Transcriptome analyses in the interaction of Neisseria meningitidis with mammalian host cells

Infectious disease research has been revolutionized by two recent developments in the field of genome biology: (1) the sequencing of the human genome as well as many pathogen genomes and (2) the development of high-throughput technologies including microarray technology, proteomics, and metabolomics. Microarray studies enable a deeper understanding of the genetic evolution of pathogens and investigation of the determinants of pathogenicity on a whole-genome scale. Host studies, in turn, allow for an unprecedented holistic appreciation of the complexities of 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. In this chapter, we briefly explain the principles underlying DNA microarrays including the major points to consider when planning and analyzing microarray experiments and we describe in detail their practical application, using the interaction of Neisseria meningitidis with human endothelial or epithelial cells as examples.