Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome

Ashani T. Weeraratna, Dorothea Becker, Kristen M. Carr, Paul H. Duray, Kevin P. Rosenblatt, Sherry Yang, Yidong Chen, Michael Bittner, Robert L. Strausberg, Gregory J. Riggins, Urs Wagner, Olli P. Kallioniemi, Jeffrey M. Trent, Patrice J. Morin, Paul S. Meltzer

Research output: Contribution to journalArticle

58 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2264-2274
Number of pages11
JournalOncogene
Volume23
Issue number12
DOIs
StatePublished - Mar 18 2004
Externally publishedYes

Keywords

  • CD74
  • Calpain
  • Melanoma
  • SAGE
  • Tissue microarray
  • Wnt5a

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Cancer Research

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