Changes in protein expression during melanoma differentiation determined by computer analysis of 2-D gels

A systems biology analysis of metastatic melanoma using in-depth three-dimensional protein profiling

Melanoma is an excellent model to study molecular mechanisms of tumor progression because melanoma usually develops through a series of architecturally and phenotypically distinct stages that are progressively more aggressive, culminating in highly metastatic cells. In this study, we used an in-depth, 3-D protein level, comparative proteome analysis of two genetically, very closely related melanoma cell lines with low- and high-metastatic potentials to identify proteins and key pathways involved in tumor progression. This proteome comparison utilized fluorescent tagging of cell lysates followed by microscale solution IEF prefractionation and subsequent analysis of each fraction on narrow-range 2-D gels. LC-MS/MS analysis of gel spots exhibiting significant abundance changes identified 110 unique proteins. The majority of observed abundance changes closely correlate with biological processes central to cancer progression, such as cell death and growth and tumorigenesis. In addition, the vast majority of protein changes mapped to six cellular networks, which included known oncogenes (JNK, c-myc, and N-myc) and tumor suppressor genes (p53 and transforming growth factor-β) as critical components. These six networks showed substantial connectivity, and most of the major biological functions associated with these pathways are involved in tumor progression. These results provide novel insights into cellular pathways implicated in melanoma metastasis.

Clinical applications of two-dimensional electrophoresis

Two-dimensional electrophoresis is increasingly being used as an important tool for biological research although it continues to have few direct clinical applications. In the absence of simple systems to identify and quantify individual proteins or groups of proteins it is unlikely that clinical applications will increase. Measurement of some individual proteins, for example a single acute phase reactant, often yields as much clinically useful information as could be currently expected from quantitation of several proteins with the same physiological role. Cost-containment pressures within the clinical laboratory will prevent the technique from becoming widely used in the clinical laboratory until it can clearly demonstrate that it can produce clinically important and necessary information that can not be obtained by other means. We continue to believe that the technique's greatest potential lies in identifying a protein or proteins whose concentration can be correlated with a disease and whose concentration varies with the progress of the disease. Antibodies to such proteins can then be produced and used to quantify the disease-associated proteins by a simple procedure, such as nephelometry. In spite of our belief of the likely clinical application of the technique there appears to be no systematic use of two-dimensional electrophoresis for this purpose. With clinical specimens a few investigators still run gels of serum or urine from patients with apparently unusual disorders and compare them visually with gels from healthy individuals. Nevertheless, the technique continues to have considerable unmet promise for clinical applications.

Protein patterns of benign and malignant human melanocytes show consistent changes in gene expression

For human malignant melanoma, no pattern of oncogene activation has yet been identified which consistently occurs in the malignant cells. In order to better understand the transformation process, we studied the overall gene expression at the protein level in human melanoma cells in vitro by two-dimensional gel electrophoresis. For that, four established cell lines, MEWO, M5, SKMEL13, and IGR39, were used and compared with newly established cultures of normal human melanocytes. Considerable variations in the protein patterns of the different melanoma cell lines were found, whereas the patterns of normal human melanocytes correlated fairly well with each other. With respect to the expression of single proteins, we identified four major proteins which were consistently found in cultured melanocytes and stringently repressed in the four melanoma cell lines examined. On the other hand, induction of new proteins in the different melanoma cell lines was found to be less stringent and also less uniform. We propose that malignant transformation of melanocytes may be more associated with the suppression of melanocytic proteins rather than with new expression of melanoma specific proteins.