title: Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome.
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.
authors.affiliation: Laboratory of Immunology, National Institutes of Health, The National Institute on Aging, Baltimore, MD 21224, USA. weerarat@grc.nia.nih.gov
authors.forename: Ashani T
authors.initials: AT
authors.lastname: Weeraratna
authors.forename: Dorothea
authors.initials: D
authors.lastname: Becker
authors.forename: Kristen M
authors.initials: KM
authors.lastname: Carr
authors.forename: Paul H
authors.initials: PH
authors.lastname: Duray
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Rosenblatt
authors.forename: Sherry
authors.initials: S
authors.lastname: Yang
authors.forename: Yidong
authors.initials: Y
authors.lastname: Chen
authors.forename: Michael
authors.initials: M
authors.lastname: Bittner
authors.forename: Robert L
authors.initials: RL
authors.lastname: Strausberg
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Riggins
authors.forename: Urs
authors.initials: U
authors.lastname: Wagner
authors.forename: Olli P
authors.initials: OP
authors.lastname: Kallioniemi
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Trent
authors.forename: Patrice J
authors.initials: PJ
authors.lastname: Morin
authors.forename: Paul S
authors.initials: PS
authors.lastname: Meltzer
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000944:Antigens, Differentiation, B-Lymphocyte / Q000378:metabolism; D002154:Calpain / Q000378:metabolism; D045744:Cell Line, Tumor; D019295:Computational Biology; D020224:Expressed Sequence Tags; D005260:Female; D015723:Gene Library; D000949:Histocompatibility Antigens Class II / Q000378:metabolism; D006801:Humans; D007150:Immunohistochemistry; D007527:Isoenzymes / Q000378:metabolism; D008297:Male; D008545:Melanoma / Q000235:genetics* / Q000473:pathology; D008875:Middle Aged; D009124:Muscle Proteins; D009367:Neoplasm Staging; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results
chemical_list: D000944:Antigens, Differentiation, B-Lymphocyte; D000949:Histocompatibility Antigens Class II; D007527:Isoenzymes; D009124:Muscle Proteins; C045084:invariant chain; C105884:CAPN3 protein, human; D002154:Calpain