In this study, we generated three SAGE libraries from melanoma tissues.
Using bioinformatics tools usually applied to microarray data, we
identified several genes, including novel transcripts, which are
preferentially expressed in melanoma. SAGE results converged with
previous microarray analysis on the importance of intracellular calcium
and G-protein signaling, and the Wnt/Frizzled family. We also examined
the expression of CD74, which was specifically, albeit not abundantly,
expressed in the melanoma libraries using a melanoma progression tissue
microarray, and demonstrate that this protein is expressed by melanoma
cells but not by benign melanocytes. Many genes involved in
intracellular calcium and G-protein signaling were highly expressed in
melanoma, results we had observed earlier from microarray studies (Bittner et al., 2000).
One of the genes most highly expressed in our melanoma SAGE libraries
was a calcium-regulated gene, calpain 3 (p94). Immunohistochemical
analysis demonstrated that calpain 3 moves from the nuclei of
non-neoplastic cells to the cytoplasm of malignant cells, suggesting
activation of this intracellular proteinase. Our SAGE results and the
clinical validation data demonstrate how SAGE profiles can highlight
specific links between signaling pathways as well as associations with
tumor progression. This may provide insights into new genes that may be
useful for the diagnosis and therapy of melanoma.
- tissue microarray