Transcriptome Analyses in the Interaction of Neisseria meningitidis with Mammalian Host Cells

  • Alexandra Schubert-Unkmeir
  • Anja Schramm-Glück
  • Matthias Frosch
  • Christoph Schoen
Part of the Methods in Molecular Biology book series (MIMB, volume 470)


As in many other areas of basic and applied biology, research in infectious diseases has been revolutionized by two recent developments in the field of genome biology: first, the sequencing of the human genome as well as that of many pathogen genomes; and second, the development of high-throughput technologies such as microarray technology, proteomics, and metabolomics. Microarray studies enable a deeper understanding of genetic evolution of pathogens and investigation of determinants of pathogenicity on a whole-genome scale. Host studies in turn permit an unprecedented holistic appreciation of the complexities of the host cell responses at the molecular level. In combination, host-pathogen studies allow global analysis of gene expression in the infecting bacterium as well as in the infected host cell during pathogenesis providing a comprehensive picture of the intricacies of pathogen-host interactions. This chapter briefly explains the principles underlying DNA microarrays including major points to consider when planning and analyzing microarray experiments and highlights in detail their practical application using the interaction of Neisseria meningitidis with endothelial cells as an example.

Key words

Neisseria meningitidis infection biology cellular microbiology gene expression transcriptomics microarrays 


  1. 1.
    Lander, E. S., Linton, L. M., Birren, B., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.CrossRefPubMedGoogle Scholar
  2. 2.
    Venter, J. C., Adams, M. D., Myers, E. W., et al. (2001) The sequence of the human genome. Science 291, 1304–51.CrossRefPubMedGoogle Scholar
  3. 3.
    Hacker, J. and Dobrindt, U., eds. (2006) Pathogenomics. Weinheim: Wiley-VCH.Google Scholar
  4. 4.
    Schena, M., Shalon, D., Davis, R. W. and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–70.CrossRefPubMedGoogle Scholar
  5. 5.
    Grifantini, R., Bartolini, E., Muzzi, A., et al. (2002) Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat Biotechnol 20, 914–21.CrossRefPubMedGoogle Scholar
  6. 6.
    Dietrich, G., Kurz, S., Hubner, C., et al. (2003) Transcriptome analysis of Neisseria meningitidis during infection. J Bacteriol 185, 155–64.CrossRefPubMedGoogle Scholar
  7. 7.
    Schubert-Unkmeir, A., Sokolova, O., Panzner, U., Eigenthaler, M. and Frosch, M. (2007) Gene expression pattern in human brain endothelial cells in response to Neisseria meningitidis. Infect Immun 75, 899–914.CrossRefPubMedGoogle Scholar
  8. 8.
    Hossain, H., Tchatalbachev, S. and Chakraborty, T. (2006) Host gene expression profiling in pathogen-host interactions. Curr Opin Immunol 18, 422–29.CrossRefPubMedGoogle Scholar
  9. 9.
    Claus, H., Vogel, U., Swiderek, H., Frosch, M. and Schoen, C. (2007) Microarray analyses of meningococcal genome composition and gene regulation: a review of the recent literature. FEMS Microbiol Rev 31, 43–51.CrossRefPubMedGoogle Scholar
  10. 10.
    Lipshutz, R. J., Fodor, S. P., Gingeras, T. R. and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat Genet 21, 20–24.CrossRefPubMedGoogle Scholar
  11. 11.
    Bowtell, D. and Sambrook, J., eds. (2002) DNA Microarrays. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.Google Scholar
  12. 12.
    Churchill, G. A. (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32, 490–95.CrossRefPubMedGoogle Scholar
  13. 13.
    Yang, Y. H. and Speed, T. (2002) Design issues for cDNA microarray experiments. Nat Rev Genet 3, 579–88.PubMedGoogle Scholar
  14. 14.
    Stekel, D. (2003) Microarray Bioinformatics. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
  15. 15.
    Parmigiani, G., Garret, E. S., Irizarry, R. A. and Zeger, S. L., eds. (2003) The Analysis of Gene Expression Data. Berlin: Springer.Google Scholar
  16. 16.
    Tilstone, C. (2003) DNA microarrays: vital statistics. Nature 424, 610–2.CrossRefPubMedGoogle Scholar
  17. 17.
    Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A. and Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18, 96–104.Google Scholar
  18. 18.
    Cleveland, W. S. (1979) Robust locally weighted regression and smoothing scatterplots. J Am Statist Assoc 74, 829–36.CrossRefGoogle Scholar
  19. 19.
    Brazma, A., Hingamp, P., Quackenbush, J., et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29, 365–71.CrossRefPubMedGoogle Scholar
  20. 20.
    Tinsley, C. R. and Heckels, J. E. (1986) Variation in the expression of pili and outer membrane protein by Neisseria meningitidis during the course of meningococcal infection. J Gen Microbiol 132, 2483–90.PubMedGoogle Scholar
  21. 21.
    Stins, M. F., Gilles, F. and Kim, K. S. (1997) Selective expression of adhesion molecules on human brain microvascular endothelial cells. J Neuroimmunol 76, 81–90.CrossRefPubMedGoogle Scholar
  22. 22.
    Stins, M. F., Badger, J. and Sik Kim, K. (2001) Bacterial invasion and transcytosis in transfected human brain microvascular endothelial cells. Microb Pathog 30, 19–28.CrossRefPubMedGoogle Scholar
  23. 23.
    Sambrook, J., Fritsch, E. F., and Maniatis, T., eds. (1989) Molecular Cloning: A Laboratory Handbook, 2nd ed. Cold Spring Harbour: Cold Spring Harbor Laboratory Press.Google Scholar
  24. 24.
    Unkmeir, A., Latsch, K., Dietrich, G., et al. (2002) Fibronectin mediates Opc-dependent internalization of Neisseria meningitidis in human brain microvascular endothelial cells. Mol Microbiol 46, 933–46.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Alexandra Schubert-Unkmeir
    • 1
  • Anja Schramm-Glück
    • 2
  • Matthias Frosch
    • 3
  • Christoph Schoen
    • 3
  1. 1.Institute for Hygiene and Microbiology, Julius-Maximilians-University WürzburgGermany
  2. 2.Institute for Hygiene and Microbiology, University of WürzburgGermany
  3. 3.Institute for Hygiene and MicrobiologyGermany

Personalised recommendations