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

Ashani T. Weeraratna (Corresponding Author), 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 Kallioniemi, Jeffrey M. Trent, Patrice J. Morin, Paul S. Meltzer (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

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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
Pages (from-to)2264-2274
JournalOncogene
Volume23
Issue number12
DOIs
Publication statusPublished - 2004
MoE publication typeA1 Journal article-refereed

Fingerprint

Transcriptome
Melanoma
Genes
Calcium
GTP-Binding Proteins
Protein Array Analysis
Calpain
Melanocytes
Microarray Analysis
Computational Biology
Libraries
Cytoplasm
Peptide Hydrolases
Neoplasms

Keywords

  • SAGE
  • melanoma
  • tissue microarray
  • CD74
  • calpain
  • Wnt5a

Cite this

Weeraratna, A. T., Becker, D., Carr, K. M., Duray, P. H., Rosenblatt, K. P., Yang, S., ... Meltzer, P. S. (2004). Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome. Oncogene, 23(12), 2264-2274. https://doi.org/10.1038/sj.onc.1207337
Weeraratna, Ashani T. ; Becker, Dorothea ; Carr, Kristen M. ; Duray, Paul H. ; Rosenblatt, Kevin P. ; Yang, Sherry ; Chen, Yidong ; Bittner, Michael ; Strausberg, Robert L. ; Riggins, Gregory J. ; Wagner, Urs ; Kallioniemi, Olli ; Trent, Jeffrey M. ; Morin, Patrice J. ; Meltzer, Paul S. / Generation and analysis of melanoma SAGE libraries : SAGE advice on the melanoma transcriptome. In: Oncogene. 2004 ; Vol. 23, No. 12. pp. 2264-2274.
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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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Weeraratna, AT, Becker, D, Carr, KM, Duray, PH, Rosenblatt, KP, Yang, S, Chen, Y, Bittner, M, Strausberg, RL, Riggins, GJ, Wagner, U, Kallioniemi, O, Trent, JM, Morin, PJ & Meltzer, PS 2004, 'Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome', Oncogene, vol. 23, no. 12, pp. 2264-2274. https://doi.org/10.1038/sj.onc.1207337

Generation and analysis of melanoma SAGE libraries : SAGE advice on the melanoma transcriptome. / Weeraratna, Ashani T. (Corresponding Author); Becker, Dorothea; Carr, Kristen M.; Duray, Paul H.; Rosenblatt, Kevin P.; Yang, Sherry; Chen, Yidong; Bittner, Michael; Strausberg, Robert L.; Riggins, Gregory J.; Wagner, Urs; Kallioniemi, Olli; Trent, Jeffrey M.; Morin, Patrice J.; Meltzer, Paul S. (Corresponding Author).

In: Oncogene, Vol. 23, No. 12, 2004, p. 2264-2274.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Generation and analysis of melanoma SAGE libraries

T2 - SAGE advice on the melanoma transcriptome

AU - Weeraratna, Ashani T.

AU - Becker, Dorothea

AU - Carr, Kristen M.

AU - Duray, Paul H.

AU - Rosenblatt, Kevin P.

AU - Yang, Sherry

AU - Chen, Yidong

AU - Bittner, Michael

AU - Strausberg, Robert L.

AU - Riggins, Gregory J.

AU - Wagner, Urs

AU - Kallioniemi, Olli

AU - Trent, Jeffrey M.

AU - Morin, Patrice J.

AU - Meltzer, Paul S.

PY - 2004

Y1 - 2004

N2 - 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.

AB - 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.

KW - SAGE

KW - melanoma

KW - tissue microarray

KW - CD74

KW - calpain

KW - Wnt5a

U2 - 10.1038/sj.onc.1207337

DO - 10.1038/sj.onc.1207337

M3 - Article

VL - 23

SP - 2264

EP - 2274

JO - Oncogene

JF - Oncogene

SN - 0950-9232

IS - 12

ER -

Weeraratna AT, Becker D, Carr KM, Duray PH, Rosenblatt KP, Yang S et al. Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome. Oncogene. 2004;23(12):2264-2274. https://doi.org/10.1038/sj.onc.1207337