Large-scale protein expression analysis provides a discovery-driven approach in studying the detailed mechanism behind the pathogenesis of various diseases. We have intended in this study to classify proteins differentially expressed in the glomerulus, cortex and medulla of normal human kidney in an attempt to contribute to understanding the pathogenesis of renal diseases. Kidney tissues with normal appearance, far from the tumor mass, were obtained from patients under surgical nephrectomy due to renal cell carcinoma, and pieces of cortex and outer medulla were excised. Glomeruli were further purified from the cortices to an apparent homogeneity under a phase-contrast microscopy. The tissues were solubilized in a conventional extraction buffer (urea/NP-40/DTT), separated by 2-DE with 18 cm IPG strips of pH 3-10 range in the 1st dimension and 20 x 20 cm separation gels of 12.5 % in the 2nd dimension, and silver-stained. 2-DE gel images of the three tissues obtained from each of 4 subjects with no apparent pathologic manifestations were subjected to analysis by PDQuest, a 2-DE analysis software (Bio-Rad) to detect protein spots differentially expressed. We detected 1,810 valid spots in the glomerulus, 1,758 spots in the cortex, and 1,275 spots in medulla Statistical assessment of significance differences in expression among the three tissues was made by one-way ANOVE followed by Tukey's post-hoc test. Differences were considered significant at p<0.05. The statistical analyses revealed 204 protein spots abundantly expressed in the glomerulus, 138 protein spots in the cortex and 89 spots in the medulla. These spot proteins were now under identification by peptide mass fingerprinting with a MALDI-TOF mass spectrometer. These results were combined with the proteome database for the glomerulus of normal human kidney, which we have recently constructed and discussed in the view of physiological significance.
