Limits...
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.

Show MeSH

Related in: MedlinePlus

p38 MAPK canonical signalling pathway. Genes are colored according to the log ratio gene expression values between tumors with concomitant CIS and tumors without concomitant CIS. Yellow gene-symbols indicate up-regulation and blue gene symbols indicate down-regulation. The pathway is from the Ingenuity software.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2268699&req=5

Figure 1: p38 MAPK canonical signalling pathway. Genes are colored according to the log ratio gene expression values between tumors with concomitant CIS and tumors without concomitant CIS. Yellow gene-symbols indicate up-regulation and blue gene symbols indicate down-regulation. The pathway is from the Ingenuity software.

Mentions: We found that the ability to predict CIS status based on the TFs in the P38 MAPK pathway (Figure 1) was most interesting since it contained a relative large number of TFs. Further, it has previously been suggested to have a role in bladder cancer development [9]. Moreover, the FGF pathway (Figure 2) was also interesting because it, among other genes, contained the well described FGF receptor, FGFR3. We calculated the mean log ratios of all expressed genes from the tumors with concomitant CIS compared to the expression in tumors without concomitant CIS and superimposed the gene expression data to the FGF and p38/MAPK canonical pathways. The canonical pathway for p38 MAPK signalling showed that the majority of genes were up regulated in tumors with adjacent CIS compared to tumors without adjacent CIS (Figure 1). For example interleukine 1 (IL-1), which activates the pathway, was found to be up regulated together with its receptor, interleukin 1 receptor beta (IL1R). Further, the kinases mitogen activated kinase kinase kinases, MAP3K5 and MAP3K7 were both up regulated like the kinase-kinase MAP2K4 and the mitogen activated kinase p38 MAPK α. In the nucleus, p38 MAPK α regulates transcription of several targets, and our data showed that in tumors with concomitant CIS the majority of these targets were up regulated, like cAMP responsive element binding protein 1 (CREB1), activating transcription factor 1 and 2 (ATF1, ATF2), MADS box transcription enhancer factor 2, polypeptide A and C (MEF2A, MEF2C), signal transducer and activator of transcription 1 (STAT1), while DNA-damage-inducible transcript 3 (DDIT3 = CHOP) was down regulated.


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)

p38 MAPK canonical signalling pathway. Genes are colored according to the log ratio gene expression values between tumors with concomitant CIS and tumors without concomitant CIS. Yellow gene-symbols indicate up-regulation and blue gene symbols indicate down-regulation. The pathway is from the Ingenuity software.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: p38 MAPK canonical signalling pathway. Genes are colored according to the log ratio gene expression values between tumors with concomitant CIS and tumors without concomitant CIS. Yellow gene-symbols indicate up-regulation and blue gene symbols indicate down-regulation. The pathway is from the Ingenuity software.
Mentions: We found that the ability to predict CIS status based on the TFs in the P38 MAPK pathway (Figure 1) was most interesting since it contained a relative large number of TFs. Further, it has previously been suggested to have a role in bladder cancer development [9]. Moreover, the FGF pathway (Figure 2) was also interesting because it, among other genes, contained the well described FGF receptor, FGFR3. We calculated the mean log ratios of all expressed genes from the tumors with concomitant CIS compared to the expression in tumors without concomitant CIS and superimposed the gene expression data to the FGF and p38/MAPK canonical pathways. The canonical pathway for p38 MAPK signalling showed that the majority of genes were up regulated in tumors with adjacent CIS compared to tumors without adjacent CIS (Figure 1). For example interleukine 1 (IL-1), which activates the pathway, was found to be up regulated together with its receptor, interleukin 1 receptor beta (IL1R). Further, the kinases mitogen activated kinase kinase kinases, MAP3K5 and MAP3K7 were both up regulated like the kinase-kinase MAP2K4 and the mitogen activated kinase p38 MAPK α. In the nucleus, p38 MAPK α regulates transcription of several targets, and our data showed that in tumors with concomitant CIS the majority of these targets were up regulated, like cAMP responsive element binding protein 1 (CREB1), activating transcription factor 1 and 2 (ATF1, ATF2), MADS box transcription enhancer factor 2, polypeptide A and C (MEF2A, MEF2C), signal transducer and activator of transcription 1 (STAT1), while DNA-damage-inducible transcript 3 (DDIT3 = CHOP) was down regulated.

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