Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma <it>in situ </it>in the urinary bladder
<p>Abstract</p> <p>Background</p> <p>Carcinoma <it>in situ </it>(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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-01-01
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| Series: | BMC Cancer |
| Online Access: | http://www.biomedcentral.com/1471-2407/8/37 |
| _version_ | 1818049751894982656 |
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| author | Ørntoft Torben F Borre Michael Wiuf Carsten Thykjaer Thomas Christensen Ole F Herbsleb Malene Dyrskjøt Lars |
| author_facet | Ørntoft Torben F Borre Michael Wiuf Carsten Thykjaer Thomas Christensen Ole F Herbsleb Malene Dyrskjøt Lars |
| author_sort | Ørntoft Torben F |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Carcinoma <it>in situ </it>(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.</p> <p>Methods</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>We conclude that it is possible to use pathway analysis for molecular classification of bladder tumors.</p> |
| first_indexed | 2024-12-10T10:42:34Z |
| format | Article |
| id | doaj.art-eba6608b5ac241ce919a3babc93cfc02 |
| institution | Directory Open Access Journal |
| issn | 1471-2407 |
| language | English |
| last_indexed | 2024-12-10T10:42:34Z |
| publishDate | 2008-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj.art-eba6608b5ac241ce919a3babc93cfc022022-12-22T01:52:15ZengBMCBMC Cancer1471-24072008-01-01813710.1186/1471-2407-8-37Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma <it>in situ </it>in the urinary bladderØrntoft Torben FBorre MichaelWiuf CarstenThykjaer ThomasChristensen Ole FHerbsleb MaleneDyrskjøt Lars<p>Abstract</p> <p>Background</p> <p>Carcinoma <it>in situ </it>(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.</p> <p>Methods</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>We conclude that it is possible to use pathway analysis for molecular classification of bladder tumors.</p>http://www.biomedcentral.com/1471-2407/8/37 |
| spellingShingle | Ørntoft Torben F Borre Michael Wiuf Carsten Thykjaer Thomas Christensen Ole F Herbsleb Malene Dyrskjøt Lars Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma <it>in situ </it>in the urinary bladder BMC Cancer |
| title | Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma <it>in situ </it>in the urinary bladder |
| title_full | Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma <it>in situ </it>in the urinary bladder |
| title_fullStr | Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma <it>in situ </it>in the urinary bladder |
| title_full_unstemmed | Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma <it>in situ </it>in the urinary bladder |
| title_short | Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma <it>in situ </it>in the urinary bladder |
| title_sort | bioinformatic identification of fgf p38 mapk and calcium signalling pathways associated with carcinoma it in situ it in the urinary bladder |
| url | http://www.biomedcentral.com/1471-2407/8/37 |
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