Use of cDNA Representational Difference Analysis to Identify Disease-Specific Genes in Human Atherosclerotic Plaques

  • Kerry Tyson
  • Catherine Shanahan
Part of the Methods in Molecular Medicine™ book series (MIMM, volume 30)

Abstract

Changes in gene expression underlie many biological phenomena, including cellular differentiation and activation, embryonic development, and pathological processes. In recent years, much attention has been focused on the identification of genes that are differentially expressed between normal and disease states: the isolation of disease-specific genes is not only essential for our understanding of the molecular basis of pathological conditions, but may potentially highlight novel therapeutic targets.

Keywords

Vortex Agarose MgCl2 Diethyl Isopropanol 

References

  1. 1.
    Hubank, M. and Schatz, D. (1994) Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucl. Acids. Res., 22, 5640–5648.CrossRefPubMedGoogle Scholar
  2. 2.
    Tyson, K. L., Weissberg, P. L., and Shanahan, C. M. Unpublished observations.Google Scholar
  3. 3.
    Duguid, J. R., Rohwer, R. G., and Seed, B. (1988) Isolation of cDNAs of scrapie-modulated RNAs by subtractive hybridization of a cDNA library. Proc. Natl. Acad. Sci., 85, 5738–5742.CrossRefPubMedGoogle Scholar
  4. 4.
    Duguid, J. R. and Dinauer, M. C. (1990) Library subtraction of cDNA libraries to identify differentially expressed genes in scrapie infection. Nucl. Acids Res., 18, 2789–2792.CrossRefPubMedGoogle Scholar
  5. 5.
    Shanahan, C. M., Weissberg, P. L., and Metcalfe, J. C. (1993) Isolation of gene markers of differentiated and proliferating vascular smooth-muscle cells. Circ. Res., 73, 193–204.PubMedGoogle Scholar
  6. 6.
    Liang, P. and Pardee, A. B. (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science, 257, 967–971.CrossRefPubMedGoogle Scholar
  7. 7.
    Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995) Serial analysis of gene expression. Science, 270, 484–487.CrossRefPubMedGoogle Scholar
  8. 8.
    Utans, U., Liang, P., Wyner, L. R., Kamovsky, M. J., and Russell, M. E. (1994) Chronic cardiac rejection: identification of five upregulated genes in transplanted hearts by differential mRNA display. Proc. Natl. Acad. Sci., 91, 6463–6467.CrossRefPubMedGoogle Scholar
  9. 9.
    Hu, E., Liang, P., and Spiegelman, B. M. (1996) AdipoQ is a novel adiposespecific gene dysregulated in obesity. J. Biol. Chem., 271, 10,697–10,703.CrossRefPubMedGoogle Scholar
  10. 10.
    Lee, I. J., Soh, Y. J., and Song, B.J. (1997) Molecular characterization of fetal alcohol syndrome using mRNA differential display. Biochem. Biophys. Res. Comm., 240, 309–313.CrossRefPubMedGoogle Scholar
  11. 11.
    Li, Y. L. and Youssoufian, H. (1997) MxA overexpression reveals a common genetic link in four Fanconi anemia complementation groups. J. Clin. Invest. 100, 2873–2880.CrossRefPubMedGoogle Scholar
  12. 12.
    Patel, I. R., Attur, M. G., Patel, R. N., Stuchin, S. A., Abagyan, R. A., Abramson, S. B., and Amin, A. R. (1998) TNFα convertase enzyme from human arthritisaffected cartilage: Isolation of cDNA by differential display, expression of the active enzyme and regulation of TNFα. J. Immunol., 160, 4570–4579.PubMedGoogle Scholar
  13. 13.
    Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D. E., Hieter, P., Vogelstein, B., and Kinzler, W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243–251.CrossRefPubMedGoogle Scholar
  14. 14.
    Madden, S. L., Galella, E.A., Zhu, J. S., Bertelsen, A. H., and Beaudry, G. A. (1997) SAGE transcript profiles for p53-dependent growth regulation. Oncogene, 15, 1079–1085.CrossRefPubMedGoogle Scholar
  15. 15.
    Gonzalez-Zulueta, M., Ensz, L. M., Mukhina, G., Lebovitz, R. M., Zwacka, R. M., Engelhardt, J.F., Oberley, L. W., Dawson., V. L., and Dawson, T. M. (1998) Manganese superoxide dismutase protects nNOS neurons from NMDA and nitric oxide-mediated neurotoxicity. J. Neurosci., 18, 2040–2055.PubMedGoogle Scholar
  16. 16.
    Wada, J., Kumar, A., Ota, K., Wallner, E. I., Batlle, D. C., and Kanwar, Y. S. (1997) Representational difference analysis of cDNA of genes expressed in embryonic kidney. Kidney Int., 51, 1629–1638.CrossRefPubMedGoogle Scholar
  17. 17.
    O’Neill, M. J. and Sinclair, A.H. (1997) Isolation of rare transcripts by representational difference analysis. Nucl. Acids Res. 25, 2681,2682.CrossRefPubMedGoogle Scholar
  18. 18.
    Don, M. and Manuelidis, L. (1996) Visualization of viral candidate cDNAs in infectious brain fractions from Creutzfeldt-Jakob disease by representational difference analysis. J. Neurovirol. 2, 240–248.CrossRefGoogle Scholar
  19. 19.
    Niwa, H., Harrison, L. C., DeAizpurua, H., and Cram, D. S. (1997) Identification of pancreatic beta cell-related genes by representational difference analysis. Endocrinology 138, 1419–1426.CrossRefPubMedGoogle Scholar
  20. 20.
    Gress, T. M., Wallrapp, C., Frohme, M., MullerPillasch, F., Lacher, U., Friess, H., Buchler, M., Adler, G., and Hoheisel, J. D. (1997) Identification of genes with specific expression in pancreatic cancer by cDNA representational difference analysis. Genes Chromosomes and Cancer 19, 97–103.CrossRefPubMedGoogle Scholar
  21. 21.
    Tajima, Y., Tashiro, K., and Camerini, D. (1997) Cloning of human chromosome 17-specific cDNAs using representational difference analysis and human-mouse hybrid cells. Genomics 42, 353–355.CrossRefPubMedGoogle Scholar
  22. 22.
    Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. 2nd ed., Cold Spring Harbor Laboratory Press, New York.Google Scholar
  23. 23.
    Gubler, U. and Hoffman, B. J. (1983) A simple and very efficient method for generating cDNA libraries. Gene 25, 263.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 1999

Authors and Affiliations

  • Kerry Tyson
    • 1
  • Catherine Shanahan
    • 1
  1. 1.Department of Medicine, Addenbrooke’s HospitalUniversity of CambridgeCambridgeUK

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