Review
Chips with everything: DNA microarrays in infectious diseases

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Summary

Two developments are set to revolutionise research in and clinical management of infectious diseases. First, the completion of the human genome project together with the sequencing of many pathogen genomes, and second, the development of microarray technology. This review explains the principles underlying DNA microarrays and highlights the uses to which they are being put to investigate the molecular basis of infectious diseases. Pathogen studies enable identification of both known and novel organisms, understanding of genetic evolution, and investigation of determinants of pathogenicity. Host studies show the complexities of development and activation of both innate and adaptive immunity. Host-pathogen studies allow global analysis of gene expression during pathogenesis. Microarray technology will accelerate our understanding of the complex genetic processes underlying the interaction between microorganisms and the host, with consequent improvements in the diagnosis, treatment, and prevention of infectious diseases.

Section snippets

What are DNA microarrays?

A microarray is a series of nucleic acid targets immobilised on a solid substrate. Hybridisation of fluorescently labelled probes made from nucleic acids in the test sample to these targets allows analysis of the relative concentrations of mRNA or DNA in the sample (figure 1).

Diagnosis

Organisms can be identified by analysing either their DNA content or their gene-expression profiles. The large number of DNA sequences that can be spotted on a microarray, together with the high specificity of binding to the immobilised gene targets, allow the detection of a broad range of organisms with high discriminatory ability.

Outbreak investigation

One of the most common applications of microarrays in infectious disease has been in epidemiological investigation. By characterising both major and minor genomic variations, microarrays can be used to differentiate between strains. Chizhikov et al14 used the highly conserved rotavirus VP7 gene to create a genotype-specific oligonucleotide array to classify 20 rotaviruses into five known strains. Unlike PCR, the use of microarrays allowed the detection of random mutations since each isolate

Pathogenicity

While molecular techniques have long been at the core of investigating pathogenicity, the advent of microarray technology for the first time allows a global analysis of the genetic determinants that contribute to pathogenicity. Table 1 cites examples of how microarrays have been used to investigate molecular mechanisms of host invasion, defence avoidance, and survival strategies.

Host studies

An understanding of the host immune system is vital to a thorough understanding of infectious disease. Global expression analysis is helping to unravel the complexities of immunology. Examining cells of both the innate and adaptive immune system at various stages of differentiation, maturation, and activation shows the power of unbiased approaches.

Innate immunity

Innate immune responses initiated by the recognition of microbial surface or secreted components are increasingly recognised as being important. Microarrays have been used to advance our understanding of the genetic processes involved in immune cell development.31, 34 Le Naour et al33 used oligonucleotide arrays to show that 255 genes were expressed during differentiation of dendritic cells, including genes involved with cell adhesion, signalling, and lipid metabolism. Many of them had not

Adaptive immunity

Microarrays have also helped to further the understanding of how B and T cell immunity develops.35, 38 Genes are uniquely expressed during the various stages of B-cell differentiation, activation, and the acquisition of tolerance (table 3). Shaffer e t al37 used cDNA microarrays to study germinal centre B cells, which are a discrete stage of differentiation when B cells encounter antigen in secondary lymphoid tissue. They reported a unique gene-expression signature for this stage, including

Differences between hosts

Even in the absence of infection, gene expression in immune cells can vary. Using cDNA microarrays Whitney et al44 reported that age, sex, time of day, and the proportions of different cell types in the blood all affected gene expression in healthy volunteers. Although they did not expose these immune cells to infective organisms, they compared the magnitude of global gene expression changes in samples from these healthy individuals with samples from patients with either bacterial infection or

Host-pathogen interaction studies

While the isolated study of either infectious organisms or host cells is revealing, the key to an infectious disease process is the interaction between the pathogen and the host.

Drug and vaccine research

Investigation of both host and pathogen has already provided insights into therapeutic modalities.

Analysis and interpretation of microarray data

The amount of data generated by microarray experiments is enormous. A simple experiment comparing stimulation of immune cells by two different bacteria in two individuals at three different time points requires at least 12 microarrays. With up to 20 000 genes on an array, the number of data points leaps to 240 000. Such quantities of data require specialised statistical expertise and software to decipher patterns from the entire expression repertoire. The bottleneck in genetic analysis has

Conclusion

Microarrays offer the potential to revolutionise research in many fields and the management of many diseases. While their use in the investigation of infectious diseases is still in its infancy, this emerging technology will illuminate our understanding of the molecular basis of the host-pathogen interaction. The biological insights thus gained are likely to lead to major shifts in our approach to the diagnosis, treatment, assessment of prognosis, and prevention in many types of infectious

Search strategy and selection criteria

Data for this review were identified by searches of Medline and references from relevant articles. Search terms were: “microarray”, “DNA microarray”, “DNA microchip”, “genomic”, “genome”, “infection”, “infectious disease”, “infect*”, “bacterial”, “bact*”, “viral”, “vir*”, “fungal”, “fung*”, “parasitic”, “parasit*”, “vaccine”, and “vacc*”. Papers were chosen based on their importance (including numbers of references by other authors) and their ability to show how microarrays have advanced

References (83)

  • M Schena et al.

    Parallel human genome analysis: microarray-based expression monitoring of 1000 genes

    Proc Natl Acad Sci USA

    (1996)
  • DJ Lockhart et al.

    Expression monitoring by hybridization to high-density oligonucleotide arrays

    Nat Biotechnol

    (1996)
  • HC King et al.

    Gene expression profile analysis by DNA microarrays: promise and pitfalls

    JAMA

    (2001)
  • M Bilban et al.

    Normalizing DNA microarray data

    Curr Issues Mol Biol

    (2002)
  • J Quackenbush

    Microarray data normalization and transformation

    Nat Genet

    (2002)
  • V Chizhikov et al.

    Microarray analysis of microbial virulence factors

    Appl Environ Microbiol

    (2001)
  • D Wang et al.

    Microarray-based detection and genotyping of viral pathogens

    Proc Natl Acad Sci USA

    (2002)
  • SN Gardner et al.

    Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis A, B, C, and E viruses and human immunodeficiency virus

    J Clin Microbiol

    (2003)
  • M Schalling et al.

    A role for a new herpes virus (KSHV) in different forms of Kaposi's sarcoma

    Nat Med

    (1995)
  • DA Relman

    The search for unrecognized pathogens

    Science

    (1999)
  • DA Relman

    Genome-wide responses of a pathogenic bacterium to its host

    J Clin Invest

    (2002)
  • CA Cummings et al.

    Using DNA microarrays to study host-microbe interactions

    Emerg Infect Dis

    (2000)
  • DA Relman

    New technologies, human-microbe interactions, and the search for previously unrecognized pathogens

    J Infect Dis

    (2002)
  • V Chizhikov et al.

    Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization

    J Clin Microbiol

    (2002)
  • EE Leonard et al.

    Use of an open-reading frame-specific Campylobacter jejuni DNA microarray as a new genotyping tool for studying epidemiologically related isolates

    J Infect Dis

    (2003)
  • JC Smoot et al.

    Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks

    Proc Natl Acad Sci USA

    (2002)
  • R Hakenbeck et al.

    Mosaic genes and mosaic chromosomes: intra- and interspecies genomic variation of Streptococcus pneumoniae

    Infect Immun

    (2001)
  • U Dobrindt et al.

    Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays

    J Bacteriol

    (2003)
  • MA Behr et al.

    Comparative genomics of BCG vaccines by whole-genome DNA microarray

    Science

    (1999)
  • R Grifantini et al.

    Gene expression profile in Neisseria meningitidis and Neisseria lactamica upon host-cell contact: from basic research to vaccine development

    Ann N Y Acad Sci

    (2002)
  • DS Merrell et al.

    Host-induced epidemic spread of the cholera bacterium

    Nature

    (2002)
  • N Salama et al.

    A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains

    Proc Natl Acad Sci USA

    (2000)
  • WC Yang et al.

    General and specific alterations in programming of global viral gene expression during infection by VP16 activation-deficient mutants of herpes simplex virus type 1

    J Virol

    (2002)
  • C Fradin et al.

    Stage-specific gene expression of Candida albicans in human blood

    Mol Microbiol

    (2003)
  • C Ben Mamoun et al.

    Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis

    Mol Microbiol

    (2001)
  • JM Voyich et al.

    Genome-wide protective response used by group A Streptococcus to evade destruction by human polymorphonuclear leukocytes

    Proc Natl Acad Sci USA

    (2003)
  • BJ Staudinger et al.

    mRNA expression profiles for Escherichia coli ingested by normal and phagocyte oxidase-deficient human neutrophils

    J Clin Invest

    (2002)
  • GJ Nau et al.

    Human macrophage activation programs induced by bacterial pathogens

    Proc Natl Acad Sci USA

    (2002)
  • SW Stingley et al.

    Global analysis of herpes simplex virus type 1 transcription using an oligonucleotide-based DNA microarray

    J Virol

    (2000)
  • Q Huang et al.

    The plasticity of dendritic cell responses to pathogens and their components

    Science

    (2001)
  • E Izmailova et al.

    HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages

    Nat Med

    (2003)

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