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Proteomics in Bladder Cancer Research: Protein Profiling of Bladder Squamous Cell Carcinomas, Rev C

ematic analysis of the proteome expression profile of tumors, other cell types in the urinary tract, their secreted and/or externalized proteins, as well as the patients urine. The strategy is straightforward although its implementation requires a full knowledge of the protein composition of all cell types in the urinary tract.


Characterization of SCC Proteins Utilizing the Keratinocyte 2-D PAGE Database
To date, the identification and characterization of SCC proteins has been greatly facilitated by the fact that SCC cells exhibit similar protein expression profiles as keratinocytes, a cell type for which we have identified about 35% of the 3,500 proteins resolved by high-resolution 2-D gel electrophoresis (2-D PAGE) (Celis et al. 1995, 1996a). In addition, we have gathered a substantial amount of behavioral protein data (identity, cellular localization, regulatory properties, etc.) that has greatly speeded up the analysis of the tumors (Celis et al. 1996b, stergaard et al. 1997). This information is currently stored in 2-D PAGE proteomic databases that are available through the Internet thanks to custom software developed by Protein Databases, Inc., now owned by Bio-Rad. Figure 1 shows the synthetic master (IEF = isoelectric focusing) 2-D PAGE image of noncultured human keratinocyte proteins as depicted on the Web (http://biobase.dk/cgi-bin/celis).

Proteins flagged with a red cross correspond to known polypeptides. About 1,200 polypeptides have been identified in this database (IEF and NEPHGE). Both microsequencing (Vandekerckhove and Rasmussen 1994, Nika and Aebersold 1994) and mass spectrometry (Wilm et al. 1996, Yates 1996, Pappin 1997) are instrumental for the id
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