Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA View Full Text


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Article Info

DATE

2013-08-01

AUTHORS

Virginia López, Pilar González-Peramato, Javier Suela, Alvaro Serrano, Ferrán Algaba, Juan C Cigudosa, August Vidal, Joaquim Bellmunt, Oscar Heredero, Marta Sánchez-Carbayo

ABSTRACT

BackgroundArray-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.MethodsUrinary 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).ResultsQuality 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.ConclusionsGenomic 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. More... »

PAGES

182

References to SciGraph publications

  • 2006-11-12. Regional copy number–independent deregulation of transcription in cancer in NATURE GENETICS
  • 1998-10. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays in NATURE GENETICS
  • 2006-09. Application of multiplex FISH, CGH and MSSCP techniques for cytogenetic and molecular analysis of transitional cell carcinoma (TCC) cells in voided urine specimens in JOURNAL OF APPLIED GENETICS
  • 1998-05. Chromatin remodelling by the glucocorticoid receptor requires the BRG1 complex in NATURE
  • 2005-06. Array comparative genomic hybridization and its applications in cancer in NATURE GENETICS
  • 2004-12-14. Expressional patterns of chaperones in ten human tumor cell lines in PROTEOME SCIENCE
  • 2007-11-26. Inactivation of the Rb pathway and overexpression of both isoforms of E2F3 are obligate events in bladder tumours with 6p22 amplification in ONCOGENE
  • 2004-02-16. High-resolution analysis of genomic copy number alterations in bladder cancer by microarray-based comparative genomic hybridization in ONCOGENE
  • 2002-03-22. Chromosomal aberrations in benign and malignant Bilharzia-associated bladder lesions analyzed by comparative genomic hybridization in BMC CANCER
  • 2004-01-15. Identification of a novel function of TWIST, a bHLH protein, in the development of acquired taxol resistance in human cancer cells in ONCOGENE
  • 1997-02-06. 20q gain associates with immortalization: 20q13.2 amplification correlates with genome instability in human papillomavirus 16 E7 transformed human uroepithelial cells in ONCOGENE
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    30 schema:description BackgroundArray-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.MethodsUrinary 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).ResultsQuality 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.ConclusionsGenomic 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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    37 schema:keywords DNA
    38 K oligonucleotide array
    39 alterations
    40 amplification
    41 analysis
    42 array
    43 array CGH
    44 biomarkers
    45 bladder cancer
    46 bladder cancer patients
    47 bladder cancer progression
    48 bladder tumors
    49 body fluids
    50 cancer
    51 cancer patients
    52 cancer progression
    53 candidate mappings
    54 candidates
    55 clustering
    56 comparative genomic hybridization array
    57 comprehensive tool
    58 control
    59 dilution experiments
    60 disease alterations
    61 disease-specific survival
    62 experiments
    63 fish
    64 fluid
    65 fluorescent
    66 frequent genomic alterations
    67 gain
    68 genomic alterations
    69 grade
    70 hierarchical clustering
    71 high reproducibility
    72 hybridization
    73 hybridization arrays
    74 identification
    75 immunohistochemistry
    76 independent set
    77 loss
    78 mapping
    79 means
    80 molecular profiling
    81 oligonucleotide arrays
    82 overexpression
    83 patients
    84 pool
    85 poor disease-specific survival
    86 prefoldin
    87 profile
    88 profiling
    89 prognostic biomarker
    90 progression
    91 q24.1
    92 reference pool
    93 region
    94 report
    95 reproducibility
    96 samples
    97 set
    98 situ hybridization
    99 specimens
    100 stage
    101 stratification
    102 survival
    103 tissue arrays
    104 tool
    105 tumor grade
    106 tumor stratification
    107 tumors
    108 urinary DNA
    109 urinary samples
    110 urinary specimens
    111 validation analysis
    112 schema:name Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA
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