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Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situ in the urinary bladder.

Herbsleb M, Christensen OF, Thykjaer T, Wiuf C, Borre M, Orntoft TF, Dyrskjøt L - BMC Cancer (2008)

Bottom Line: The expression in the CIS group was comparable to the expression of twenty-three patients suffering from muscle-invasive bladder carcinoma.Finally, we validated our results in an independent test set and found that prediction of CIS status was possible using TF expression of the p38 MAPK pathway.We conclude that it is possible to use pathway analysis for molecular classification of bladder tumors.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Diagnostic Laboratory, Aarhus University Hospital Skejby, Brendstrupgaardsvej 100, DK-8200 Aarhus N, Denmark. herbsleb@ki.au.dk

ABSTRACT

Background: Carcinoma in situ (CIS) is believed to be a precursor of invasive bladder cancer. Identification of CIS is a valuable prognostic factor since radical treatment strategies can be offered these patients before the disease becomes invasive.

Methods: We developed a pathway based classifier approach to predict presence or absence of CIS in patients suffering from non muscle invasive bladder cancer. From Ingenuity Pathway Analysis we considered four canonical signalling pathways (p38 MAPK, FGF, Calcium, and cAMP pathways) with most coherent expression of transcription factors (TFs) across samples in a set of twenty-eight non muscle invasive bladder carcinomas. These pathways contained twelve TFs in total. We used the expression of the TFs to predict presence or absence of CIS in a Leave-One-Out Cross Validation classification.

Results: We showed that TF expression levels in three pathways (FGF, p38 MAPK, and calcium signalling) or the expression of the twelve TFs together could be used to predict presence or absence of concomitant CIS. A cluster analysis based on expression of the twelve TFs separated the samples in two main clusters: one branch contained 11 of the 15 patients without concomitant CIS and with the majority of the genes being down regulated; the other branch contained 10 of 13 patients with concomitant CIS, and here genes were mostly up regulated. The expression in the CIS group was comparable to the expression of twenty-three patients suffering from muscle-invasive bladder carcinoma. Finally, we validated our results in an independent test set and found that prediction of CIS status was possible using TF expression of the p38 MAPK pathway.

Conclusion: We conclude that it is possible to use pathway analysis for molecular classification of bladder tumors.

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Related in: MedlinePlus

Cluster analysis of 9 normal samples and 10 samples from cystectomies with CIS. Top: TFs from p38 MAPK signalling pathway. Bottom: All 12 TFs used for clustering. The color bar indicates the clinical diagnosis, blue, histologically normal urothelial samples; pink, cystectomy specimens.
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Figure 6: Cluster analysis of 9 normal samples and 10 samples from cystectomies with CIS. Top: TFs from p38 MAPK signalling pathway. Bottom: All 12 TFs used for clustering. The color bar indicates the clinical diagnosis, blue, histologically normal urothelial samples; pink, cystectomy specimens.

Mentions: After identification of pathways with relevance for identification of concomitant CIS in non muscle invasive bladder carcinomas we investigated if these pathways were also important in actual CIS lesions. For this we used a set of nine urothelial samples from healthy individuals and ten biopsies from cystectomy specimens (five were CIS lesions and five were histological normal samples located adjacent to CIS). The five histologically normal samples located adjacent to CIS were previously shown to express the CIS signature [6] and this set was previously used to validate the CIS classifier developed by Dyrskjøt et al. [6] We used a hierarchical cluster analysis approach for classification of the samples (see Additional File 8). The p38 MAPK signalling pathway showed a significant correlation to CIS status for the patients in these independent test samples (p = 0.0198), while the other pathways showed no significant correlation to CIS status in this small sample set. The TFs from the four pathways combined did not show a statistically significant correlation to CIS status, although the p-value was borderline (p = 0.0698; Figure 6). Like in the papillary tumors, the cluster analysis showed that the expression of the majority of the twelve genes was down regulated in normal biopsies compared to the ten biopsies from cystectomy specimens. The biopsies from the cystectomy specimens clustered together, and this was independent of whether the specimen was a CIS lesion or a histological normal sample located adjacent to CIS, underscoring the tight relation between CIS-and "normal" looking biopsies in this urothelium. DDIT3 was up-regulated in the normal samples compared to the biopsies from cystectomy specimens, while MYC was up regulated in the cystectomy specimens but not differentially expressed in the papillary tumors.


Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situ in the urinary bladder.

Herbsleb M, Christensen OF, Thykjaer T, Wiuf C, Borre M, Orntoft TF, Dyrskjøt L - BMC Cancer (2008)

Cluster analysis of 9 normal samples and 10 samples from cystectomies with CIS. Top: TFs from p38 MAPK signalling pathway. Bottom: All 12 TFs used for clustering. The color bar indicates the clinical diagnosis, blue, histologically normal urothelial samples; pink, cystectomy specimens.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2268699&req=5

Figure 6: Cluster analysis of 9 normal samples and 10 samples from cystectomies with CIS. Top: TFs from p38 MAPK signalling pathway. Bottom: All 12 TFs used for clustering. The color bar indicates the clinical diagnosis, blue, histologically normal urothelial samples; pink, cystectomy specimens.
Mentions: After identification of pathways with relevance for identification of concomitant CIS in non muscle invasive bladder carcinomas we investigated if these pathways were also important in actual CIS lesions. For this we used a set of nine urothelial samples from healthy individuals and ten biopsies from cystectomy specimens (five were CIS lesions and five were histological normal samples located adjacent to CIS). The five histologically normal samples located adjacent to CIS were previously shown to express the CIS signature [6] and this set was previously used to validate the CIS classifier developed by Dyrskjøt et al. [6] We used a hierarchical cluster analysis approach for classification of the samples (see Additional File 8). The p38 MAPK signalling pathway showed a significant correlation to CIS status for the patients in these independent test samples (p = 0.0198), while the other pathways showed no significant correlation to CIS status in this small sample set. The TFs from the four pathways combined did not show a statistically significant correlation to CIS status, although the p-value was borderline (p = 0.0698; Figure 6). Like in the papillary tumors, the cluster analysis showed that the expression of the majority of the twelve genes was down regulated in normal biopsies compared to the ten biopsies from cystectomy specimens. The biopsies from the cystectomy specimens clustered together, and this was independent of whether the specimen was a CIS lesion or a histological normal sample located adjacent to CIS, underscoring the tight relation between CIS-and "normal" looking biopsies in this urothelium. DDIT3 was up-regulated in the normal samples compared to the biopsies from cystectomy specimens, while MYC was up regulated in the cystectomy specimens but not differentially expressed in the papillary tumors.

Bottom Line: The expression in the CIS group was comparable to the expression of twenty-three patients suffering from muscle-invasive bladder carcinoma.Finally, we validated our results in an independent test set and found that prediction of CIS status was possible using TF expression of the p38 MAPK pathway.We conclude that it is possible to use pathway analysis for molecular classification of bladder tumors.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Diagnostic Laboratory, Aarhus University Hospital Skejby, Brendstrupgaardsvej 100, DK-8200 Aarhus N, Denmark. herbsleb@ki.au.dk

ABSTRACT

Background: Carcinoma in situ (CIS) is believed to be a precursor of invasive bladder cancer. Identification of CIS is a valuable prognostic factor since radical treatment strategies can be offered these patients before the disease becomes invasive.

Methods: We developed a pathway based classifier approach to predict presence or absence of CIS in patients suffering from non muscle invasive bladder cancer. From Ingenuity Pathway Analysis we considered four canonical signalling pathways (p38 MAPK, FGF, Calcium, and cAMP pathways) with most coherent expression of transcription factors (TFs) across samples in a set of twenty-eight non muscle invasive bladder carcinomas. These pathways contained twelve TFs in total. We used the expression of the TFs to predict presence or absence of CIS in a Leave-One-Out Cross Validation classification.

Results: We showed that TF expression levels in three pathways (FGF, p38 MAPK, and calcium signalling) or the expression of the twelve TFs together could be used to predict presence or absence of concomitant CIS. A cluster analysis based on expression of the twelve TFs separated the samples in two main clusters: one branch contained 11 of the 15 patients without concomitant CIS and with the majority of the genes being down regulated; the other branch contained 10 of 13 patients with concomitant CIS, and here genes were mostly up regulated. The expression in the CIS group was comparable to the expression of twenty-three patients suffering from muscle-invasive bladder carcinoma. Finally, we validated our results in an independent test set and found that prediction of CIS status was possible using TF expression of the p38 MAPK pathway.

Conclusion: We conclude that it is possible to use pathway analysis for molecular classification of bladder tumors.

Show MeSH
Related in: MedlinePlus