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

Oncogene volume 23, pages 2264–2274 (2004)Cite this article

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.

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Acknowledgements

We extend our appreciation to Ms Cheryl Sherman-Baust for assistance with the SAGE technique, and Dr Galen Hostetter for assistance with the tissue microarray. We also thank Agencourt Biosciences for sequencing of these libraries via collaboration with the Cancer Genome Anatomy project.

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Authors and Affiliations

  1. The National Institute on Aging, Baltimore, MD, USA

    Ashani T Weeraratna & Sherry Yang

  2. Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA

    Dorothea Becker

  3. The National Cancer Institute, Bethesda, MD, USA

    Kristen M Carr, Paul H Duray & Kevin P Rosenblatt

  4. The National Human Genome Research Institute, Bethesda, MD, USA

    Yidong Chen & Paul S Meltzer

  5. The Translational Genomics Research Institute, Phoenix, AZ, USA

    Michael Bittner & Jeffrey M Trent

  6. The Institute for Genomic Research, Rockville, MD, USA

    Robert L Strausberg

  7. Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA

    Gregory J Riggins

  8. Institute of Pathology, University of Basel, Basel, Switzerland

    Urs Wagner

  9. Medical Biotechnology Group, Technical Research Centre of Finland and University of Turku, Turku, Finland

    Olli P Kallioniemi & Patrice J Morin

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  1. Ashani T Weeraratna
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Correspondence to Ashani T Weeraratna or Paul S Meltzer.

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Weeraratna, A., Becker, D., Carr, K. et al. Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome. Oncogene 23, 2264–2274 (2004). https://doi.org/10.1038/sj.onc.1207337

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  • DOI: https://doi.org/10.1038/sj.onc.1207337

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