Proteomics and the Kidney

Abstract

Proteomics can be defined as "the systematic analysis of proteins for their identity, quantity, and function." The central concept is "multiplexing," i.e., simultaneous analysis of all proteins in a defined protein population, rather than investigation of one protein at a time, as in traditional biochemistry. Two major approaches have been described: (1) mass spectrometry-based approaches and (2) protein micro-array approaches. The purpose of this Science Watch article is to describe the fundamental features of these two approaches and to speculate on how proteomics will be useful in nephrology and nephrology research in the coming years.

Discovery of Protein Biomarkers for Renal Diseases

“…These methods were reviewed recently (43)(44)(45)(46). The advantages and disadvantages of commonly used methods are summarized in Table 4 and Appendix 1.…”

“…One then hopes that protein will follow RNA levels, which is not always the case (34 -37), and that the protein will be detectable in serum or urine. Alternatively, one may use differential proteomic approaches (2-D differential in-gel electrophoresis, isotope-coded affinity tags [ICAT]) on proteins obtained from normal and diseased tissue samples (37)(38)(39). These subtractive strategies can work well if the question is presence or absence of disease, the disease itself is uniform, and the differential diagnosis is short (e.g., pregnant versus not pregnant).…”

“…The spots can be robotically removed, trypsinized, and subjected to matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (TOF) or TOF-TOF for identification (reviewed in ref. 43). This method is good for high-abundant, moderate-pI, moderate-molecularweight soluble proteins but is not good for membrane, lowmolecular-weight, or very acidic or basic proteins.…”

Challenges of Genomics and Proteomics in Nephrology

“…[21,22] Several renal centers have initiated proteomic analysis to their research areas. Promising areas of research include a description of altered protein expression in tissues and biological fluids (serum and urine), the development of novel biomarkers for diagnosis and early detection of kidneys undergoing end-stage renal disease, the identification of new targets for therapeutics, and the potential for accelerating drug development through more effective strategies to evaluate therapeutic effect and toxicity.…”

Practice guidelines for the renal biopsy

“…New directions include [45][46][47][48][49][50][51] genomics and proteomics of renal disease. This arena is currently handicapped by the need for tissue fixation that may limit recovery for RNA and protein analysis.…”