title: Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situ in the urinary bladder.
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.
  
  
  CONCLUSIONS
  We conclude that it is possible to use pathway analysis for molecular classification of bladder tumors.
authors.affiliation: Molecular Diagnostic Laboratory, Aarhus University Hospital Skejby, Brendstrupgaardsvej 100, DK-8200 Aarhus N, Denmark. herbsleb@ki.au.dk
authors.forename: Malene
authors.initials: M
authors.lastname: Herbsleb
authors.forename: Ole F
authors.initials: OF
authors.lastname: Christensen
authors.forename: Thomas
authors.initials: T
authors.lastname: Thykjaer
authors.forename: Carsten
authors.initials: C
authors.lastname: Wiuf
authors.forename: Michael
authors.initials: M
authors.lastname: Borre
authors.forename: Torben F
authors.initials: TF
authors.lastname: Orntoft
authors.forename: Lars
authors.initials: L
authors.lastname: Dyrskjøt
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D001706:Biopsy; D020013:Calcium Signaling / Q000235:genetics*; D002278:Carcinoma in Situ / Q000737:chemistry* / Q000473:pathology; D016000:Cluster Analysis; D019295:Computational Biology; D005346:Fibroblast Growth Factors / Q000235:genetics*; D015870:Gene Expression; D005819:Genetic Markers / Q000235:genetics; D006801:Humans; D016013:Likelihood Functions; D040081:Protein Array Analysis; D014157:Transcription Factors / Q000302:isolation & purification*; D001749:Urinary Bladder Neoplasms / Q000737:chemistry* / Q000473:pathology; D048051:p38 Mitogen-Activated Protein Kinases / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; D005819:Genetic Markers; D014157:Transcription Factors; D005346:Fibroblast Growth Factors; D048051:p38 Mitogen-Activated Protein Kinases