Skip to main content
SpringerLink
Log in
Book cover

Expression Profiling of Human Tumors pp 47–60Cite as

Serial Analysis of Gene Expression (SAGE) in Cancer Research

  • Chapter

  • 80 Accesses

Abstract

Due to considerable research investment in the Human Genome Project, we will have access to the complete sequence information on all the genes encoded by the human genome within the next few years. Although this information will be of great value, it will not be sufficient to provide full understanding of the complex pathophysiology of diseases such as cancer. A more daunting task that lies ahead in this “postgenome era,” is to understand how the different genes are altered in the various cancers and how complex gene interactions produce particular outcomes.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Riggins, G. J. and Strausberg, R. L. (2001) Genome and genetic resources from the Cancer Genome Anatomy Project. Hum. Mol. Genet. 10, 663–667.

    Google Scholar 

  2. Adams, M. D., Soares, M. B., Kerlavage, A. R., Fields, C., and Venter, J. C. (1993) Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nat. Genet. 4, 373–380.

    Article  PubMed  CAS  Google Scholar 

  3. Williamson, A. R. (1999) The Merck Gene Index project. Drug Discov. Today 4, 115–122.

    Article  PubMed  CAS  Google Scholar 

  4. Velculescu, E., Zhang, L., Volgelstein, B., and Kinzler, W. (1995) Serial analysis of gene expression. Science 270, 484–487.

    Article  PubMed  CAS  Google Scholar 

  5. Gruvberger, S., Ringner, M., Chen, Y., et al. (2001) Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res. 61, 5979–5984.

    PubMed  CAS  Google Scholar 

  6. Perou, C. M., Sorlie, T., Eisen, M. B., et al. (2000) Molecular portraits of human breast tumours. Nature 406, 747–752.

    Article  PubMed  CAS  Google Scholar 

  7. Kuo, W. P., Jenssen, T. K., Butte, A. J., Ohno-Machado, L., and Kohane, I. S. (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18, 405–412.

    Article  PubMed  CAS  Google Scholar 

  8. Zhang, L., Zhou, W., Velculescu, V., et al. (1997) Gene expression profiles in normal and cancer cells. Science 276, 1268–1272.

    Article  PubMed  CAS  Google Scholar 

  9. Velculescu, E., Zhang, L., Zhou, W., et al. (1997) Characterization of the yeast transcriptome. Cell 88, 243–251.

    Article  PubMed  CAS  Google Scholar 

  10. Eisen, M. B Spellman, P T., Brown, P. 0., and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95 14,86314,868.

    Google Scholar 

  11. Lal, A., Lash, A. E., Altschul, S. F., et al. (1999) A public database for gene expression in human cancers. Cancer Res. 59, 5403–5407.

    PubMed  CAS  Google Scholar 

  12. Datson, N. A., van der Perk-de Jong, J., van den Berg, M. P., de Kloet, E. R., and Vreugdenhil, E. (1999) MicroSAGE: a modified procedure for serial analysis of gene expression in limited amounts of tissue. Nucleic Acids Res. 27, 1300–1307.

    Google Scholar 

  13. Peters, D. G., Kassam, A. B., Yonas, H., O’Hare, E. H., Ferrell, R. E., and Brufsky, A. M. (1999) Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite. Nucleic Acids Res. 27, e39.

    Google Scholar 

  14. Virlon, B.., Cheval, L., Buhler, J. M., Billon, E., Doucet, A., and Elalouf, J. M. (1999) Serial microanalysis of renal transcriptomes. Proc. Natl. Acad. Sci. USA 96, 15,286–15, 291.

    Google Scholar 

  15. St. Croix, B., Rago, C., Velculescu, V., et al. (2000) Genes expressed in human tumor endothelium. Science 289, 1197–1202.

    Article  Google Scholar 

  16. Saha, S., Bardelli, A., Buckhaults, P., et al. (2001) A phosphatase associated with metastasis of colorectal cancer. Science 294, 1343–1346.

    Article  PubMed  CAS  Google Scholar 

  17. Saha, S., Sparks, A. B., Rago, C., et al. (2002) Using the transcriptome to annotate the genome. Nat. Biotechnol. 20, 508–512.

    Article  PubMed  CAS  Google Scholar 

  18. Caron, H van Schaik, B van der Mee, M., et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291 12891292.

    Google Scholar 

  19. Zhou, W., Sokoll, L. J., Bruzek, D. J., et al. (1998) Identifying markers for pancreatic cancer by gene expression analysis. Cancer Epidemiol. Biomarkers Prey. 7, 109–112.

    CAS  Google Scholar 

  20. Argani, P., Rosty, C., Reiter, R. E., et al. (2001) Discovery of new markers of cancer through serial analysis of gene expression: prostate stem cell antigen is overexpressed in pancreatic adenocarcinoma. Cancer Res. 61, 4320–4324.

    PubMed  CAS  Google Scholar 

  21. Michiels, E. M., Oussoren, E., Van Groenigen, M., et al. (1999) Genes differentially expressed in medulloblastoma and fetal brain. Physiol. Genomics 1, 83–91.

    PubMed  CAS  Google Scholar 

  22. van Limpt, V., Chan, A., Caron, H., et al. (2000) SAGE analysis of neuroblastoma reveals a high expression of the human homologue of the Drosophila Delta gene. Med. Pediatr. Oncol 35, 554–558.

    Google Scholar 

  23. Sasaki, M., Nakahira, K., Kawano, Y., et al. (2001) MAGE-El, a new member of the melanoma-associated antigen gene family and its expression in human glioma. Cancer Res 61, 4809–4814.

    CAS  Google Scholar 

  24. Polyak, K. and Riggins, G. J. (2001) Gene discovery using the serial analysis of gene expression technique: implications for cancer research. J. Clin. Oncol. 19, 2948–2958.

    PubMed  CAS  Google Scholar 

  25. Vandeputte, D. A., Meije, C. B., van Dartel, M., et al. (2001) GOA, a novel gene encoding a ring finger B-box coiled-coil protein, is overexpressed in astrocytoma. Biochem. Biophys. Res. Commun 286, 574–579.

    Google Scholar 

  26. Hibi, K., Westra, W. H., Borges, M., Goodman, S., Sidransky, D., and Jen, J. (1999) PGP9.5 as a candidate tumor marker for non-small-cell lung cancer. Am. J. Pathol. 155, 711–715.

    Google Scholar 

  27. Nacht, M., Dracheva, T., Gao, Y., et al. (2001) Molecular characteristics of non-small cell lung cancer. Proc. Natl. Acad. Sci. USA 98, 15,203–15, 208.

    Google Scholar 

  28. Hough, C. D., Sherman-Baust, C. A., Pizer, E. S., et al. (2000) Large-scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer. Cancer Res. 60, 6281–6287.

    PubMed  CAS  Google Scholar 

  29. Argani, P Iacobuzio-Donahue, C., Ryu, B., et al. (2001) Mesothelin is overexpressed in the vast majority of ductal adenocarcinomas of the pancreas: identification of a new pancreatic cancer marker by serial analysis of gene expression (SAGE). Clin. Cancer Res. 7,3862–3868.

    Google Scholar 

  30. Porter, D. A., Krop, I. E., Nasser, S., et al. (2001) A SAGE (serial analysis of gene expression) view of breast tumor progression. Cancer Res. 61, 5697–5702.

    PubMed  CAS  Google Scholar 

  31. Krop, I. E., Sgroi, D., Porter, D. A., et al. (2001) HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells. Proc. Natl. Acad. Sci. USA 98, 9796–9801.

    PubMed  CAS  Google Scholar 

  32. Ferguson, A. T., Evron, E., Umbricht, C. B., et al. (2000) High frequency of hypermethylation at the 14–3–3 sigma locus leads to gene silencing in breast cancer. Proc. Natl. Acad. Sci. USA 97, 6049 – 6054.

    Google Scholar 

  33. Charpentier, A. H., Bednarek, A. K., Daniel, R. L., et al. (2000) Effects of estrogen on global gene expression: identification of novel targets of estrogen action. Cancer Res. 60, 5977–5983.

    PubMed  CAS  Google Scholar 

  34. Bouras, T., Southey, M. C., Chang, A. C., et al. (2002) Stanniocalcin 2 is an estrogen-responsive gene coexpressed with the estrogen receptor in human breast cancer. Cancer Res. 62, 1289–1295.

    PubMed  CAS  Google Scholar 

  35. Aldaz, C. M., Hawkins, K., Drake, J, Laflin, K., Gaddis, S., and Sahin, A. (2002) High resolution transcriptome analysis of breast cancer using SAGE. Proc. Am. Assoc. Cancer Res. 43, 2236.

    Google Scholar 

  36. Waghray, A., Schober, M., Feroze, F., Yao, F., Virgin, J., and Chen, Y. Q. (2001) Identification of differentially expressed genes by serial analysis of gene expression in human prostate cancer. Cancer Res. 61, 4283–4286.

    PubMed  CAS  Google Scholar 

  37. Xu, L. L., Shanmugam, N., Segawa, T., et al. (2000) A novel androgen-regulated gene, PMEPAI, located on chromosome 20813 exhibits high level expression in prostate. Genomics 66, 257–263.

    Article  PubMed  CAS  Google Scholar 

  38. He, T. C., Sparks, A. B., Rago, C., et al. (1998) Identification of c-MYC as a target of the APC pathway. Science 281, 1509–1512.

    Article  PubMed  CAS  Google Scholar 

  39. Hermeking, H Rago, C., Schuhmacher, M., et al. (2000) Identification of CDK4 as a target of c-MYC. Proc. Natl. Acad. Sci. USA 97 2229–2234.

    Google Scholar 

  40. He, T. C., Chan, T. A., Vogelstein, B., and Kinzler, K. W. (1999) PPARdelta is an APCregulated target of nonsteroidal anti-inflammatory drugs. Cell 99, 335–345.

    CAS  Google Scholar 

  41. Polyak, K., Xia, Y., Zweier, J. L., Kinzler, K. W., and Vogelstein, B. (1997) A model for p53-induced apoptosis. Nature 389, 300–305.

    Article  PubMed  CAS  Google Scholar 

  42. Hermeking, H., Lengauer, C., Polyak, K., et al. (1997) 14–3–3 sigma is a p53–regulated inhibitor of G2/M progression. Mol. Cell 1, 3 – 11.

    Google Scholar 

  43. Boon, K., Caron, H. N., van Asperen, R., et al. (2001) N-myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis. EMBO J 20, 1383–1393.

    CAS  Google Scholar 

  44. Lal, A., Peters, H., St. Croix, B., et al. (2001) Transcriptional response to hypoxia in human tumors. J. Natl. Cancer Inst. 93, 1337–1343.

    Article  PubMed  CAS  Google Scholar 

  45. Aldaz, C. M., Hu, Y., Daniel, R Gaddis, S., Kittrell, F., and Medina, D. (2002) Serial analysis of gene expression in normal p53 null mammary epithelium. Oncogene 21 63666376.

    Google Scholar 

  46. Klein, R. D. Hawkins, K. A., Lubet, R., Fischer, S. M., and Aldaz, C. M. (2002) Comparative serial analysis of gene expression (SAGE) studies of normal mouse skin and UV-induced carcinomas. Proc. Am. Assoc. Cancer Res. 43 5676.

    Google Scholar 

Download references

Authors
  1. C. Marcelo Aldaz
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

    Marc Ladanyi MD  & William L. Gerald MD, PhD  & 

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer Science+Business Media New York

About this chapter

Cite this chapter

Aldaz, C.M. (2003). Serial Analysis of Gene Expression (SAGE) in Cancer Research. In: Ladanyi, M., Gerald, W.L. (eds) Expression Profiling of Human Tumors. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-386-6_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-59259-386-6_4

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61737-375-6

  • Online ISBN: 978-1-59259-386-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation