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

López V, González-Peramato P, Suela J, Serrano A, Algaba F, Cigudosa JC, Vidal A, Bellmunt J, Heredero O, Sánchez-Carbayo M - J Transl Med (2013)

Bottom Line: Supervised hierarchical clustering identified the gain at 1q23.3-q24.1 significantly correlated to stage (p = 0.011), and grade (p = 0.002).Moreover, PFND2 overexpression was significantly associated with poor disease-specific survival (p ≤0.0005).Genomic profiles of urinary DNA mirrowed bladder tumors.

View Article: PubMed Central - HTML - PubMed

Affiliation: Tumor Markers Group, Molecular Pathology Program, Spanish National Cancer Center, Melchor Fernandez Almagro 3, Madrid E-28029, Spain.

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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Array-CGH analysis showing the 1q23.3- q24.1 region that harbors the PFND2 gene. A. The ideogram of chromosome 1 for the urinary specimen 131HG belonging to a pT1G2 bladder tumor is shown to the left. The central red tracings represent the mean signal ratio of each of the clones along the chromosome generated by the CGH Analytics software. Displacement of this red line to the right of the centre indicates relative genomic gains. B. Gene view of the gain at 1q23.3-q24.1 displaying probes as dots. The color of each dot represents normal (black) or gains (red). The gain of PFND2 identified by array-CGH is highlighted.
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Figure 3: Array-CGH analysis showing the 1q23.3- q24.1 region that harbors the PFND2 gene. A. The ideogram of chromosome 1 for the urinary specimen 131HG belonging to a pT1G2 bladder tumor is shown to the left. The central red tracings represent the mean signal ratio of each of the clones along the chromosome generated by the CGH Analytics software. Displacement of this red line to the right of the centre indicates relative genomic gains. B. Gene view of the gain at 1q23.3-q24.1 displaying probes as dots. The color of each dot represents normal (black) or gains (red). The gain of PFND2 identified by array-CGH is highlighted.

Mentions: Supervised hierarchical clustering was performed to identify top discriminatory genomic imbalances among the minimal recurrent regions of gain and loss associated with tumor stage and grade, by means of ANOVA test analyses. Regarding tumor stage, 1q23.3-q24.1 was found differentially expressed between the urinary specimens (p = 0.011, FDR =0.068) (Figure 2A). 1q23.3-q24.1 was also the region differentially expressed regarding their tumor grade (p = 0.002, FDR = 0.016) (Figure 2B). Overall, these results confirmed the clinical relevance of the gain at 1q23.3-q24.1 as a minimal recurrent region associated with clinicopathologic variables of bladder cancer (Figure 3A). Localization of the minimal recurrent regions of aberration in the urinary specimens associated with histopathologic variables prompted us the search for genes potentially involved in bladder cancer in the most recurrent region at 1q23.3-q24.1. This region harboured a set of genes commonly gained in 3 out of the 14 urinary samples analyzed, with 116 probes showing this gain (Table 2). Among these genes identified in this region showing the highest log-ratio gains (Additional file 4: Table S1), PFND2 was selected for further validation analyses (Figure 3B).


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

López V, González-Peramato P, Suela J, Serrano A, Algaba F, Cigudosa JC, Vidal A, Bellmunt J, Heredero O, Sánchez-Carbayo M - J Transl Med (2013)

Array-CGH analysis showing the 1q23.3- q24.1 region that harbors the PFND2 gene. A. The ideogram of chromosome 1 for the urinary specimen 131HG belonging to a pT1G2 bladder tumor is shown to the left. The central red tracings represent the mean signal ratio of each of the clones along the chromosome generated by the CGH Analytics software. Displacement of this red line to the right of the centre indicates relative genomic gains. B. Gene view of the gain at 1q23.3-q24.1 displaying probes as dots. The color of each dot represents normal (black) or gains (red). The gain of PFND2 identified by array-CGH is highlighted.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3750577&req=5

Figure 3: Array-CGH analysis showing the 1q23.3- q24.1 region that harbors the PFND2 gene. A. The ideogram of chromosome 1 for the urinary specimen 131HG belonging to a pT1G2 bladder tumor is shown to the left. The central red tracings represent the mean signal ratio of each of the clones along the chromosome generated by the CGH Analytics software. Displacement of this red line to the right of the centre indicates relative genomic gains. B. Gene view of the gain at 1q23.3-q24.1 displaying probes as dots. The color of each dot represents normal (black) or gains (red). The gain of PFND2 identified by array-CGH is highlighted.
Mentions: Supervised hierarchical clustering was performed to identify top discriminatory genomic imbalances among the minimal recurrent regions of gain and loss associated with tumor stage and grade, by means of ANOVA test analyses. Regarding tumor stage, 1q23.3-q24.1 was found differentially expressed between the urinary specimens (p = 0.011, FDR =0.068) (Figure 2A). 1q23.3-q24.1 was also the region differentially expressed regarding their tumor grade (p = 0.002, FDR = 0.016) (Figure 2B). Overall, these results confirmed the clinical relevance of the gain at 1q23.3-q24.1 as a minimal recurrent region associated with clinicopathologic variables of bladder cancer (Figure 3A). Localization of the minimal recurrent regions of aberration in the urinary specimens associated with histopathologic variables prompted us the search for genes potentially involved in bladder cancer in the most recurrent region at 1q23.3-q24.1. This region harboured a set of genes commonly gained in 3 out of the 14 urinary samples analyzed, with 116 probes showing this gain (Table 2). Among these genes identified in this region showing the highest log-ratio gains (Additional file 4: Table S1), PFND2 was selected for further validation analyses (Figure 3B).

Bottom Line: Supervised hierarchical clustering identified the gain at 1q23.3-q24.1 significantly correlated to stage (p = 0.011), and grade (p = 0.002).Moreover, PFND2 overexpression was significantly associated with poor disease-specific survival (p ≤0.0005).Genomic profiles of urinary DNA mirrowed bladder tumors.

View Article: PubMed Central - HTML - PubMed

Affiliation: Tumor Markers Group, Molecular Pathology Program, Spanish National Cancer Center, Melchor Fernandez Almagro 3, Madrid E-28029, Spain.

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.

Show MeSH
Related in: MedlinePlus