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Spasova V, Mladenov B, Rangelov S, Hammoudeh Z, Nesheva D, Serbezov D, Staneva R, Hadjidekova S, Ganev M, Balabanski L, Vazharova R, Slavov C, Toncheva D, Antonova O. Clinical impact of copy number variation changes in bladder cancer samples. Exp Ther Med 2021; 22:901. [PMID: 34257714 PMCID: PMC8243332 DOI: 10.3892/etm.2021.10333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to detect copy number variations (CNVs) related to tumour progression and metastasis of urothelial carcinoma through whole-genome scanning. A total of 30 bladder cancer samples staged from pTa to pT4 were included in the study. DNA was extracted from freshly frozen tissue via standard phenol-chloroform extraction and CNV analysis was performed on two alternative platforms (CytoChip Oligo aCGH, 4x44K and Infinium OncoArray-500K BeadChip; Illumina, Inc.). Data were analysed with BlueFuse Multi software and Karyostudio, respectively. The results highlight the role of genomic imbalances in regions containing genes with metastatic and proliferative potential for tumour invasion. A high level of genomic instability in uroepithelial tumours was observed and a total of 524 aberrations, including 175 losses and 349 gains, were identified. The most prevalent genetic imbalances affected the following regions: 1p, 1q, 2q, 4p, 4q, 5p, 5q, 6p, 6q, 7q, 8q, 9p, 9q, 10p, 10q, 11q, 13q and 17q. High-grade tumours more frequently harboured genomic imbalances (n=227) than low-grade tumours (n=103). A total of 36 CNVs in high-grade bladder tumours were detected in chromosomes 1-5, 8-11, 14, 17, 19 and 20. Furthermore, five loss of heterozygosity variants containing 176 genes were observed in high-grade bladder cancer and may be used as potential targets for precision therapy. Revealing specific chromosomal regions related to the metastatic potential of uroepithelial tumours may lay a foundation for implementing molecular CNV profiling of bladder tumours as part of a routine progression risk estimation strategy, thus expanding the personalized therapeutic approach.
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Affiliation(s)
- Victoria Spasova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Boris Mladenov
- Department of Urology, UMBALSM N.I. Pirogov, 1606 Sofia, Bulgaria
| | - Simeon Rangelov
- Department of Urology, Tsaritsa Yoanna University Hospital, 1527 Sofia, Bulgaria
| | - Zora Hammoudeh
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, Nadezhda Women's Health Hospital, 1373 Sofia, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, Nadezhda Women's Health Hospital, 1373 Sofia, Bulgaria
| | - Mihail Ganev
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Lubomir Balabanski
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, GARH Malinov, 1680 Sofia, Bulgaria
| | - Radoslava Vazharova
- Medical Genetics Laboratory, GARH Malinov, 1680 Sofia, Bulgaria.,Department of Biology, Medical Genetics and Microbiology, Faculty of Medicine, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology, Tsaritsa Yoanna University Hospital, 1527 Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Olga Antonova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
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Abstract
In the nearly 60 years since prenatal diagnosis for genetic disease was first offered, the field of prenatal diagnosis has progressed far past rudimentary uterine puncture to provide fetal material to assess gender and interpret risk. Concurrent with the improvements in invasive fetal sampling came technological advances in cytogenetics and molecular biology that widened both the scope of genetic disorders that could be diagnosed and also the resolution at which the human genome could be interrogated. Nowadays, routine blood work available to all pregnant women can determine the risk for common chromosome abnormalities; chorionic villus sampling (CVS) and amniocentesis can be used to diagnose nearly all conditions with a known genetic cause; and the genome and/or exome of a fetus with multiple anomalies can be sequenced in an attempt to determine the underlying etiology. This chapter will discuss some of the major advances in prenatal sampling and prenatal diagnostic laboratory techniques that have occurred over the past six decades.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
| | - Melissa Stosic
- Department of Obstetrics and Gynecology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
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ACGH detects distinct genomic alterations of primary intrahepatic cholangiocarcinomas and matched lymph node metastases and identifies a poor prognosis subclass. Sci Rep 2018; 8:10637. [PMID: 30006612 PMCID: PMC6045619 DOI: 10.1038/s41598-018-28941-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/03/2018] [Indexed: 12/17/2022] Open
Abstract
Lymph node metastases (LNM) are an important prognostic factor for patients with intrahepatic cholangiocarcinoma, but underlying genetic alterations are poorly understood. Whole genome array comparative genomic hybridization (aCGH) was performed in 37 tumors and 14 matched LNM. Genomic analyses of tumors confirmed known and identified new (gains in 19q) copy number alterations (CNA). Tumors with LNM (N1) had more alterations and exclusive gains (3p, 4q, 5p, 13q) and losses (17p and 20p). LNM shared most alterations with their matched tumors (86%), but 79% acquired new isolated gains [12q14 (36%); 1p13, 2p23, 7p22, 7q11, 11q12, 13q13 and 14q12 (>20%)]. Unsupervised clustering revealed a poor prognosis subclass with increased alterations significantly associated to tumor differentiation and survival. TP53 and KRAS mutations occurred in 19% of tumors and 6% of metastases. Pathway analyses revealed association to cancer-associated pathways. Advanced tumor stage, microvascular/perineural invasion, and microscopic positive resection margin (R1) were significantly correlated to metastases, while N1-status, R1-resection, and poor tumor differentiation were significantly correlated to survival. ACGH identified clear differences between N0 (no LNM) and N1 tumors, while N1 tumors and matched LNM displayed high clonality with exclusive gains in the metastases. A novel subclass with increased CNAs and poor tumor differentiation was significantly correlated to survival.
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Smits JPH, Niehues H, Rikken G, van Vlijmen-Willems IMJJ, van de Zande GWHJF, Zeeuwen PLJM, Schalkwijk J, van den Bogaard EH. Immortalized N/TERT keratinocytes as an alternative cell source in 3D human epidermal models. Sci Rep 2017; 7:11838. [PMID: 28928444 PMCID: PMC5605545 DOI: 10.1038/s41598-017-12041-y] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/01/2017] [Indexed: 12/24/2022] Open
Abstract
The strong societal urge to reduce the use of experimental animals, and the biological differences between rodent and human skin, have led to the development of alternative models for healthy and diseased human skin. However, the limited availability of primary keratinocytes to generate such models hampers large-scale implementation of skin models in biomedical, toxicological, and pharmaceutical research. Immortalized cell lines may overcome these issues, however, few immortalized human keratinocyte cell lines are available and most do not form a fully stratified epithelium. In this study we compared two immortalized keratinocyte cell lines (N/TERT1, N/TERT2G) to human primary keratinocytes based on epidermal differentiation, response to inflammatory mediators, and the development of normal and inflammatory human epidermal equivalents (HEEs). Stratum corneum permeability, epidermal morphology, and expression of epidermal differentiation and host defence genes and proteins in N/TERT-HEE cultures was similar to that of primary human keratinocytes. We successfully generated N/TERT-HEEs with psoriasis or atopic dermatitis features and validated these models for drug-screening purposes. We conclude that the N/TERT keratinocyte cell lines are useful substitutes for primary human keratinocytes thereby providing a biologically relevant, unlimited cell source for in vitro studies on epidermal biology, inflammatory skin disease pathogenesis and therapeutics.
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Affiliation(s)
- Jos P H Smits
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), PO BOX 9101, 6500 HB, Nijmegen, The Netherlands
| | - Hanna Niehues
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), PO BOX 9101, 6500 HB, Nijmegen, The Netherlands
| | - Gijs Rikken
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), PO BOX 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ivonne M J J van Vlijmen-Willems
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), PO BOX 9101, 6500 HB, Nijmegen, The Netherlands
| | - Guillaume W H J F van de Zande
- Department of Human Genetics, Radboud University Medical Center (Radboudumc), PO BOX 9101, 6500 HB, Nijmegen, The Netherlands
| | - Patrick L J M Zeeuwen
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), PO BOX 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joost Schalkwijk
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), PO BOX 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ellen H van den Bogaard
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
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Hoffmann MJ, Koutsogiannouli E, Skowron MA, Pinkerneil M, Niegisch G, Brandt A, Stepanow S, Rieder H, Schulz WA. The New Immortalized Uroepithelial Cell Line HBLAK Contains Defined Genetic Aberrations Typical of Early Stage Urothelial Tumors. Bladder Cancer 2016; 2:449-463. [PMID: 28035326 PMCID: PMC5181672 DOI: 10.3233/blc-160065] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Background: Cell culture models of normal urothelial cells are important for studying differentiation, disease mechanisms and anticancer drug development. Beyond primary cultures with their limitations in lifespan, interindividual heterogeneity and supply, few conditionally immortalized cell lines with limited applicability due to partial transformation or impaired differentiation capacity are available. We describe characteristics of the new spontaneously immortalized cell line HBLAK derived from a primary culture of uroepithelial cells. Objective: To characterize utility and limitations of HBLAK cells as an urothelial cell culture model. Methods: Differentiation markers were investigated by immunofluorescence and RT-PCR, genetic changes by standard karyotyping, array-CGH, PCR, RT-PCR and exome sequencing; expression of p53 and p21 by Western blotting. Results: HBLAK cells proliferated for >50 passages without senescing. They expressed cytokeratins of basal urothelial cells. Terminal differentiation markers appeared only after induction of differentiation by specific protocols. The karyotype was stable, with few chromosomal changes, especially gains of chromosomes 5 and 20 and a chromosome 9p21 deletion resulting in p16INK4A loss. A C228T TERT promoter mutation was present, but no other mutation typical of urothelial carcinoma. TP53 was wild-type and the cell cycle was arrested in response to genomic stress. Conclusions: HBLAK cells retain some differentiation potential and respond to cytotoxic agents similar to normal urothelial cells, but contain genetic changes contributing to immortalization in urothelial tumors. HBLAK may be valuable for evaluating the tumor specificity of novel cancer drugs, but may also be applied as an urothelial in vitro carcinogenesis model.
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Affiliation(s)
- Michèle J Hoffmann
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | | | - Margaretha A Skowron
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Maria Pinkerneil
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Artur Brandt
- Institute for Human Genetics, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Stefanie Stepanow
- Biological and Medical Research Center (BMFZ), Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Harald Rieder
- Institute for Human Genetics, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf , Düsseldorf, Germany
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6
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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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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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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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Keck B, Ellmann C, Stoehr R, Weigelt K, Goebell PJ, Kunath F, Taubert H, Hartmann A, Wullich B, Wach S. Comparative genomic hybridization shows complex genomic changes of plasmacytoid urothelial carcinoma. Urol Oncol 2014; 32:1234-9. [PMID: 25087089 DOI: 10.1016/j.urolonc.2014.06.016] [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: 04/06/2014] [Revised: 06/27/2014] [Accepted: 06/27/2014] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To describe genomic imbalances in plasmacytoid urothelial carcinoma (PUC), which is a rare and aggressive variant of urothelial carcinoma (UC). METHODS AND MATERIALS In total, 25 formalin-fixed paraffin-embedded PUCs were analyzed by metaphase comparative genomic hybridization. Genomic imbalances were considered to be characteristic if they were detected in ≥ 20% of the cases. Chromosome regions deviating by ≥ 3 standard deviations from the average chromosome profile were scored as chromosomal gains or losses. Copy-number variations (CNVs) of CDH1 (16q 22.1), SNAI1 (20q 13.1), CCND1 (11q13.3), ERBB2 (17q12), and FOXO3 (6q21) were validated using quantitative polymerase chain reaction. RESULTS Chromosomal aberrations were detected in every PUC analyzed, and the average number of aberrations was 10.24 (ranging from 1-15). Characteristic aberrations were gains on 1q (48%), 3p (20%), 6p (32%), 11q (72%), 15q (36%), 16q (44%), 17p (76%), 17q (88%), and 20q (88%) and losses on 2q (24%) 4p (36%), 4q (84%), 5q (44%), 6q (68%), 13q (20%), and Xq (52%). polymerase chain reaction-based analysis of CNV for CCND1 (11q13) showed a deletion in 73% of the cases. CDH1 (16q22) was deleted in 72% and amplified in 5%. ERBB2 (17q12) displayed remarkably few copy-number alterations, with only 14% showing an amplification. SNAI1 (20q13) showed reduced gene copy numbers in 59.1% of the cases, whereas no copy-number gains were detected. FOXO3 (6q21) exhibited the lowest number of copy-number alterations, with 9% of all cases showing an amplification. CONCLUSIONS In PUCs, the frequency of aneuploidy and the complexity of genomic changes per tumor are greater than those described in conventional UC. The aberrations described in PUC involve the same regions that are associated with aggressive biological behavior in conventional UC. Gains on 11q, 17q, 17p, and 20q and losses on 4q and 6q affect most PUCs and seem to harbor important chromosomal regions for PUC carcinogenesis. Large-scale deletions on chromosome 9 were not detected. CNV analysis indicates heterozygous deletion of CDH1 as one underlying mechanism of loss of membranous E-cadherin in PUC. Loss of CCND1 and SNAI1 is a common molecular feature and could contribute to the aggressive biological behavior of PUC.
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Affiliation(s)
- Bastian Keck
- Department of Urology, University Hospital Erlangen, Erlangen, Germany.
| | - Christina Ellmann
- Department of Urology, University Hospital Erlangen, Erlangen, Germany
| | - Robert Stoehr
- Department of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Katrin Weigelt
- Department of Urology, University Hospital Erlangen, Erlangen, Germany
| | - Peter J Goebell
- Department of Urology, University Hospital Erlangen, Erlangen, Germany
| | - Frank Kunath
- Department of Urology, University Hospital Erlangen, Erlangen, Germany
| | - Helge Taubert
- Department of Urology, University Hospital Erlangen, Erlangen, Germany
| | - Arndt Hartmann
- Department of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Bernd Wullich
- Department of Urology, University Hospital Erlangen, Erlangen, Germany
| | - Sven Wach
- Department of Urology, University Hospital Erlangen, Erlangen, Germany
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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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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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Gamage DG, Hendrickson TL. GPI Transamidase and GPI anchored proteins: Oncogenes and biomarkers for cancer. Crit Rev Biochem Mol Biol 2013; 48:446-64. [DOI: 10.3109/10409238.2013.831024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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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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14
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Nascimento e Pontes MG, da Silveira SM, de Souza Trindade Filho JC, Rogatto SR, Viana de Camargo JL. Chromosomal imbalances in successive moments of human bladder urothelial carcinoma. Urol Oncol 2013; 31:827-35. [DOI: 10.1016/j.urolonc.2011.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 05/02/2011] [Accepted: 05/24/2011] [Indexed: 02/06/2023]
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15
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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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16
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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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17
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Novel amplifications in pediatric medulloblastoma identified by genome-wide copy number profiling. J Neurooncol 2011; 107:37-49. [PMID: 21979893 DOI: 10.1007/s11060-011-0716-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 09/16/2011] [Indexed: 12/21/2022]
Abstract
Medulloblastoma (MB) is a WHO grade IV, invasive embryonal CNS tumor that mainly affects children. The aggressiveness and response to therapy can vary considerably between cases, and despite treatment, ~30% of patients die within 2 years from diagnosis. Furthermore, the majority of survivors suffer long-term side-effects due to severe management modalities. Several distinct morphological features have been associated with differences in biological behavior, but improved molecular-based criteria that better reflect the underlying tumor biology are in great demand. In this study, we profiled a series of 25 MB with a 32K BAC array covering 99% of the current assembly of the human genome for the identification of genetic copy number alterations possibly important in MB. Previously known aberrations as well as several novel focally amplified loci could be identified. As expected, the most frequently observed alteration was the combination of 17p loss and 17q gain, which was detected in both high- and standard-risk patients. We also defined minimal overlapping regions of aberrations, including 16 regions of gain and 18 regions of loss in various chromosomes. A few noteworthy narrow amplified loci were identified on autosomes 1 (38.89-41.97 and 84.89-90.76 Mb), 3 (27.64-28.20 and 35.80-43.50 Mb), and 8 (119.66-139.79 Mb), aberrations that were verified with an alternative platform (Illumina 610Q chips). Gene expression levels were also established for these samples using Affymetrix U133Plus2.0 arrays. Several interesting genes encompassed within the amplified regions and presenting with transcript upregulation were identified. These data contribute to the characterization of this malignant childhood brain tumor and confirm its genetic heterogeneity.
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18
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Panzeri E, Conconi D, Antolini L, Redaelli S, Valsecchi MG, Bovo G, Pallotti F, Viganò P, Strada G, Dalprà L, Bentivegna A. Chromosomal aberrations in bladder cancer: fresh versus formalin fixed paraffin embedded tissue and targeted FISH versus wide microarray-based CGH analysis. PLoS One 2011; 6:e24237. [PMID: 21909424 PMCID: PMC3164716 DOI: 10.1371/journal.pone.0024237] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/03/2011] [Indexed: 01/08/2023] Open
Abstract
Bladder carcinogenesis is believed to follow two alternative pathways driven by the loss of chromosome 9 and the gain of chromosome 7, albeit other nonrandom copy number alterations (CNAs) were identified. However, confirmation studies are needed since many aspects of this model remain unclear and considerable heterogeneity among cases has emerged. One of the purposes of this study was to evaluate the performance of a targeted test (UroVysion assay) widely used for the detection of Transitional Cell Carcinoma (TCC) of the bladder, in two different types of material derived from the same tumor. We compared the results of UroVysion test performed on Freshly Isolated interphasic Nuclei (FIN) and on Formalin Fixed Paraffin Embedded (FFPE) tissues from 22 TCCs and we didn't find substantial differences. A second goal was to assess the concordance between array-CGH profiles and the targeted chromosomal profiles of UroVysion assay on an additional set of 10 TCCs, in order to evaluate whether UroVysion is an adequately sensitive method for the identification of selected aneuploidies and nonrandom CNAs in TCCs. Our results confirmed the importance of global genomic screening methods, that is array based CGH, to comprehensively determine the genomic profiles of large series of TCCs tumors. However, this technique has yet some limitations, such as not being able to detect low level mosaicism, or not detecting any change in the number of copies for a kind of compensatory effect due to the presence of high cellular heterogeneity. Thus, it is still advisable to use complementary techniques such as array-CGH and FISH, as the former is able to detect alterations at the genome level not excluding any chromosome, but the latter is able to maintain the individual data at the level of single cells, even if it focuses on few genomic regions.
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Affiliation(s)
- Elena Panzeri
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, Monza, Italy
- Medical Genetics Laboratory, S. Gerardo Hospital, Monza, Italy
| | - Donatella Conconi
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, Monza, Italy
- Medical Genetics Laboratory, S. Gerardo Hospital, Monza, Italy
| | - Laura Antolini
- Department of Clinical Medicine and Prevention, Center of Biostatistics for Clinical Epidemiology, University of Milan-Bicocca, Monza, Italy
| | - Serena Redaelli
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, Monza, Italy
- Medical Genetics Laboratory, S. Gerardo Hospital, Monza, Italy
| | - Maria Grazia Valsecchi
- Department of Clinical Medicine and Prevention, Center of Biostatistics for Clinical Epidemiology, University of Milan-Bicocca, Monza, Italy
| | - Giorgio Bovo
- Department of Pathology, S. Gerardo Hospital, Monza, Italy
| | - Francesco Pallotti
- Department of Pathology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milano, Italy
| | - Paolo Viganò
- Urology Division, Bassini ICP Hospital, Milano, Italy
| | - Guido Strada
- Urology Division, Bassini ICP Hospital, Milano, Italy
| | - Leda Dalprà
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, Monza, Italy
- Medical Genetics Laboratory, S. Gerardo Hospital, Monza, Italy
| | - Angela Bentivegna
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, Monza, Italy
- Medical Genetics Laboratory, S. Gerardo Hospital, Monza, Italy
- * E-mail:
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19
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Kim TJ, Lee A, Lee SJ, Lee WC, Choi YJ, Lee KY, Kang CS. Prognostic Significance of Amplification of the c-MYCGene in Surgically Treated Stage IB-IIB Cervical Cancer. KOREAN JOURNAL OF PATHOLOGY 2011. [DOI: 10.4132/koreanjpathol.2011.45.6.596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Tae-Jung Kim
- Department of Hospital Pathology, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Ahwon Lee
- Department of Hospital Pathology, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Sung-Jong Lee
- Department of Obstetrics and Gynecology, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Won-Chul Lee
- Department of Preventive Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Yeong-Jin Choi
- Department of Hospital Pathology, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Kyo-Young Lee
- Department of Hospital Pathology, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Chang Suk Kang
- Department of Hospital Pathology, The Catholic University of Korea College of Medicine, Seoul, Korea
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20
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Bruin SC, Klijn C, Liefers GJ, Braaf LM, Joosse SA, van Beers EH, Verwaal VJ, Morreau H, Wessels LF, van Velthuysen MLF, Tollenaar RAEM, Van't Veer LJ. Specific genomic aberrations in primary colorectal cancer are associated with liver metastases. BMC Cancer 2010; 10:662. [PMID: 21126340 PMCID: PMC3027605 DOI: 10.1186/1471-2407-10-662] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 12/02/2010] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Accurate staging of colorectal cancer (CRC) with clinicopathological parameters is important for predicting prognosis and guiding treatment but provides no information about organ site of metastases. Patterns of genomic aberrations in primary colorectal tumors may reveal a chromosomal signature for organ specific metastases. METHODS Array Comparative Genomic Hybridization (aCGH) was employed to asses DNA copy number changes in primary colorectal tumors of three distinctive patient groups. This included formalin-fixed, paraffin-embedded tissue of patients who developed liver metastases (LM; n = 36), metastases (PM; n = 37) and a group that remained metastases-free (M0; n = 25).A novel statistical method for identifying recurrent copy number changes, KC-SMART, was used to find specific locations of genomic aberrations specific for various groups. We created a classifier for organ specific metastases based on the aCGH data using Prediction Analysis for Microarrays (PAM). RESULTS Specifically in the tumors of primary CRC patients who subsequently developed liver metastasis, KC-SMART analysis identified genomic aberrations on chromosome 20q. LM-PAM, a shrunken centroids classifier for liver metastases occurrence, was able to distinguish the LM group from the other groups (M0&PM) with 80% accuracy (78% sensitivity and 86% specificity). The classification is predominantly based on chromosome 20q aberrations. CONCLUSION Liver specific CRC metastases may be predicted with a high accuracy based on specific genomic aberrations in the primary CRC tumor. The ability to predict the site of metastases is important for improvement of personalized patient management.
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Affiliation(s)
- Sjoerd C Bruin
- Division of Experimental Therapy, Department of Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
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21
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Bladder cancer: translating molecular genetic insights into clinical practice. Hum Pathol 2010; 42:455-81. [PMID: 21106220 DOI: 10.1016/j.humpath.2010.07.007] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 07/03/2010] [Accepted: 07/08/2010] [Indexed: 11/21/2022]
Abstract
Transitional cell (urothelial) carcinoma of the bladder is the second most common urologic malignancy and is one of the best understood neoplasms, with relatively well-defined pathogenetic pathways, natural history, and tumor biology. Conventional clinical and pathologic parameters are widely used to grade and stage tumors and to predict clinical outcome of transitional cell carcinoma; but the predictive ability of these parameters is limited, and there is a lack of indices that could allow prospective assessment of risk for individual patients. In the last decade, a wide range of candidate biomarkers representing key pathways in carcinogenesis have been reported to be clinically relevant and potentially useful as diagnostic and prognostic molecular markers, and as potential therapeutic targets. The use of molecular markers has facilitated the development of novel and more accurate diagnostic, prognostic, and therapeutic strategies. FGFR3 and TP53 mutations have been recognized as key genetic pathways in the carcinogenesis of transitional cell carcinoma. FGFR3 appears to be the most frequently mutated oncogene in transitional cell carcinoma; its mutation is strongly associated with low tumor grade, early stage, and low recurrence rate, which confer a better overall prognosis. In contrast, TP53 mutations are associated with higher tumor grade, more advanced stage, and more frequent tumor recurrences. These molecular markers offer the potential to characterize individual urothelial neoplasms more completely than is possible by histologic evaluation alone. Areas in which molecular markers may prove valuable include prediction of tumor recurrence, molecular staging of transitional cell carcinoma, detection of lymph node metastasis and circulating cancer cells, identification of therapeutic targets, and prediction of response to therapy. With accumulating molecular knowledge of transitional cell carcinoma, we are closer to the goal of bridging the gap between molecular findings and clinical outcomes. Assessment of key genetic pathways and expression profiles could ultimately establish a set of molecular markers to predict the biological nature of tumors and to establish new standards for molecular tumor grading, classification, and prognostication. The main focus of this review is to discuss clinically relevant biomarkers that might be useful in the management of transitional cell carcinoma and to provide approaches in the analysis of molecular pathways that influence the clinical course of bladder cancer.
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22
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Eguchi S, Yamamoto Y, Sakano S, Chochi Y, Nakao M, Kawauchi S, Furuya T, Oga A, Matsuyama H, Sasaki K. The loss of 8p23.3 is a novel marker for predicting progression and recurrence of bladder tumors without muscle invasion. ACTA ACUST UNITED AC 2010; 200:16-22. [PMID: 20513529 DOI: 10.1016/j.cancergencyto.2010.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 03/16/2010] [Indexed: 10/19/2022]
Abstract
There are few reliable markers to distinguish tumors with aggressive characteristics from others at the time of initial diagnosis in non-muscle-invasive bladder cancer. The purpose of this study was to identify a genomic marker that allows the prediction of prognosis for non-muscle-invasive bladder cancers. We screened the genome-wide copy number in 41 patients with non-muscle-invasive urothelial carcinoma of the bladder by array-based comparative genomic hybridization using arrays spotted with 4,030 bacterial artificial chromosome clones. A loss of 8p23.3 (clone 923) was correlated significantly with a higher histological grade (P = 0.0026) and advanced pathological stage (P = 0.0148). Both recurrence-free and progression-free survival rates were lower in patients with tumors without 8p23.3, compared with those with 8p23.3 (P = 0.0146 and 0.0473, respectively; log-rank test). These data suggest that the loss of 8p23.3 is a novel genomic marker allowing estimation of biological characteristics of non-muscle-invasive bladder cancer.
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Affiliation(s)
- Satoshi Eguchi
- Department of Urology, Yamaguchi University Graduate School of Medicine, Ube, Japan
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23
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Ryan D, Rafferty M, Hegarty S, O'Leary P, Faller W, Gremel G, Bergqvist M, Agnarsdottir M, Strömberg S, Kampf C, Pontén F, Millikan RC, Dervan PA, Gallagher WM. Topoisomerase I amplification in melanoma is associated with more advanced tumours and poor prognosis. Pigment Cell Melanoma Res 2010; 23:542-53. [PMID: 20465595 DOI: 10.1111/j.1755-148x.2010.00720.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this study, we used array-comparative genomic hybridization (aCGH) and fluorescent in situ hybridization (FISH) to examine genetic aberrations in melanoma cell lines and tissues. Array-comparative genomic hybridization revealed that the most frequent genetic changes found in melanoma cell lines were amplifications on chromosomes 7p and 20q, along with disruptions on Chr 9, 10, 11, 12, 22 and Y. Validation of the results using FISH on tissue microarrays (TMAs) identified TOP1 as being amplified in melanoma tissues. TOP1 amplification was detected in a high percentage (33%) of tumours and was associated with thicker, aggressive tumours. These results show that TOP1 amplification is associated with advanced tumours and poor prognosis in melanoma. These observations open the possibility that TOP1-targeted therapeutics may be of benefit in a particular subgroup of advanced stage melanoma patients.
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Affiliation(s)
- Denise Ryan
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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24
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Amplification of 8q21 in breast cancer is independent of MYC and associated with poor patient outcome. Mod Pathol 2010; 23:603-10. [PMID: 20139910 DOI: 10.1038/modpathol.2010.5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Copy number gains involving the long arm of chromosome 8, including high-level amplifications at 8q21 and 8q24, have been frequently reported in breast cancer. Although the role of the MYC gene as the driver of the 8q24 amplicon is well established, the significance of the 8q21 amplicon is less clear. The breast cancer cell line SK-BR-3 contains three separate 8q21 amplicons, the distal two of which correspond to putative target genes TPD52 and WWP1. To understand the effect of proximal 8q21 amplification on breast cancer phenotype and patient prognosis, we analyzed 8q21 copy number changes using fluorescence in situ hybridization (FISH) in a tissue microarray containing more than 2000 breast cancers. Amplification at 8q21 was found in 3% of tumors, and was associated with medullary type (P<0.03), high tumor grade (P<0.0001), high Ki67 labeling index (P<0.05), amplification of MYC (P<0.0001), HER2, MDM2, and CCND1 (P<0.05 each), as well as the total number of gene amplifications (P<0.0001). 8q21 copy number gains were significantly related to unfavorable patient outcome in univariate analysis. However, multivariate Cox regression analysis did not reveal an independent prognostic value of 8q21 amplification. The position of our FISH probe and data of a previously performed high-resolution CGH study in the breast cancer cell line SK-BR-3 involve TCEB1 and TMEM70 as new possible candidate oncogenes at 8q21 in breast cancer.
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25
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Quantitative loss of heterozygosity analysis for urothelial carcinoma detection and prognosis. Urology 2010; 76:515.e1-7. [PMID: 20206968 DOI: 10.1016/j.urology.2009.11.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 10/14/2009] [Accepted: 11/14/2009] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To evaluate loss of heterozygosity (LOH) using microsatellite polymorphism analysis as a diagnostic and prognostic marker at the time of transurethral resection and as a follow-up marker preceding cystoscopic evidence of recurrence compared with cytology. METHODS A total of 127 urothelial carcinoma (UC) patients were included. Tumors were staged and graded according to the International Union Against Cancer-tumor, node, metastases system and to the 2004 World Health Organization classification. LOH urinalysis was performed using 8 markers and marker-specific LOH thresholds. Thirty control samples, obtained from healthy volunteers, were used to determine the positive cut-off for each marker. RESULTS LOH was significantly more sensitive than cytology in low-grade (64.8% vs 38.5%, P <.001) and low-stage UC (68.6% vs 45.5%, P <.001). The cumulative sensitivity of cytology and LOH reached 74.7% (P <.001) for low-grade and 80.2% (P <.001) for low-stage tumors. Both urinary LOH at TP53 and chromosome 9p markers were associated with an increased risk of recurrence (relative risk = 1.73 [1.30-2.31], P = .0002) and occurred more frequently in the initial urine samples of patients who later relapsed from primary tumors (36.4% vs 0.0%, P <.05 and 57.6% vs 15.8%, P = .0001). Among 32 relapse patients, LOH was positive alongside cystoscopy in 25 of 32 cases and tested positive before cystoscopy detected recurrence in a further 5 of 25 cases. CONCLUSIONS UC diagnosis and monitoring would greatly benefit from supplementing conventional cytology with LOH urinalysis, using a panel of 8 microsatellite markers with specific threshold levels. Given the limitations of both cystoscopy and cytology, novel molecular markers are needed for detection and follow-up of UC.
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26
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Nord H, Segersten U, Sandgren J, Wester K, Busch C, Menzel U, Komorowski J, Dumanski JP, Malmström PU, Díaz de Ståhl T. Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinoma. Int J Cancer 2010; 126:1390-402. [PMID: 19821490 DOI: 10.1002/ijc.24954] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Urinary bladder cancer is a heterogeneous disease with tumors ranging from papillary noninvasive (stage Ta) to solid muscle infiltrating tumors (stage T2+). The risk of progression and death for the most frequent diagnosed type, Ta, is low, but the high incidence of recurrences has a significant effect on the patients' quality of life and poses substantial costs for health care systems. Consequently, the purpose of this study was to search for predictive factors of recurrence on the basis of genetic profiling. A clinically well characterized cohort of Ta bladder carcinomas, selected by the presence or absence of recurrences, was evaluated by an integrated analysis of DNA copy number changes and gene expression (clone-based 32K, respectively, U133Plus2.0 arrays). Only a few chromosomal aberrations have previously been defined in superficial bladder cancer. Surprisingly, the profiling of Ta tumors with a high-resolution array showed that DNA copy alterations are relatively common in this tumor type. Furthermore, we observed an overrepresentation of focal amplifications within high-grade and recurrent cases. Known (FGFR3, CCND1, MYC, MDM2) and novel candidate genes were identified within the loci. For example, MYBL2, a nuclear transcription factor involved in cell-cycle progression; YWHAB, an antiapoptotic protein; and SDC4, an important component of focal adhesions represent interesting candidates detected within two amplicons on chromosome 20, for which DNA amplification correlated with transcript up-regulation. The observed overrepresentation of amplicons within high-grade and recurrent cases may be clinically useful for the identification of patients who will benefit from a more aggressive therapy.
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Affiliation(s)
- Helena Nord
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden
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27
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Lukasiewicz KB, Lingle WL. Aurora A, centrosome structure, and the centrosome cycle. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2009; 50:602-619. [PMID: 19774610 DOI: 10.1002/em.20533] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The centrosome, also known as the microtubule organizing center of the cell, is a membrane-less organelle composed of a pair of barrel-shaped centrioles surrounded by electron-dense pericentriolar material. The centrosome progresses through the centrosome cycle in step with the cell cycle such that centrosomes are duplicated in time to serve as the spindle poles during mitosis and that each resultant daughter cell contains a single centrosome. Regulation of the centrosome cycle with relation to the cell cycle is an essential process to maintain the ratio of one centrosome per new daughter cell. Numerous mitosis-specific kinases have been implicated in this regulation, and phosphorlyation plays an important role in coordinating the centrosome and cell cycles. Centrosome amplification can occur when the cycles are uncoupled, and this amplification is associated with cancer and with an increase in the levels of chromosomal instability. The aurora kinases A, B, and C are serine/threonine kinases that are active during mitosis. Aurora A is associated with centrosomes, being localized at the centrosome just prior to the onset of mitosis and for the duration of mitosis. Overexpression of aurora A leads to centrosome amplification and cellular transformation. The activity of aurora A is regulated by phosphorlyation and proteasomal degradation.
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Affiliation(s)
- Kara B Lukasiewicz
- Section on Cell Cycle Regulation, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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28
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Prat E, del Rey J, Ponsa I, Nadal M, Camps J, Plaja A, Campillo M, Algaba F, Gelabert A, Miró R. Comparative genomic hybridization analysis reveals new different subgroups in early-stage bladder tumors. Urology 2009; 75:347-55. [PMID: 19647297 DOI: 10.1016/j.urology.2009.04.080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 03/16/2009] [Accepted: 04/14/2009] [Indexed: 10/20/2022]
Abstract
OBJECTIVES To classify bladder tumors according to their genomic imbalances and evaluate their association with patient's outcome. METHODS Sixty-three superficially and minimally invasive bladder tumors were analyzed by conventional comparative genomic hybridization. Subtelomeric screening in 15 of these tumors was performed by multiplex ligation-dependent probe amplification. RESULTS Losses of 9q and 9p (32% and 25% of all cases, respectively) as well as gains of chromosomes Xq and Xp (28% and 25%, respectively) were the most frequent chromosome imbalances. Losses of 8p and gains in 1q and 8q were detected in >20% of cases. Tumors were classified into 3 groups according to their individualized pattern of gains and losses. The largest group was characterized by few chromosome imbalances, presenting 77% and 49% of the Ta and T1 tumors, respectively. Another group characterized by chromosomal gains, was composed of equal number of Ta and T1 tumors, with +1q and +17q gains being the most common imbalances. A minority group was characterized by chromosomal losses on 11q, 5q, and 6q. The multiplex ligation-dependent probe amplification study showed good correlation with comparative genomic hybridization results. With regard to the biological significance of this classification, a remarkable fact is that this minority group composed mainly of T1 tumors, showed a significant decrease in patient overall survival. CONCLUSIONS Our data suggest that superficial carcinomas of the bladder can be subdivided into a larger number of subclasses than had previously been expected. Our results also demonstrate a decreased survival among patients whose tumors show more genomic losses than gains.
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Affiliation(s)
- Esther Prat
- Institut de Biotecnologia i Biomedicina and Department de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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Approaches to Carcinoma In Situ (CIS). Bladder Cancer 2009. [DOI: 10.1007/978-1-59745-417-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
Mycosis fungoides (MF), the most common cutaneous T-cell lymphoma, is a malignancy of mature, skin-homing T cells. Sézary syndrome (Sz) is often considered to represent a leukemic phase of MF. In this study, the pattern of numerical chromosomal alterations in MF tumor samples was defined using array-based comparative genomic hybridization (CGH); simultaneously, gene expression was analyzed using microarrays. Highly recurrent chromosomal alterations in MF include gain of 7q36, 7q21-7q22 and loss of 5q13 and 9p21. The pattern characteristic of MF differs markedly from chromosomal alterations observed in Sz. Integration of data from array-based CGH and gene-expression analysis yielded several candidate genes with potential relevance in the pathogenesis of MF. We confirmed that the FASTK and SKAP1 genes, residing in loci with recurrent gain, demonstrated increased expression. The RB1 and DLEU1 tumor suppressor genes showed diminished expression associated with loss. In addition, it was found that the presence of chromosomal alterations on 9p21, 8q24, and 1q21-1q22 was associated with poor prognosis in patients with MF. This study provides novel insight into genetic alterations underlying MF. Furthermore, our analysis uncovered genomic differences between MF and Sz, which suggest that the molecular pathogenesis and therefore therapeutic requirements of these cutaneous T-cell lymphomas may be distinct.
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Veerakumarasivam A, Scott HE, Chin SF, Warren A, Wallard MJ, Grimmer D, Ichimura K, Caldas C, Collins VP, Neal DE, Kelly JD. High-resolution array-based comparative genomic hybridization of bladder cancers identifies mouse double minute 4 (MDM4) as an amplification target exclusive of MDM2 and TP53. Clin Cancer Res 2008; 14:2527-34. [PMID: 18451213 DOI: 10.1158/1078-0432.ccr-07-4129] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Loss of p53 function in urothelial cell carcinoma (UCC) by mutation or inactivation disrupts normal cell cycle checkpoints, generating a favorable milieu for genomic instability, a hallmark of UCC. The aim of this study was to characterize novel DNA copy number changes to identify putative therapeutic targets. EXPERIMENTAL DESIGN We report our findings using array comparative genomic hybridization on a whole-genome BAC/PAC/cosmid array with a median clone interval of 0.97 Mb to study a series of UCC cases. TP53 status was determined by direct sequencing, and an in-house tissue microarray was constructed to identify protein expression of target genes. RESULTS Array comparative genomic hybridization allowed identification of novel regions of copy number changes in addition to those already known from previous studies. A novel amplification previously unreported in UCC was identified at 1q32. A chromosome 1 tile path array was used to analyze tumors that showed gains and amplification; the mouse double minute 4 (MDM4) homologue was identified as the amplified gene. MDM4 mRNA expression correlated with copy number and tumor grade. Copy number changes of MDM4 and MDM2 occurred exclusively in tumors with wild-type p53. Overexpression of MDM4 corresponded to disruption of p53 transcriptional activity. Immunohistochemistry on an independent series by tissue microarray identified an inverse relationship between Mdm4 and Mdm2, with Mdm4 expression highest in invasive UCC. CONCLUSION The data indicate that gain/amplification and overexpression of MDM4 is a novel molecular mechanism by which a subset of UCC escapes p53-dependent growth control, thus providing new avenues for therapeutic intervention.
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Burum-Auensen E, DeAngelis PM, Schjølberg AR, Røislien J, Mjåland O, Clausen OPF. Reduced level of the spindle checkpoint protein BUB1B is associated with aneuploidy in colorectal cancers. Cell Prolif 2008; 41:645-59. [PMID: 18699967 DOI: 10.1111/j.1365-2184.2008.00539.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES The majority of solid human malignancies demonstrate DNA aneuploidy as a consequence of chromosomal instability. We wanted to investigate whether Aurora A, Aurora B, BUB1B and Mad2 were associated with the development of aneuploidy in colorectal adenocarcinomas as suggested by several in vitro studies, and if their protein levels were related to alterations at the corresponding chromosomal loci. MATERIALS AND METHODS Expression levels of these spindle proteins were investigated by immunohistochemistry using tissue micro-arrays in a series of DNA aneuploid and diploid colorectal adenocarcinomas previously examined for genomic aberrations by comparative genomic hybridization. RESULTS All proteins were overexpressed in malignant tissues compared to controls (P < 0.001 for all). BUB1B level was significantly reduced in aneuploid compared to diploid cancers (P = 0.001), whereas expression of the other proteins was not associated with DNA ploidy status. High levels of Aurora A (P = 0.049) and low levels of Aurora B (P = 0.031) were associated with poor prognosis, but no associations were revealed between protein expression and genomic aberration. CONCLUSIONS A significant reduction of BUB1B level was detected in aneuploid compared to diploid colorectal cancers, consistent with earlier studies showing that loss of spindle checkpoint function may be involved in development of DNA aneuploidy. Our data also show that spindle proteins are overexpressed in colorectal cancers, and that expression of the Aurora kinases is associated with prognosis in colorectal cancer.
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Affiliation(s)
- E Burum-Auensen
- The Pathology Clinic, Rikshospitalet-Radiumhospitalet Medical Center, University of Oslo, Faculty of Medicine, 0027 Oslo, Norway.
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DeVries S, Gray JW, Pinkel D, Waldman FM, Sudar D. Comparative genomic hybridization. ACTA ACUST UNITED AC 2008; Chapter 4:Unit4.6. [PMID: 18428281 DOI: 10.1002/0471142905.hg0406s06] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Comparative Genomic Hybridization (CGH) is a powerful molecular cytogenetic technique that permits assessment of DNA copy number on a genome-wide scale. Of note, this methodology uses tumor DNA as a probe for fluorescence in situ hybridization (FISH) to normal metaphase chromosomes and does not require dividing cells from the tumor specimen. This unit provides protocols for CGH, for preparation of metaphase chromosomes, tumor and normal DNAs for FISH and for the microscopy and image analysis of CGH experiments.
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Affiliation(s)
- S DeVries
- University of California at San Francisco, San Francisco, USA
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Wolff DJ. The genetics of bladder cancer: a cytogeneticist's perspective. Cytogenet Genome Res 2007; 118:177-81. [PMID: 18000368 DOI: 10.1159/000108298] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 03/06/2007] [Indexed: 12/29/2022] Open
Abstract
Cytogenetic studies of bladder cancer have helped to define two clinically distinct subtypes: benign tumors with few genetic mutations and a stable karyotype and aggressive cancers with chromosomal instability and many non-random cytogenetic aberrations. While the cytogenetic data does not provide complete information, these studies have been important for suggesting pathways for bladder carcinoma initiation and its progression. In addition, molecular cytogenetic studies have proven useful for diagnosing bladder cancer and for monitoring patients for cancer recurrence. More detailed molecular genetic studies and expression array analyses are needed to fully comprehend the biologic processes associated with urothelial cancers, but cytogenetics studies have laid the foundation for further investigation.
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Affiliation(s)
- D J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA.
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Inactivation of the Rb pathway and overexpression of both isoforms of E2F3 are obligate events in bladder tumours with 6p22 amplification. Oncogene 2007; 27:2716-27. [PMID: 18037967 DOI: 10.1038/sj.onc.1210934] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
E2F3 and CDKAL1 are candidate genes from the 6p22 region frequently amplified in bladder cancer. Expression of E2F3 isoforms (E2F3a and b) and CDKAL1 were examined and modulated in 6p22-amplified bladder cell lines. Eight lines with amplification showed overexpression of both E2F3 isoforms and CDKAL1. shRNA-mediated knockdown of CDKAL1 had no effect on proliferation. Knockdown of E2F3a or E2F3b alone induced antiproliferative effects, with the most significant effect on proliferation being observed when both isoforms were knocked down together. As E2Fs interact with the Rb tumour suppressor protein, Rb expression was analysed. There was a striking relationship between 6p22.3 amplification, E2F3 overexpression and lack of Rb expression. This was also examined in primary bladder tumours. Array-CGH detected 6p22.3 amplification in 8/91 invasive tumours. Five were studied in more detail. Four showed 13q14.2 loss (including RB1) and expressed no Rb protein. In the fifth, 13q was unaltered but the CDKN2A locus was deleted. This tumour was negative for p16 and positive for Rb protein. As p16 is a negative regulator of the Rb pathway, its loss represents an alternative mechanism for inactivation. Indeed, a phospho-specific Rb antibody showed much Rb protein in a hyperphosphorylated (inactive) form. We conclude that inactivation of the Rb pathway is required in addition to E2F3 overexpression in this subset of bladder tumours.
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Hsu LI, Chiu AW, Pu YS, Wang YH, Huan SK, Hsiao CH, Hsieh FI, Chen CJ. Comparative genomic hybridization study of arsenic-exposed and non-arsenic-exposed urinary transitional cell carcinoma. Toxicol Appl Pharmacol 2007; 227:229-38. [PMID: 18201742 DOI: 10.1016/j.taap.2007.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 10/02/2007] [Accepted: 10/03/2007] [Indexed: 10/22/2022]
Abstract
To compare the differences in DNA aberrations between arsenic-exposed and non-arsenic-exposed transitional cell carcinoma (TCC), we analyzed 19 arsenic-exposed and 29 non-arsenic-exposed urinary TCCs from Chi-Mei Hospital using comparative genomic hybridization. DNA aberrations were detected in 42 TCCs including 19 arsenic-exposed and 23 non-arsenic-exposed TCCs. Arsenic-exposed TCCs had more changes than unexposed TCCs (mean+/-SD, 6.6+/-2.9 vs. 2.9+/-2.2). Arsenic exposure was significantly associated with the number of DNA aberrations after adjustment for tumor stage, tumor grade and cigarette smoking in multiple regression analysis. The most frequent DNA gains, which were strikingly different between arsenic-exposed and non-arsenic-exposed TCCs, included those at 1p, 4p, 4q and 8q. A much higher frequency of DNA losses in arsenic-exposed TCCs compared with non-arsenic-exposed TCCs was observed in 10q, 11p and 17p. Chromosomal loss in 17p13 was associated not only with arsenic exposure, but also with tumor stage and grade. The p53 immunohistochemistry staining showed that chromosome 17p13 loss was associated with either p53 no expression (25%) or p53 overexpression (75%). The findings suggest that long-term arsenic exposure may increase the chromosome abnormality in TCC, and 17p loss plays an important role in arsenic-induced urinary carcinogenesis.
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Affiliation(s)
- Ling-I Hsu
- The Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Appanna TC, Doak SH, Jenkins SA, Kynaston HG, Stephenson TP, Parry JM. Comparative genomic hybridization (CGH) of augmentation cystoplasties. Int J Urol 2007; 14:539-44. [PMID: 17593101 DOI: 10.1111/j.1442-2042.2006.01724.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Tumors arising within augmentation cystoplasties are aggressive, have poor prognosis and the majority are not detected at follow-up cystoscopy. Genetic changes in tumors precede morphological abnormalities. Therefore, the aim of this study was to investigate whether genetic abnormalities detected by comparative genomic hybridization (CGH) could be used to identify those patients with augmentation cystoplasties at increased risk of tumorigenesis. METHODS Bladder biopsy samples were obtained from 16 augmentation cystoplasty patients both distant from and near to the enterovesical anastomosis. CGH was used to detect genetic abnormalities in DNA extracted from the biopsies, archival specimens of two augmentation cystoplasties and two de novo bladder adenocarcinomas. RESULTS A greater number of amplifications on 2p, 3q, 8q, 9p, 17p, 18pq and 20pq, were observed in bladder biopsies obtained near to the enterovesical anastomosis compared to those taken distant to the suture line. CGH of archival augmentation cystoplasty tumor DNA indicated abnormalities at several loci with amplifications at 2q, 5q, 10p and 21pq, while deletions occurred at 5p and 16p. CONCLUSIONS The results of this study suggest that the urothelium adjacent to the bladder and/or bowel anastomosis in augmentation cystoplasties is genetically unstable. Furthermore, longitudinal studies are required to establish whether or not patients exhibiting genetic instability following augmentation cystoplasty are at greater risk of developing tumors than those with genetically stable epithelia.
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Affiliation(s)
- Timson C Appanna
- Department of Urology, University Hospital of Wales, Cardiff, UK
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Junker K, Fritsch T, Hartmann A, Schulze W, Schubert J. Multicolor fluorescence in situ hybridization (M-FISH) on cells from urine for the detection of bladder cancer. Cytogenet Genome Res 2006; 114:279-83. [PMID: 16954667 DOI: 10.1159/000094214] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 04/18/2006] [Indexed: 11/19/2022] Open
Abstract
Bladder cancer is the fifth most common cancer in adults. Because of the high recurrence rate (up to 70%) new tumor markers for urine are necessary for monitoring patients. In this study, we investigated the value of M-FISH on cells from urine for the detection of bladder cancer. Urine samples from 141 patients suspicious of bladder cancer were analyzed in this study. Cells were isolated from urine before surgical therapy. For FISH analysis, a commercial kit (UroVysion) containing hybridization probes for chromosomes 3, 7, 9p21 and 17, was used. Twenty-five cells were analyzed in each case by two observers. A FISH result was obtained in 121 cases. Overall, sensitivity was 60% and specificity reached 82.6%. Sensitivity and specificity by cytology were 24.1% and 90.5%, respectively. Analyzing results concerning T-category, sensitivity of FISH and cytology was 36.1% and 15% in pTa, 65.2 and 25.7% in pT1, 100% and 66.7% in pT2-3 tumors, respectively. Concerning tumor grade, similar results were obtained: sensitivity was 37% and 14% in G1, 65.4% and 40% in G2, 91.7% and 50% in G3 tumors, for FISH and cytology, respectively. In conclusion, FISH on cells from urine has been shown in all studies to be highly sensitive and specific for detection of bladder cancer. Sensitivity of FISH is higher than conventional cytology and can be used in routine diagnosis additionally to conventional cytology especially in doubtful or negative cases. FISH can detect recurrence earlier than other methods like cytology, cystoscopy or biopsy histological examination.
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Affiliation(s)
- K Junker
- Department of Urology, Friedrich-Schiller-University, Jena, Germany.
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Frau DV, Usai P, Dettori T, Caria P, De Lisa A, Vanni R. Fluorescence in situ hybridization patterns in newly diagnosed superficial bladder lesions and corresponding bladder washings. ACTA ACUST UNITED AC 2006; 169:21-6. [PMID: 16875932 DOI: 10.1016/j.cancergencyto.2006.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2005] [Revised: 03/02/2006] [Accepted: 03/06/2006] [Indexed: 10/24/2022]
Abstract
A multiprobe interphase fluorescence in situ hybridization (I-FISH) approach has become a useful ancillary tool in the follow-up protocol for patients with low-grade superficial bladder tumors. Nevertheless, reports contextually comparing I-FISH patterns in primary superficial tumor cells with those in concomitant washing cells at the time of initial tumor appearance are sparse. We comparatively evaluated I-FISH patterns of chromosomes 3, 7, 9, and 17 and of the CDKN2A and TP53 loci in newly diagnosed superficial bladder lesions and in corresponding bladder washings, to verify representatives of the latter type of sampling and to improve the efficacy of I-FISH follow-up. A total of 21 biopsies and 12 washings were examined. Samples obtained at the time of the tumor's first appearance showed the presence of cytogenetically abnormal clones in 80% of washings and 70% of biopsies. Five cases showed overlapping washing and biopsy I-FISH patterns; in three cases (and to a lesser extent in two others), consistent discrepancies between the two patterns was observed. The results indicate that knowledge of I-FISH patterns in both washing and biopsy cells on first tumor appearance may be of help in interpreting further follow-up I-FISH patterns, and that these should be considered in the context of the patient's entire clinical history.
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Affiliation(s)
- Daniela V Frau
- Department of Biomedical Sciences and Technologies, University of Cagliari, Monserrato CA, Italy
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Qin SL, Chen XJ, Xu X, Shou JZ, Bi XG, Ji L, Han YL, Cai Y, Wei F, Ma JH, Wu M, Zhan QM, Wang MR. Detection of chromosomal alterations in bladder transitional cell carcinomas from Northern China by comparative genomic hybridization. Cancer Lett 2006; 238:230-9. [PMID: 16125302 DOI: 10.1016/j.canlet.2005.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 07/08/2005] [Accepted: 07/10/2005] [Indexed: 12/16/2022]
Abstract
To identify chromosome alterations in Chinese bladder cancer, forty-six transitional cell carcinomas of the bladder were analyzed by comparative genomic hybridization. Frequent gains of DNA copy number were observed on 1p (13/46), 1q (13/46), 5p (8/46), 6p (9/46), 7p (7/46), 8q (12/46), 11q (8/46), 17q (11/46), 19q (7/46), 20q (8/46) and Yq (8/46), with minimal overlapping regions at 1p32-pter (10/46), 1q21-q24 (12/46), 5p (8/46), 6p22-p23 (7/46), 7p11.2-p14 (7/46), 8q22-q24 (12/46), 11q13-q14 (8/46), 17q22-qter (11/46), 19q11-13.2 (7/46), 20q11-q13.2 (8/46) and Yq11 (8/46). Losses were predominantly found on 2q (16/46), 5q (8/46), 8p (7/46), 9p (8/46), 9q (13/46), 11p (7/46), 13q (7/46), 17p (12/46), 18q (7/46), Xp (18/46) and Xq (19/46), with smallest overlapping regions at 2q32-qter (16/46), 5q12-q31 (8/46), 8p12-pter (7/46), 9p21-pter (10/46), 9q (13/46), 11p (7/46), 13q13-q22 (7/46), 17p (12/46), 18q21-qter (7/46), Xp (18/46) and Xq (19/46). There were significantly higher frequencies of gains of 1q21-q24 and 17q22-qter in moderately differentiated tumors as compared with those in well-differentiated tumors, indicating a possible association of these two abnormalities with the dedifferentiation of tumor cells. Gains of 1p32-pter, 5p, 6p22-p23, 11q13-q14, 17q22-qter and losses of 2q32-qter, 9q, 17p were more frequent in pT1 as compared with those in pTa carcinomas. Gains at 1q21-q24, 7p11.2-p14, 8q22-q24, 19q, 20q11-q13.2 and losses at 5q12-q31, 8p12-pter, 9p21-pter, 11p, 13q13-q22 and 18q21-qter were unique to pT1 and higher stage tumors, suggesting that genes responsible for the invasion and progression of bladder cancer might be located at these chromosomal regions. In multiple tumors from the same patients, consistent alterations such as gains of 8q, 11q13-q14, 12q13-q15, 13q12, 20q and losses of 2q32-qter, 8p, 9, 11p, 11q21-qter, 13q13-qter, X were detected. These abnormalities were possibly earlier events, which might play a critical role during the genesis of the tumors. Further detailed studies to the recurrent aberration regions may lead to the identification of oncogenes and tumor suppressor genes involved in the development and progression of Chinese bladder cancer.
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Affiliation(s)
- Si-Long Qin
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College, Chinese Academy of Medical Sciences, P.O. Box 2258, Beijing 100021, China
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Jones JS. DNA–based molecular cytology for bladder cancer surveillance. Urology 2006; 67:35-45; discussion 45-7. [PMID: 16530074 DOI: 10.1016/j.urology.2006.01.039] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 01/11/2006] [Indexed: 11/17/2022]
Abstract
Surveillance strategies for urothelial cancer (UC) recurrence have historically relied on the diagnostic combination of cystoscopy and conventional urinary cytology. In this review, results of studies evaluating the role of the fluorescence in situ hybridization (FISH) assay in bladder cancer surveillance are critically examined. The published research on FISH compared with conventional cytology and cystoscopy for bladder cancer was identified using a Medline search and was critically analyzed. Sensitivity and specificity data were tabulated and compared. FISH outperformed conventional cytology across all stages and grades in all published reports, and it detected malignancy before the development of lesions visible by cystoscopy. Although overall sensitivity was 48% for cytology and 74% for FISH, its greatest advantage was in the detection of high-grade UC, including carcinoma in situ (CIS). Cumulative data from comparative studies showed the sensitivity of cytology compared with FISH was 19% versus 58% for grade 1, 50% versus 77% for grade 2, and 71% versus 96% for grade 3. Similar findings occurred by stage, where cytology compared with FISH sensitivity was 35% versus 64% for Ta, 66% versus 83% for T1, and 76% versus 94% for muscle-invasive carcinoma. Notably, cytology detected only 67% of CIS versus 100% detection by FISH. Specificity data were comparable. Unlike conventional urinary cytology and cystoscopy, which depend on subjective visible microscopic or macroscopic changes, FISH allows identification of chromosomal abnormalities associated with malignant development before phenotypic expression of those alterations. Use of morphologic cellular changes allows more rapid detection of such alterations, combining the benefits of conventional cytology with molecular diagnostics. It is apparent that we are in the early phases of realizing the potential of molecular diagnostics.
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Affiliation(s)
- J Stephen Jones
- The Glickman Urological Institute, The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA.
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Abstract
Cancer of the bladder shows divergent clinical behaviour following diagnosis and it has been proposed that two major groups of tumours exist that develop via different molecular pathways. Low-grade, non-invasive papillary tumours recur frequently, but patients with these tumours do not often suffer progression of disease to muscle invasion. In contrast, tumours that are invading muscle at diagnosis are aggressive and associated with significant mortality. Molecular studies have identified distinct genetic, epigenetic and expression changes in these groups. However, it is not yet clear whether there is direct progression of low-grade superficial tumours to become invasive (a Jeckell and Hyde scenario) or whether in those patients who apparently progress from one form of the disease to the other, different tumour clones are involved and that the two tumour groups are mutually exclusive ('chalk and cheese'). If the latter is true, then attempts to identify molecular markers to predict progression of low-grade superficial bladder tumours may be fruitless. Similarly, it is not clear whether other subgroups of tumours exist that arise via different molecular pathways. There is now a large amount of molecular information about bladder cancer that facilitates examination of these possibilities. Some recent studies provide evidence for the existence of at least one further group of tumours, high-grade superficial papillary tumours, which may develop via a distinct molecular pathway. Patients with such tumours do show increased risk of disease progression and for these there may exist a real progression continuum from non-invasive to invasive. If this is the case, definition of the molecular signature of this pathway and improved understanding of the biological consequences of the events involved will be pivotal in disease management.
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Affiliation(s)
- Margaret A Knowles
- Cancer Research UK Clinical Centre, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK.
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Blaveri E, Brewer JL, Roydasgupta R, Fridlyand J, DeVries S, Koppie T, Pejavar S, Mehta K, Carroll P, Simko JP, Waldman FM. Bladder Cancer Stage and Outcome by Array-Based Comparative Genomic Hybridization. Clin Cancer Res 2005; 11:7012-22. [PMID: 16203795 DOI: 10.1158/1078-0432.ccr-05-0177] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Bladder carcinogenesis is believed to follow alternative pathways of disease progression driven by an accumulation of genetic alterations. The purpose of this study was to evaluate associations between measures of genomic instability and bladder cancer clinical phenotype. EXPERIMENTAL DESIGN Genome-wide copy number profiles were obtained for 98 bladder tumors of diverse stages (29 pT(a), 14 pT1, 55 pT(2-4)) and grades (21 low-grade and 8 high-grade superficial tumors) by array-based comparative genomic hybridization (CGH). Each array contained 2,464 bacterial artificial chromosome and P1 clones, providing an average resolution of 1.5 Mb across the genome. A total of 54 muscle-invasive cases had follow-up information available. Overall outcome analysis was done for patients with muscle-invasive tumors having "good" (alive >2 years) versus "bad" (dead in <2 years) prognosis. RESULTS Array CGH analysis showed significant increases in copy number alterations and genomic instability with increasing stage and with outcome. The fraction of genome altered (FGA) was significantly different between tumors of different stages (pT(a) versus pT1, P = 0.0003; pT(a) versus pT(2-4), P = 0.02; and pT1 versus pT(2-4), P = 0.03). Individual clones that differed significantly between different tumor stages were identified after adjustment for multiple comparisons (false discovery rate < 0.05). For muscle-invasive tumors, the FGA was associated with patient outcome (bad versus good prognosis patients, P = 0.002) and was identified as the only independent predictor of overall outcome based on a multivariate Cox proportional hazards method. Unsupervised hierarchical clustering separated "good" and "bad" prognosis muscle-invasive tumors into clusters that showed significant association with FGA and survival (Kaplan-Meier, P = 0.019). Supervised tumor classification (prediction analysis for microarrays) had a 71% classification success rate based on 102 unique clones. CONCLUSIONS Array-based CGH identified quantitative and qualitative differences in DNA copy number alterations at high resolution according to tumor stage and grade. Fraction genome altered was associated with worse outcome in muscle-invasive tumors, independent of other clinicopathologic parameters. Measures of genomic instability add independent power to outcome prediction of bladder tumors.
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Affiliation(s)
- Ekaterini Blaveri
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California 94143-0808, USA
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Hazra A, Grossman HB, Zhu Y, Luo S, Spitz MR, Wu X. Benzo[a]pyrene diol epoxide-induced 9p21 aberrations associated with genetic predisposition to bladder cancer. Genes Chromosomes Cancer 2005; 41:330-8. [PMID: 15390186 DOI: 10.1002/gcc.20093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
CDKN2A, 9p21, encodes two alternatively spiked, functionally distinct, tumor-suppressor proteins, P16INK4A and P14ARF, which play active roles in the RB1 and TP53 pathways, respectively. Deletion of 9p is one of the most frequent genomic alterations in bladder cancer. In addition, alterations of 9p21 and P16 are frequently seen in the epithelial cells of chronic smokers. This pilot study evaluated whether 9p21 aberrations induced by exposure in vitro to benzo[a]pyrene diol epoxide (BPDE), the metabolic product of benzo[a]pyrene, a constituent of tobacco smoke, were more common in the peripheral blood lymphocytes of 61 bladder cancer patients compared to 64 matched controls. Our hypothesis was that 9p21 sensitivity to BPDE reflects the susceptibility of a specific locus to damage from carcinogens in tobacco smoke. We found that BPDE-induced chromosome band 9p21 aberrations were significantly higher in lymphocytes of bladder cancer cases (24.97 +/- 5.26 per 1,000) than in controls (20.72 +/- 4.51 per 1,000; P < 0.0001). However, no difference was observed for CEP9, a control locus. After adjustment for age, sex, ethnicity, and smoking status, 9p BPDE sensitivity had an odds ratio (OR) of 9.01 [95% confidence interval (95% CI) 3.75, 21.67] for bladder cancer. We further observed a gradient of elevated bladder cancer risk associated with increasing chromosomal damage. The adjusted ORs for subjects in the second, third, and highest quartiles of BPDE-induced 9p21 aberrations relative to the first quartile were 0.48 (0.04, 5.69), 5.14 (1.12, 23.59), and 21.51 (4.75, 97.34), respectively, providing increasing dose-response evidence of the locus-specific alterations. Thus, 9p21 may be a molecular target for BPDE-induced damage in bladder cancer cases.
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Affiliation(s)
- Aditi Hazra
- Department of Epidemiology, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
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Venter DJ, Ramus SJ, Hammet FMA, de Silva M, Hutchins AM, Petrovic V, Price G, Armes JE. Complex CGH alterations on chromosome arm 8p at candidate tumor suppressor gene loci in breast cancer cell lines. ACTA ACUST UNITED AC 2005; 160:134-40. [PMID: 15993269 DOI: 10.1016/j.cancergencyto.2004.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 12/01/2004] [Accepted: 12/08/2004] [Indexed: 02/08/2023]
Abstract
Loss of genetic material from chromosome arm 8p occurs frequently in human breast carcinomas, consistent with this region of the genome harboring one or more tumor suppressor genes (TSGs). We used the complementary techniques of microsatellite-based LOH, high-density FISH, and conventional CGH on 6 breast cancer cell lines (MCF7, SKBR3, T47D, MDA MB453, BT549, and BT474) to investigate the molecular cytogenetic changes occurring on chromosome 8 during tumorigenesis, with particular emphasis on 6 potential TSGs on 8p. We identified multiple alterations of chromosome 8, including partial or complete deletion of 8p or 8q, duplication of 8q, and isochromosome 8q. The detailed FISH analysis showed several complex rearrangements of 8p with differing breakpoints of varying proximity to the genes of interest. High rates of LOH were observed at markers adjacent to or within PCM1, DUSP4/MKP2, NKX3A, and DLC1, supporting their status as candidate TSGs. Due to the complex ploidy status of these cell lines, relative loss of 8p material detected by CGH did not always correlate with microsatellite-based LOH results. These results extend our understanding of the mechanisms accompanying the dysregulation of candidate tumor suppressor loci on chromosome arm 8p, and identify appropriate cellular systems for further investigation of their biological properties.
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Affiliation(s)
- Deon J Venter
- Department of Pathology, University of Melbourne, Melbourne, Australia
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Poeaim S, Rerkamnuaychoke B, Jesdapatarakul S, Campiranon A. Chromosome alterations in colorectal cancer in Thai patients. ACTA ACUST UNITED AC 2005; 160:152-9. [PMID: 15993271 DOI: 10.1016/j.cancergencyto.2004.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2004] [Revised: 11/16/2004] [Accepted: 12/03/2004] [Indexed: 12/01/2022]
Abstract
Much information has been reported on the genetic and genomic alterations in colorectal cancer (CRC) in various countries; however, nonrandom chromosomal alterations in Thai patients have not been described. As a first step toward understanding the underlying genetic changes and determining early chromosomal changes of tumor development in this population, we used comparative genomic hybridization (CGH) to screen for losses and gains of DNA sequences along chromosomes in 20 morphologically normal tumor surroundings (MNTS) and 40 CRC tissues from 40 patients. In CRC, we detected gains of chromosome arms 20q (60%), 8q (25%), 19q (22.5%), and 19p (20%), as well as losses of chromosome arms 18q (25%) and 4q (20%). There were no differences in genetic alteration between colon and rectal cancer. In morphologically normal tumor surroundings (MNTS) tissues, gains on 19p and 19q were most frequent. We suggest that gains of this chromosome are early events in the progression of CRC, followed by gains on 8q and 20q and losses on 4q and 18q at later stages. Based on our cytogenetic data by comparison of 2 tissue groups in the same cases, we discuss the monoclonal model followed by lateral epithelial spread as an explanation of multiple CRC. Identification and characterization of the causative genes for these cancer syndromes have enabled precise pre-symptomatic detection of mutations in individuals who bear a prior risk of developing CRC.
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Affiliation(s)
- S Poeaim
- Department of Applied Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Road, Bangkok 10520, Thailand.
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Adams J, Cuthbert-Heavens D, Bass S, Knowles MA. Infrequent mutation of TRAIL receptor 2 (TRAIL-R2/DR5) in transitional cell carcinoma of the bladder with 8p21 loss of heterozygosity. Cancer Lett 2005; 220:137-44. [PMID: 15766588 DOI: 10.1016/j.canlet.2004.06.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Revised: 06/28/2004] [Accepted: 06/30/2004] [Indexed: 10/26/2022]
Abstract
Loss of heterozygosity (LOH) on 8p is a frequent event in many cancers and is often associated with more aggressive disease. Tumour necrosis factor-related apoptosis inducing ligand (TRAIL) receptor 2 (TRAIL-R2) also known as TNFRSF10B (tumour necrosis factor receptor (TNFR) super family 10b) or KILLER/DR5, a member of the TNFR family, is a promising candidate tumour suppressor gene at 8p21-22. Mutations in this gene have been identified in non-small cell lung cancer, head and neck cancer, breast cancer and non-Hodgkin's lymphoma. We carried out mutation analysis of TRAIL-R2 in bladder cancer cell lines and in primary bladder tumours. One novel protein truncating mutation was identified in a bladder cancer cell line. Our results suggest that if TRAIL-R2 is the target of LOH events in these cancers, inactivation of the remaining allele is by a mechanism other than mutation.
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Affiliation(s)
- Jacqui Adams
- Cancer Research UK Clinical Centre, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
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Zaharieva B, Simon R, Ruiz C, Oeggerli M, Mihatsch MJ, Gasser T, Sauter G, Toncheva D. High-throughput tissue microarray analysis ofCMYC amplificationin urinary bladder cancer. Int J Cancer 2005; 117:952-6. [PMID: 15986448 DOI: 10.1002/ijc.21253] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Alterations of chromosome 8, preferentially deletions of 8p and gains of 8q, belong to the most frequent cytogenetic changes in bladder cancer. CMYC on 8q24 is a candidate oncogene in this region. Little is known about the clinical significance of CMYC copy number changes in urinary bladder cancer because its frequency is low and a limited numbers of tumors were analyzed so far. To investigate the impact of CMYC alterations on tumor progression and patient prognosis in bladder cancer, we applied FISH to a tissue microarray containing 2317 bladder cancer samples. Presence of CMYC copy number increase was associated with advanced stage and high grade. CMYC amplifications were seen in 3 of 467 pTa (0.6%), 10 of 247 pT1 (4%) and 11 of 201 pT2-4 urothelial carcinomas (5.5%; p < 0.0001), as well as in 1 of 123 G1 (0.8%), 8 of 470 G2 (1.7%) and 17 of 365 G3 urothelial carcinomas (4.7%; p < 0.0001). CMYC gains were present in 49 of 467 pTa (10.5%), 39 of 247 pT1 (15.8%) and 43 of 201 pT2-4 urothelial carcinoma (21.4%; p < 0.0001), as well as in 7 of 123 G1 (5.7%), 56 of 470 G2 (11.9%) and 72 of 365 G3 urothelial carcinomas (19.7%; p < 0.0001). CMYC copy number changes were unrelated to prognosis of bladder cancer patients. We conclude that alterations of the CMYC gene, including copy number gains and amplifications, are linked to genetically unstable bladder cancers that are characterized by a high histologic grade and/or invasive growth. Patient prognosis was not affected by CMYC gene copy number changes.
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Affiliation(s)
- Boriana Zaharieva
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
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Dorritie K, Montagna C, Difilippantonio MJ, Ried T. Advanced molecular cytogenetics in human and mouse. Expert Rev Mol Diagn 2004; 4:663-76. [PMID: 15347260 PMCID: PMC4729310 DOI: 10.1586/14737159.4.5.663] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fluorescence in situ hybridization, spectral karyotyping, multiplex fluorescence in situ hybridization, comparative genomic hybridization, and more recently array comparative genomic hybridization, represent advancements in the field of molecular cytogenetics. The application of these techniques for the analysis of specimens from humans, or mouse models of human diseases, enables one to reliably identify and characterize complex chromosomal rearrangements resulting in alterations of the genome. As each of these techniques has advantages and limitations, a comprehensive analysis of cytogenetic aberrations can be accomplished through the utilization of a combination approach. As such, analyses of specific tumor types have proven invaluable in the identification of new tumor-specific chromosomal aberrations and imbalances (aneuploidy), as well as regions containing tumor-specific gene targets. Application of these techniques has already improved the classification of tumors into distinct categories, with the hope that this will lead to more tailored treatment strategies. These techniques, in particular the application of tumor-specific fluorescence in situ hybridization probes to interphase nuclei, are also powerful tools for the early identification of premalignant lesions.
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Affiliation(s)
| | - Cristina Montagna
- Genetics Branch, Center for CancerResearch, NCI/NIH, Bldg. 50, Rm. 1408, 50 South Drive, Bethesda, MD 20892–0913, USA, Tel: +1 301 435 3986, Fax: +1 301 402 1204
| | - Michael J. Difilippantonio
- Genetics Branch, Center for CancerResearch, NCI/NIH, Bldg. 50, Rm. 1408, 50 South Drive, Bethesda, MD 20892–8010, USA
| | - Thomas Ried
- Author for correspondence, Genetics Branch, Center for Cancer Research, NCI/NIH, Bldg. 50, Rm. 1408, 50 South Drive, Bethesda, MD, 20892–8010, USA, Tel.: +1 301 594 3118, Fax: +1 301 435 4428,
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Wullich B, Riedinger S, Brinck U, Stoeckle M, Kamradt J, Ketter R, Jung V. Evidence for gains at 15q and 20q in brain metastases of prostate cancer. ACTA ACUST UNITED AC 2004; 154:119-23. [PMID: 15474146 DOI: 10.1016/j.cancergencyto.2004.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2003] [Revised: 12/23/2003] [Accepted: 01/06/2004] [Indexed: 11/18/2022]
Abstract
Many detailed genetic studies have been reported on prostate carcinogenesis. A major shortcoming of these studies, however, is the fact that most data have been gained from investigations that were performed at a single point of time during tumor development. Only little is known on the dynamic process of genetic changes during the course of the disease. We performed comparative genomic hybridization in two cases of prostate cancer brain metastases. Tissue samples from the primary tumors, the locally recurrent tumor in one case, and the brain metastases from both cases were available for analysis. The number of chromosome abnormalities was found to be increased in the metastases. This contrasts to a remarkably stable chromosome composition of the primary tumor over several years, even in an androgen-depleted environment. When focusing on these changes, which either emerged as new common aberrations in both brain metastases, or which were commonly present in the primary and metastatic tumors, we were able to delineate five chromosomal sites that are assumed to be related to prostate cancer metastasis: 8q21 approximately q22, 8q24, 15q24 approximately q26, 20q12 approximately q13.1, and Xq12 approximately q21. These findings provide new evidence for a putative role of genes at 15q and 20q in the metastatic process of prostate cancer.
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Affiliation(s)
- Bernd Wullich
- Department of Urology and Pediatric Urology, University of the Saarland, 66421 Homburg/Saar, Germany.
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