title: Molecular Analysis of Upper Tract and Bladder Urothelial Carcinoma: Results from a Microarray Comparison.
abstract: BACKGROUND
  Prior studies have shown genetic similarities between upper tract and bladder urothelial carcinoma. However, upper tract urothelial carcinoma tends to be higher grade than bladder urothelial carcinoma and tends to form in patients with certain familial conditions (e.g. Lynch Syndrome), indicating there may be unique biologic processes in these tumors. The purpose of this study was to evaluate the differences in gene expression between upper tract and bladder urothelial carcinoma using microarray data.
  
  
  METHODS
  A search of publicly available microarray datasets identified a clinically annotated dataset of 12 upper tract and 20 bladder urothelial carcinoma specimens. Gene expression analysis of data derived from the Affymetrix HGU133Plus2 chip was performed. Bioconductor packages were used to evaluate clustering, differential gene expression, pathways relevant to oncology, and a basal/luminal signature in upper tract versus bladder urothelial carcinoma.
  
  
  RESULTS
  When separated by pathologic T stage, there was evidence of differential clustering among pT3 tumors and significant gene expression differences in 81 genes. Pathway analysis revealed differences in HGF and TNF signaling pathways. Upper tract tumors tended to have high expression of genes associated with a luminal subtype. One of the genes most highly expressed in upper tract tumors, SLITRK6, is the target of an antibody drug conjugate (AGS15E) currently in phase I clinical trials.
  
  
  CONCLUSIONS
  This study provides evidence for molecular differences between upper tract and bladder urothelial carcinoma, some of which contribute to oncologic-relevant pathways. Upper tract tumors tended to express genes consistent with a luminal subtype. We also identify a marker, SLITRK6, as a potential target for patients with advanced upper tract urothelial carcinoma.
authors: Department of Urology, University of California San Francisco, San Francisco, California, United States of America.
authors: Thomas
authors: T
authors: Sanford
authors: Department of Urology, University of California San Francisco, San Francisco, California, United States of America.
authors: Sima
authors: S
authors: Porten
authors: Department of Urology, University of California San Francisco, San Francisco, California, United States of America.
authors: Maxwell V
authors: MV
authors: Meng
mesh_terms: D000368:Aged; D002295:Carcinoma, Transitional Cell / Q000235:genetics*; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D001749:Urinary Bladder Neoplasms / Q000235:genetics*; D014551:Urinary Tract / Q000378:metabolism*