with similar patterns of array-CGH profiles therefore adds to our understanding of cancer and the treatment of patients. Various input data representations for array-CGH, dissimilarity measures between tumor samples and clustering algorithms may be used for this purpose. The choice between procedures is often difficult. An evaluation procedure is therefore required to select the best class discovery method (combination of one input data representation, one dissimilarity measure and one clustering algorithm) for array-CGH. Robustness of the resulting classes is a common requirement, but no stability-based comparison of class discovery methods for array-CGH profiles has ever been reported. RESULTS We applied several class discovery methods and evaluated the stability of their solutions, with a modified version of Bertoni's [Formula: see text]-based test [1]. Our version relaxes the assumption of independency required by original Bertoni's [Formula: see text]-based test. We conclude that Minimal Regions of alteration (a concept introduced by [2]) for input data representation, sim [3] or agree [4] for dissimilarity measure and the use of average group distance in the clustering algorithm produce the most robust classes of array-CGH profiles. AVAILABILITY The software is available from http://bioinfo.curie.fr/projects/cgh-clustering. It has also been partly integrated into "Visualization and analysis of array-CGH"(VAMP)[5]. The data sets used are publicly available from ACTuDB [6].
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Affiliation(s)
- Isabel Brito
- Institut Curie, Paris, France
- INSERM, U900, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Philippe Hupé
- Institut Curie, Paris, France
- INSERM, U900, Paris, France
- Mines ParisTech, Fontainebleau, France
- CNRS UMR144, Paris, France
| | - Pierre Neuvial
- Laboratoire Statistique & Génome, Université d′Évry Val d′Essonne, UMR CNRS 8071-USC INRA, Évry, France
| | - Emmanuel Barillot
- Institut Curie, Paris, France
- INSERM, U900, Paris, France
- Mines ParisTech, Fontainebleau, France
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Magbanua MJM, Melisko M, Roy R, Sosa EV, Hauranieh L, Kablanian A, Eisenbud LE, Ryazantsev A, Au A, Scott JH, Park JW. Molecular profiling of tumor cells in cerebrospinal fluid and matched primary tumors from metastatic breast cancer patients with leptomeningeal carcinomatosis. Cancer Res 2013; 73:7134-43. [PMID: 24142343 DOI: 10.1158/0008-5472.can-13-2051] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although leptomeningeal carcinomatosis is a well-established clinical syndrome, virtually nothing is known about the tumor cells responsible for this particularly aggressive metastatic process. To isolate cerebrospinal fluid-derived tumor cells (CSFTC) from 15 patients with metastatic breast cancer diagnosed with leptomeningeal carcinomatosis, CSF samples were subjected to a two-step method involving immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS), a technique previously used for isolating circulating tumor cells (CTC) from blood. CSFTCs were subjected to genome-wide copy number analysis by array comparative genomic hybridization. Genomic profiling was successfully performed for 13 of 15 patients (87%). Copy number analysis in CSFTCs revealed genomic alterations commonly observed in primary breast cancer and CTCs, indicating their malignant origin. Interestingly, 12 (92%) harbored high-level gains on the 8q24 locus, which includes the MYC oncogene. Comparison of CSFTCs against corresponding archival primary tumors in six patients revealed clonal relationships with some divergence. Good concordance among serial samples attested to the reproducibility of the assay. Our approach for isolation and molecular analysis of CSFTCs yielded new insights into the molecular nature of these cells. Further genomic and functional analyses may help elucidate mechanisms by which tumor cells metastasize to the central nervous system.
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Affiliation(s)
- Mark Jesus M Magbanua
- Authors' Affiliations: Division of Hematology/Oncology; Helen Diller Family Comprehensive Cancer Center; and Helen Diller Family Comprehensive Cancer Center Computational Biology Core, University of California San Francisco, San Francisco, California
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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: 198] [Impact Index Per Article: 18.0] [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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Rosser CJ, Urquidi V, Goodison S. Urinary biomarkers of bladder cancer: an update and future perspectives. Biomark Med 2013; 7:779-90. [DOI: 10.2217/bmm.13.73] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bladder cancer is one of the most prevalent cancers worldwide. Early detection of bladder tumors is critical for improved patient outcomes. The standard method for detection and surveillance of bladder tumors is cystoscopy with urinary cytology. Limitations of cystoscopy and urinary cytology have brought to light the need for more robust diagnostic assays. Ideally, such assays would be applicable to noninvasively obtained, voided urine, and be designed not only for diagnosis, but also for monitoring disease recurrence and response to therapy. Consequently, the development of a noninvasive urine-based assay would be of tremendous benefit to both patients and healthcare systems. This article reports some of the more prominent urine-based biomarkers reported in the literature. In addition, some new technologies that have been used to identify novel urinary biomarkers are highlighted.
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Affiliation(s)
- Charles J Rosser
- Department of Urology, University of Central Florida College of Medicine, Orlando, FL 32527, USA
- Nonagen Bioscience Corporation, Orlando, FL 32527, USA
| | - Virginia Urquidi
- Nonagen Bioscience Corporation, Orlando, FL 32527, USA
- Cancer Research Institute, MD Anderson Cancer Center Orlando, Orlando, FL 32527, USA
| | - Steve Goodison
- Nonagen Bioscience Corporation, Orlando, FL 32527, USA
- Cancer Research Institute, MD Anderson Cancer Center Orlando, Orlando, FL 32527, USA
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Sharron Lin X, Hu L, Sandy K, Correll M, Quackenbush J, Wu CL, Scott McDougal W. Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens. Urol Oncol 2013; 32:327-36. [PMID: 24055427 DOI: 10.1016/j.urolonc.2013.06.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/25/2013] [Accepted: 06/25/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To identify gene signatures in transitional cell carcinoma that can differentiate high-grade T1 nonprogressive (T1NP) bladder cancer (BCa) from those T1 progressive (T1P) tumors that progress to muscularis propria-invasive T2 tumors. MATERIALS AND METHODS We performed a high-throughput RNA sequencing (RNA-Seq) on formalin-fixed and paraffin-embedded BCa specimens with clinical pathologic characteristics best representing the general clinical development of the disease. For the T1NP group, only patients with long-term follow-up (6-17y) and periodic examinations (average of 4 resections and 9 cytology tests) were selected. For the T1P group, only patients in whom a complete resection was performed after a minimum of 8 months after the initial T1 diagnosis were selected, therefore eliminating the possibility of underdiagnosis. Only samples in which muscularis propria was present and uninvolved were included, further assuring a correct diagnosis. The RNA-Seq reads were mapped to the human genome build NCBI 36 (hg18) using TopHat with no mismatch. After alignment to the transcriptome and expression quantification, a linear statistical model was built using Limma between T1NP and T1P samples to identify differentially expressed genes. RESULTS Overall, 5,561 genes were mapped to all samples and used for RNA-Seq analysis to identify a gene signature that was significantly and differentially expressed between patients with T1NP BCa and patients with T1P BCa. Signature-based stratification indicated the gene signature correlated notably with the time of T1 development to T2 tumor, suggesting that the molecular signature might be used as an independent predictor for the pace of high-grade T1 BCa progression. CONCLUSIONS This is the first demonstration that RNA-Seq can be applied as a powerful tool to study BCa using formalin-fixed and paraffin-embedded specimens. We identified a gene signature that can distinguish patients diagnosed with high-grade T1 BCas that remain as non-muscle invasive tumors from those patients with cancers progressing to muscle-invasive tumors. Our findings will make future large-scale clinical cohort studies and clinical trial-based studies possible and help the development of prognostic tools for accurate prediction of T1 BCa progression that may considerably influence the clinical decision-making process, treatment regimen, and patient survival.
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Affiliation(s)
- Xuanhui Sharron Lin
- Department of Urology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Lan Hu
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Kirley Sandy
- Department of Urology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Mick Correll
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital and Harvard Medical School, Boston, MA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA.
| | - William Scott McDougal
- Department of Urology, Massachusetts General Hospital and Harvard Medical School, Boston, MA.
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Cordes I, Kluth M, Zygis D, Rink M, Chun F, Eichelberg C, Dahlem R, Fisch M, Höppner W, Wagner W, Doh O, Terracciano L, Simon R, Wilczak W, Sauter G, Minner S. PTEN deletions are related to disease progression and unfavourable prognosis in early bladder cancer. Histopathology 2013; 63:670-7. [PMID: 24004025 DOI: 10.1111/his.12209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/15/2013] [Indexed: 01/16/2023]
Abstract
AIMS This study aimed to determine the prevalence and clinical significance of deletions of the tumour suppressor gene PTEN in bladder cancer. METHODS AND RESULTS A tissue microarray with 686 bladder cancers was analysed for PTEN deletions by fluorescence in-situ hybridization. PTEN mutations were analysed in nine tumours with heterozygous PTEN deletion. Heterozygous PTEN deletions were present in 16.5% of tumours and were associated with grade (P = 0.0024) and p53 status (P = 0.0141), but not linked to stage (P = 0.0965). PTEN deletions were seen in 5.8% of pTaG1, 10.9% of pTaG2, 29.0% of pTaG3, 16.7% of pT1G2, 22.2% of pT1G3, 17.7% of pT2-4G2 and 20.9% of pT2-4G3 tumours (P = 0.0235). PTEN deletions were associated significantly with recurrences in pTa tumours (P = 0.0173), progression in pT1 tumours (P = 0.0016), but not with overall or cancer-specific survival in pT2 tumours. Multivariate analyses including grade and PTEN deletions revealed that PTEN deletions but not grade were associated independently with recurrence in pTa tumours (P = 0.0377) and progression in pT1 tumours (P = 0.0030). No inactivating PTEN mutations were found. CONCLUSIONS PTEN is linked to aggressive tumour phenotype and to unfavourable outcome in early bladder cancer. Heterozygous PTEN loss, i.e. reduced PTEN gene dosage, might be sufficient to cause aggressive tumour behaviour in bladder cancer cells.
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Affiliation(s)
- Inga Cordes
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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López V, González-Peramato P, Suela J, Serrano A, Algaba F, Cigudosa JC, Vidal A, Bellmunt J, Heredero O, Sánchez-Carbayo M. Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA. J Transl Med 2013; 11:182. [PMID: 23914742 PMCID: PMC3750577 DOI: 10.1186/1479-5876-11-182] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Array-CGH represents a comprehensive tool to discover genomic disease alterations that could potentially be applied to body fluids. In this report, we aimed at applying array-CGH to urinary samples to characterize bladder cancer. METHODS Urinary DNA from bladder cancer patients and controls were hybridized on 44K oligonucleotide arrays. Validation analyses of identified regions and candidates included fluorescent in situ hybridization (FISH) and immunohistochemistry in an independent set of bladder tumors spotted on custom-made tissue arrays (n = 181). RESULTS Quality control of array-CGH provided high reproducibility in dilution experiments and when comparing reference pools. The most frequent genomic alterations (minimal recurrent regions) among bladder cancer urinary specimens included gains at 1q and 5p, and losses at 10p and 11p. Supervised hierarchical clustering identified the gain at 1q23.3-q24.1 significantly correlated to stage (p = 0.011), and grade (p = 0.002). The amplification and overexpression of Prefoldin (PFND2), a selected candidate mapping to 1q23.3-q24.1, correlated to increasing stage and tumor grade by means of custom-designed and optimized FISH (p = 0.013 and p = 0.023, respectively), and immunohistochemistry (p ≤0.0005 and p = 0.011, respectively), in an independent set of bladder tumors included in tissue arrays. Moreover, PFND2 overexpression was significantly associated with poor disease-specific survival (p ≤0.0005). PFND2 was amplified and overexpressed in bladder tumors belonging to patients providing urinary specimens where 1q23.3q24.1 amplification was detected by array-CGH. CONCLUSIONS Genomic profiles of urinary DNA mirrowed bladder tumors. Molecular profiling of urinary DNA using array-CGH contributed to further characterize genomic alterations involved in bladder cancer progression. PFND2 was identified as a tumor stratification and clinical outcome prognostic biomarker for bladder cancer patients.
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Affiliation(s)
- Virginia López
- Tumor Markers Group, Molecular Pathology Program, Spanish National Cancer Center, Melchor Fernandez Almagro 3, Madrid E-28029, Spain
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Abstract
The development of array comparative genomic hybridization (aCGH) techniques has allowed to characterize more precisely several human neoplasms with the aim of providing prognostic markers and targets for directed therapeutic intervention. Recently, several studies applying aCGH technique have been reported in which an exhaustive genetic characterization of mycosis fungoides (MF) and Sézary syndrome (SS) has been performed. Regarding MF, a genomic profile characterized by the gains of 7q, 17q, and 8q and losses in 9p, 13q, 17p, and 10q has been described. In SS, the most common abnormalities are gains in 8q and 17q and losses at 17p and 10q. One of the main contributions of the aCGH studies in MF and SS has been the description of genetic markers associated with a poor prognosis. In MF, three specific chromosomal regions, 9p21.3 (CDKN2A, CDKN2B, and MTAP), 8q24.21 (MYC), and 10q26qter (MGMT and EBF3) have been defined as prognostic markers exhibiting a significant correlation with overall survival (P = 0.042, P = 0.017, and P = 0.022, respectively). Moreover, two MF genomic subgroups have been described, distinguishing a stable group (0-5 DNA aberrations) and an unstable group (>5 DNA aberrations), showing that the genomic unstable group had a shorter overall survival (P = 0.05).
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Affiliation(s)
- Blanca Espinet
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain.
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Chism DD, Woods ME, Milowsky MI. Neoadjuvant paradigm for accelerated drug development: an ideal model in bladder cancer. Oncologist 2013; 18:933-40. [PMID: 23883869 DOI: 10.1634/theoncologist.2013-0023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Neoadjuvant cisplatin-based combination chemotherapy for muscle-invasive bladder cancer (MIBC) has been shown to confer a survival advantage in two randomized clinical trials and a meta-analysis. Despite level 1 evidence supporting its benefit, utilization remains dismal with nearly one-half of patients ineligible for cisplatin-based therapy because of renal dysfunction, impaired performance status, and/or coexisting medical problems. This situation highlights the need for the development of novel therapies for the management of MIBC, a disease with a lethal phenotype. The neoadjuvant paradigm in bladder cancer offers many advantages for accelerated drug development. First, there is a greater likelihood of successful therapy at an earlier disease state that may be characterized by less genomic instability compared with the metastatic setting, with an early readout of activity with results determined in months rather than years. Second, pre- and post-treatment tumor tissue collection in patients with MIBC is performed as the standard of care without the need for research-directed biopsies, allowing for the ability to perform important correlative studies and to monitor tumor response to therapy in "real time." Third, pathological complete response (pT0) predicts for improved outcome in patients with MIBC. Fourth, there is a strong biological rationale with rapidly accumulating evidence for actionable targets in bladder cancer. This review focuses on the neoadjuvant paradigm for accelerated drug development using bladder cancer as the ideal model.
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Affiliation(s)
- David D Chism
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA
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Eriksson P, Aine M, Sjödahl G, Staaf J, Lindgren D, Höglund M. Detailed Analysis of Focal Chromosome Arm 1q and 6p Amplifications in Urothelial Carcinoma Reveals Complex Genomic Events on 1q, and SOX4 as a Possible Auxiliary Target on 6p. PLoS One 2013; 8:e67222. [PMID: 23825644 PMCID: PMC3688975 DOI: 10.1371/journal.pone.0067222] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 05/20/2013] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Urothelial carcinoma shows frequent amplifications at 6p22 and 1q21-24. The main target gene at 6p22 is believed to be E2F3, frequently co-amplified with CDKAL1 and SOX4. There are however reports on 6p22 amplifications that do not include E2F3. Previous analyses have identified frequent aberrations occurring at 1q21-24. However, due to complex rearrangements it has been difficult to identify specific 1q21-24 target regions and genes. METHODS We selected 29 cases with 6p and 37 cases with 1q focal genomic amplifications from 261 cases of urothelial carcinoma analyzed by array-CGH for high resolution zoom-in oligonucleotide array analyses. Genomic analyses were combined with gene expression data and genomic sequence analyses to characterize and fine map 6p22 and 1q21-24 amplifications. RESULTS We show that the most frequently amplified gene at 6p22 is SOX4 and that SOX4 can be amplified and overexpressed without the E2F3 or CDKAL1 genes being included in the amplicon. Hence, our data point to SOX4 as an auxiliary amplification target at 6p22. We further show that at least three amplified regions are observed at 1q21-24. Copy number data, combined with gene expression data, highlighted BCL9 and CHD1L as possible targets in the most proximal region and MCL1, SETDB1, and HIF1B as putative targets in the middle region, whereas no obvious targets could be determined in the most distal amplicon. We highlight enrichment of G4 quadruplex sequence motifs and a high number of intraregional sequence duplications, both known to contribute to genomic instability, as prominent features of the 1q21-24 region. CONCLUSIONS Our detailed analyses of the 6p22 amplicon suggest SOX4 as an auxiliary target gene for amplification. We further demonstrate three separate target regions for amplification at 1q21-24 and identified BCL9, CHD1L, and MCL1, SETDB1, and HIF1B as putative target genes within these regions.
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Affiliation(s)
- Pontus Eriksson
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
| | - Mattias Aine
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
| | - Gottfrid Sjödahl
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
| | - Johan Staaf
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - David Lindgren
- Center for Molecular Pathology, Department of Laboratory Medicine, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Mattias Höglund
- Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund Sweden
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Chekaluk Y, Wu CL, Rosenberg J, Riester M, Dai Q, Lin S, Guo Y, McDougal WS, Kwiatkowski DJ. Identification of nine genomic regions of amplification in urothelial carcinoma, correlation with stage, and potential prognostic and therapeutic value. PLoS One 2013; 8:e60927. [PMID: 23593348 PMCID: PMC3617176 DOI: 10.1371/journal.pone.0060927] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 03/04/2013] [Indexed: 12/16/2022] Open
Abstract
We performed a genome wide analysis of 164 urothelial carcinoma samples and 27 bladder cancer cell lines to identify copy number changes associated with disease characteristics, and examined the association of amplification events with stage and grade of disease. Multiplex inversion probe (MIP) analysis, a recently developed genomic technique, was used to study 80 urothelial carcinomas to identify mutations and copy number changes. Selected amplification events were then analyzed in a validation cohort of 84 bladder cancers by multiplex ligation-dependent probe assay (MLPA). In the MIP analysis, 44 regions of significant copy number change were identified using GISTIC. Nine gene-containing regions of amplification were selected for validation in the second cohort by MLPA. Amplification events at these 9 genomic regions were found to correlate strongly with stage, being seen in only 2 of 23 (9%) Ta grade 1 or 1–2 cancers, in contrast to 31 of 61 (51%) Ta grade 3 and T2 grade 2 cancers, p<0.001. These observations suggest that analysis of genomic amplification of these 9 regions might help distinguish non-invasive from invasive urothelial carcinoma, although further study is required. Both MIP and MLPA methods perform well on formalin-fixed paraffin-embedded DNA, enhancing their potential clinical use. Furthermore several of the amplified genes identified here (ERBB2, MDM2, CCND1) are potential therapeutic targets.
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Affiliation(s)
- Yvonne Chekaluk
- Division of Translational Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jonathan Rosenberg
- Division of Genitourinary Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Markus Riester
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Qishan Dai
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sharron Lin
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Yanan Guo
- Division of Translational Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - W. Scott McDougal
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (DJK); (WSM)
| | - David J. Kwiatkowski
- Division of Translational Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- * E-mail: (DJK); (WSM)
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Tamborero D, Lopez-Bigas N, Gonzalez-Perez A. Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression. PLoS One 2013; 8:e55489. [PMID: 23408991 PMCID: PMC3568145 DOI: 10.1371/journal.pone.0055489] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 12/23/2012] [Indexed: 01/04/2023] Open
Abstract
A well-established approach for detecting genes involved in tumorigenesis due to copy number alterations (CNAs) is to assess the recurrence of the alteration across multiple samples. Expression data can be used to filter this list of candidates by assessing whether the gene expression significantly differs between tumors depending on the copy number status. A drawback of this approach is that it may fail to detect low-recurrent drivers. Furthermore, this analysis does not provide information about expression changes for each gene as compared to the whole data set and does not take into consideration the expression of normal samples. Here we describe a novel method (Oncodrive-CIS) aimed at ranking genes according to the expression impact caused by the CNAs. The rationale of Oncodrive-CIS is based on the hypothesis that genes involved in cancer due to copy number changes are more biased towards misregulation than are bystanders. Moreover, to gain insight into the expression changes caused by gene dosage, the expression of samples with CNAs is compared to that of tumor samples with diploid genotype and also to that of normal samples. Oncodrive-CIS demonstrated better performance in detecting putative associations between copy-number and expression in simulated data sets as compared to other methods aimed to this purpose, and picked up genes likely to be related with tumorigenesis when applied to real cancer samples. In summary, Oncodrive-CIS provides a statistical framework to evaluate the in cis effect of CNAs that may be useful to elucidate the role of these aberrations in driving oncogenesis. An implementation of this method and the corresponding user guide are freely available at http://bg.upf.edu/oncodrivecis.
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Affiliation(s)
- David Tamborero
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail: (NL-B); (AG-P)
| | - Abel Gonzalez-Perez
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
- * E-mail: (NL-B); (AG-P)
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Uchino K, Takeshita F, Takahashi RU, Kosaka N, Fujiwara K, Naruoka H, Sonoke S, Yano J, Sasaki H, Nozawa S, Yoshiike M, Kitajima K, Chikaraishi T, Ochiya T. Therapeutic effects of microRNA-582-5p and -3p on the inhibition of bladder cancer progression. Mol Ther 2013; 21:610-9. [PMID: 23295946 DOI: 10.1038/mt.2012.269] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Many reports have indicated that the abnormal expression of microRNAs (miRNAs) is associated with the progression of disease and have identified miRNAs as attractive targets for therapeutic intervention. However, the bifunctional mechanisms of miRNA guide and passenger strands in RNA interference (RNAi) therapy have not yet been clarified. Here, we show that miRNA (miR)-582-5p and -3p, which are strongly decreased in high-grade bladder cancer clinical samples, regulate tumor progression in vitro and in vivo. Significantly, the overexpression of miR-582-5p or -3p reduced the proliferation and invasion of UM-UC-3 human bladder cancer cells. Furthermore, transurethral injections of synthetic miR-582 molecule suppressed tumor growth and metastasis in an animal model of bladder cancer. Most interestingly, our study revealed that both strands of miR-582-5p and -3p suppressed the expression of the same set of target genes such as protein geranylgeranyltransferase type I beta subunit (PGGT1B), leucine-rich repeat kinase 2 (LRRK2) and DIX domain containing 1 (DIXDC1). Knockdown of these genes using small interfering RNA (siRNA) resulted in the inhibition of cell growth and invasiveness of UM-UC-3. These findings uncover the unique regulatory pathway involving tumor suppression by both strands of a single miRNA that is a potential therapeutic target in the treatment of invasive bladder cancer.
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Affiliation(s)
- Keita Uchino
- National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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Höglund M. The bladder cancer genome; chromosomal changes as prognostic makers, opportunities, and obstacles. Urol Oncol 2012; 30:533-40. [PMID: 22742566 DOI: 10.1016/j.urolonc.2012.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
During the past decades, the complexity of the bladder cancer genome has become evident. Early cytogenetic studies identified several patterns of chromosomal changes, particularly the frequent loss of chromosome 9. The cytogenetic approach was replaced by molecular methods, such as comparative genome hybridization (CGH) and loss of heterozygosity (LOH) analyses that describe genomic changes at a molecular and higher resolution. With these methods, the full complexity of the bladder cancer genome has been better appreciated. Using CGH and LOH analyses, it also became apparent that premalignant lesions of the bladder, such as hyperplasia and dysplasia, as well as carcinoma in situ (CIS), showed genomic changes. Whole genome analyses showed that low stage, low grade tumors generally show fewer changes than tumors of higher stage and grade. In addition, several genomic alterations were shown to be highly specific for more aggressive and invasive tumors. Based on the general association between complex genomic changes and tumor behavior, several investigations have been directed towards the identification of prognostic genomic markers for urothelial cancer. A complicating factor in the analysis and understanding of bladder cancer genomic progression is that recurring and, hence, chronologically later tumors may show genomes less rearranged than preceding tumors. Furthermore, morphologically normal urothelium in patients with bladder cancer frequently show the same type of genomic alterations as the tumor proper. This makes an issue of to what extent information on genomic changes will produce reliable prognostic information when limited to the tumor proper.
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Affiliation(s)
- Mattias Höglund
- Department of Clinical Sciences, Oncology, Lund University, Skåne University Hospital, SE-221 85 Lund, Sweden.
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Landin Malt A, Cagliero J, Legent K, Silber J, Zider A, Flagiello D. Alteration of TEAD1 expression levels confers apoptotic resistance through the transcriptional up-regulation of Livin. PLoS One 2012; 7:e45498. [PMID: 23029054 PMCID: PMC3454436 DOI: 10.1371/journal.pone.0045498] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/17/2012] [Indexed: 11/19/2022] Open
Abstract
Background TEA domain (TEAD) proteins are highly conserved transcription factors involved in embryonic development and differentiation of various tissues. More recently, emerging evidences for a contribution of these proteins towards apoptosis and cell proliferation regulation have also been proposed. These effects appear to be mediated by the interaction between TEAD and its co-activator Yes-Associated Protein (YAP), the downstream effector of the Hippo tumour suppressor pathway. Methodology/Principal Findings We further investigated the mechanisms underlying TEAD-mediated apoptosis regulation and showed that overexpression or RNAi-mediated silencing of the TEAD1 protein is sufficient to protect mammalian cell lines from induced apoptosis, suggesting a proapoptotic function for TEAD1 and a non physiological cytoprotective effect for overexpressed TEAD1. Moreover we show that the apoptotic resistance conferred by altered TEAD1 expression is mediated by the transcriptional up-regulation of Livin, a member of the Inhibitor of Apoptosis Protein (IAP) family. In addition, we show that overexpression of a repressive form of TEAD1 can induce Livin up-regulation, indicating that the effect of TEAD1 on Livin expression is indirect and favoring a model in which TEAD1 activates a repressor of Livin by interacting with a limiting cofactor that gets titrated upon TEAD1 up-regulation. Interestingly, we show that overexpression of a mutated form of TEAD1 (Y421H) implicated in Sveinsson's chorioretinal atrophy that strongly reduces its interaction with YAP as well as its activation, can induce Livin expression and protect cells from induced apoptosis, suggesting that YAP is not the cofactor involved in this process. Conclusions/Significance Taken together our data reveal a new, Livin-dependent, apoptotic role for TEAD1 in mammals and provide mechanistic insight downstream of TEAD1 deregulation in cancers.
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Affiliation(s)
| | | | | | | | - Alain Zider
- Univ Paris Diderot, Sorbonne Paris Cité, Equipe de Génétique Moléculaire de la Différenciation, IJM, UMR 7592 CNRS, Paris, France
- * E-mail: (AZ); (DF)
| | - Domenico Flagiello
- Univ Paris Diderot, Sorbonne Paris Cité, Equipe de Génétique Moléculaire de la Différenciation, IJM, UMR 7592 CNRS, Paris, France
- * E-mail: (AZ); (DF)
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DNA copy number aberrations associated with lymphovascular invasion in upper urinary tract urothelial carcinoma. Cancer Genet 2012; 205:313-8. [PMID: 22749037 DOI: 10.1016/j.cancergen.2012.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 04/14/2012] [Accepted: 04/17/2012] [Indexed: 12/18/2022]
Abstract
Recent studies have reported that lymphovascular invasion (LVI) is a predictor of patient prognosis in upper urinary tract urothelial carcinoma (UUTUC). DNA copy number aberrations (DCNAs) identified by array-based comparative genomic hybridization (aCGH) had not previously been examined in UUTUC. We therefore examined DCNAs in UUTUC and compared them with DCNAs in LVI. We applied aCGH technology using DNA chips spotted with 4,030 BAC clones to 32 UUTUC patients. Frequent copy number gains were detected on chromosomal regions 8p23.1 and 20q13.12, whereas frequent copy number losses were detected on chromosomal regions 13q21.1, 17p13.1, 6q16.3, and 17p11.2. DCNAs occurred more frequently in tumors with LVI than in those without it (P = 0.0002), and this parameter was more closely associated with LVI than with the tumor grade or pT stage. Disease-specific survival rate was higher in tumors without LVI than in those with it (P = 0.0120); however, tumor grade and stage were not significant prognostic factors of patient outcome. These data support our hypothesis that tumors with LVI have more genetic alterations in terms of total numbers of DCNAs than those without, and provide proof that aggressive adjuvant therapy should be considered for UUTUC patients with LVI.
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Laishram RS, Kipgen P, Laishram S, Khuraijam S, Sharma DC. Urothelial tumors of the urinary bladder in Manipur: a histopathological perspective. Asian Pac J Cancer Prev 2012; 13:2477-9. [PMID: 22938407 DOI: 10.7314/apjcp.2012.13.6.2477] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To study the histomorphological pattern of urothelial tumors of the urinary bladder in Manipur and to evaluate whether any correlation exists between tumor grade and muscle invasion. METHODS A 10 year retrospective study of all consecutive cases diagnosed in the Department of Pathology RIMS - Imphal, between 1st January 2001 to 31st December 2010. RESULTS The study included 26 cases of transitional cell tumors of urinary bladder. The male to female ratio was 1.5: 1 and the ages ranged from 38 years to 73 years (medians of 60 and 64 years, respectively). Of the total, 14 (53.9%) cases were low grade, 9 (34.6%) were high grade, 2 (7.7%) were papillomas and 1 (3.9%) was a papillary urothelial neoplasm of low malignant potential (PUNLMP). Pathological staging showed that 14 (53.9%) of the cases were stage PTa, four (15.4%) PT1, and eight (30.9%) PT2. Some 18.2% of low grade tumors and 75% of high grade tumors were invasive to the detrusor muscle layer. CONCLUSION Bladder cancer is an uncommon disease, transitional tumors being the only histological type observed. It was more common in males than females, with peak incidence in seventh decade. Most of the tumors were non- invasive (PTa) and invasion to the detrusor muscle layer was seen in more than half of the high grade tumors. There is a definite correlation between advancing tumor grade and muscle invasion.
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Affiliation(s)
- Rajesh Singh Laishram
- Department of Pathology, Regional Institute of Medical Sciences Lamphelpat, Imphal, Manipur State, India.
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