Using DNA microarrays to study host-microbe interactions

Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction

Expression arrays facilitate the monitoring of changes in the expression patterns of large collections of genes. The analysis of expression array data has become a computationally-intensive task that requires the development of bioinformatics technology for a number of key stages in the process, such as image analysis, database storage, gene clustering and information extraction. Here, we review the current trends in each of these areas, with particular emphasis on the development of the related technology being carried out within our groups.

Engineering bacterial competitiveness and persistence in the phytosphere

Several tactics exist to improve the survival of an introduced microorganism of interest in the plant environment. One, derived from studies on the Agrobacterium-plant interaction and the role of opines in this interaction, proposes to promote growth of the inoculant in the plant environment via the establishment of a bias in the rhizosphere. It is supported by the occurrence of natural biases, such as those generated by opine-like molecules, by calestegins, or by mimosine. Opine-mediated biases have allowed several investigators to favor the growth of opine-degrading bacteria or communities under sterile or axenic environments or in microcosms mimicking near field conditions. Another way to favor a given microbe consists in impeding growth of competing microorganisms. Experiments performed using detergent or bacteriostatic agents as amendments under field or near field conditions yielded promising results. Research perspectives for engineering plant-microbe interactions also include specific engineering of predation and strategies designed to interfere with some of the signals perceived by the microbes, provided these signals control the expression of functions central to microbial fitness. In this respect, quorum-sensing signal molecules, such as N-acyl-homoserine lactones, may be valuable targets for the development of biocontrol agents and procedures.

GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes

Upon iron restriction, the opportunistic pathogen Pseudomonas aeruginosa produces various virulence factors, including siderophores, exotoxin, proteases and haemolysin. The ferric uptake regulator (Fur) plays a central role in this response and also controls other regulatory genes, such as pvdS, which encodes an alternative sigma factor. This circuit leads to a hierarchical cascade of direct and indirect iron regulation. We used the GeneChip to analyse the global gene expression profiles in response to iron. In iron-starved cells,the expression of 118 genes was increased at least fivefold compared with that in iron-replete cells, whereas the expression of 87 genes was decreased at least fivefold. The GeneChip data correlated well with results obtained using individual lacZ gene fusions. Strong iron regulation was observed for previously identified genes involved in biosynthesis or uptake of the siderophores pyoverdine and pyochelin, utilization of heterologous siderophores and haem and ferrous iron transport. A low-iron milieu led to increased expression of the genes encoding TonB, alkaline protease,PrpL protease, exotoxin A, as well as fumarase C, Mn-dependent superoxide dismutase SodA, a ferredoxin and ferredoxin reductase and several oxidoreductases and dehydrogenases. Iron-controlled regulatory genes included seven alternative sigma factors and five other transcriptional regulators. Roughly 20% of the iron-regulated genes encoded proteins of unknown function and lacked any conclusive homologies. Under low-iron conditions, expression of 26 genes or operons was reduced in a DeltapvdS mutant compared with wild type, including numerous novel pyoverdine biosynthetic genes. The GeneChip proved to be a very useful tool for rapid gene expression analysis and identification of novel genes controlled by Fur or PvdS.

Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays

We have used DNA microarrays to follow Neisseria meningitidis serogroup B (MenB) gene regulation during interaction with human epithelial cells. Host-cell contact induced changes in the expression of 347 genes, more than 30% of which encode proteins with unknown function. The upregulated genes included transporters of iron, chloride, amino acids, and sulfate, many virulence factors, and the entire pathway of sulfur-containing amino acids. Approximately 40% of the 189 upregulated genes coded for peripherally located proteins, suggesting that cell contact promoted a substantial reorganization of the cell membrane. This was confirmed by fluorescence activated cell sorting (FACS) analysis on adhering bacteria using mouse sera against twelve adhesion-induced proteins. Of the 12 adhesion-induced surface antigens, 5 were able to induce bactericidal antibodies in mice, demonstrating that microarray technology is a valid approach for identifying new vaccine candidates and nicely complements other genome mining strategies used for vaccine discovery.

Viruses and interferon: a fight for supremacy

The action of interferons (IFNs) on virus-infected cells and surrounding tissues elicits an antiviral state that is characterized by the expression and antiviral activity of IFN-stimulated genes. In turn, viruses encode mechanisms to counteract the host response and support efficient viral replication, thereby minimizing the therapeutic antiviral power of IFNs. In this review, we discuss the interplay between the IFN system and four medically important and challenging viruses -- influenza, hepatitis C, herpes simplex and vaccinia -- to highlight the diversity of viral strategies. Understanding the complex network of cellular antiviral processes and virus-host interactions should aid in identifying new and common targets for the therapeutic intervention of virus infection. This effort must take advantage of the recent developments in functional genomics, bioinformatics and other emerging technologies.

Redefining bacterial populations: a post-genomic reformation

Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host pathogen relationships.

Molecular diagnostics in infectious diseases and public health microbiology: cottage industry to postgenomics

Molecular methods have been used increasingly over the past ten years to improve the sensitivity and speed of diagnosis in infectious diseases. Although their routine use is still limited to the detection of pathogens that are difficult to culture in vitro,'real-time' methods, commercial kits, quantification and automation will increase potential applications. Molecular methods are now widely used for epidemiological fingerprinting of isolates of public health importance. Sequence-based identification and strain typing, together with the development of tools that can probe for thousands of markers, will allow detailed strain fingerprinting to assist in disease management and control.

Future challenges in preparing for and responding to bioterrorism events

The future success of our preparations for bioterrorism depends on many issues as presented in this article. If these issues are properly addressed, the resulting improvements in bioterrorism preparations will allow us to better deter and mitigate a bioterrorism incident and will also provide us with the added benefit of improvements in early detection, diagnosis, and treatment of natural disease outbreaks. Emergency physicians must take an active leading role in working with the various disciplines to produce a better-prepared community.

Analysis of the heat shock response of Neisseria meningitidis with cDNA- and oligonucleotide-based DNA microarrays

Oligonucleotide- and cDNA-based microarrays comprising a subset of Neisseria meningitidis genes were assessed for study of the meningococcal heat shock response and found to be highly suitable for transcriptional profiling of N. meningitidis. Employing oligonucleotide arrays encompassing the entire genome of N. meningitidis, we analyzed the meningococcal heat shock response on a global scale and identified 55 heat shock-deregulated open reading frames (34 induced and 21 repressed).

Beneficial impact of genome projects on tuberculosis control

The M. tuberculosis genome project is a landmark achievement in the history of TB research. The DNA sequence has provided valuable insights, along with a few surprises, into the complete genetic complement of M. tuberculosis. This information has been used to gain a better understanding of isoniazid-induced alteration in gene expression. It also has been used to construct a genealogy tree of different BCG strains, besides identifying genes that may be responsible for the human-specificity of M. tuberculosis. The impact of this project is far-reaching and in the next few years should yield innovative vaccines and therapeutic agents, besides aiding in the rapid and accurate diagnosis of TB.

Genetic approaches to studying virulence and pathogenesis in Toxoplasma gondii

Toxoplasma gondii is a common protozoan parasite that causes disease in immunocompromised humans. Equipped with a wide array of experimental tools, T. gondii has rapidly developed as a model parasite for genetic studies. The population structure of T. gondii is highly clonal, consisting of three distinct lineages that differ dramatically in virulence. Acute virulence is probably mediated by the genetic differences that distinguish strain types. We have utilized a combination of genetic approaches to investigate the acute virulence of toxoplasmosis using the mouse model. These studies reveal the surprising finding that pathogenicity is due to the over-stimulation of normally protective immune responses. Classical genetic linkage mapping studies indicate that genes that mediate acute virulence are linked to chromosome VII in the parasite. To increase the resolution of genetic mapping studies, single-nucleotide polymorphisms are being developed based on an extensive database of expressed sequence tags (ESTs) from T. gondii. Separately, DNA microarray studies are being used to examine the expression of parasite and host genes during infection. Collectively, these approaches should improve current understanding of virulence and pathogenicity in toxoplasmosis.

Immediate/early response to Trypanosoma cruzi infection involves minimal modulation of host cell transcription

Host cell infection by the intracellular pathogen, Trypanosoma cruzi, involves activation of signaling pathways, cytoskeletal reorganization, and targeted recruitment of host cell lysosomes. To determine the consequences of T. cruzi invasion on host cell gene expression, high density microarrays consisting of approximately 27,000 human cDNAs were hybridized with fluorescent probes generated from T. cruzi-infected human fibroblasts (HFF) at early time points following infection (2-24 h). Surprisingly, no genes were induced > or =2-fold in HFF between 2 and 6 h post-infection (hpi) in repeated experiments while immediate repression of six host cell transcripts was observed. A significant increase in transcript abundance for 106 host cell genes was observed at 24 hpi. Among the most highly induced is a set of interferon-stimulated genes, indicative of a type I interferon (IFN) response to T. cruzi. In support of this, T. cruzi-infected fibroblasts begin to secrete IFNbeta at 18 hpi following the induction of IFNbeta transcripts. As compared with global transcriptional responses evoked by other intracellular pathogens, T. cruzi is a stealth parasite that elicits few changes in host cell transcription during the initiation of infection.

Ferramentas de análise molecular e os agentes das grandes endemias

Os desenvolvimentos recentes no campo da biologia molecular abrem novas perspectivas para o estudo, diagnóstico e terapêutica das grandes endemias que afetam sobretudo as nações em desenvolvimento. As técnicas de manipulação de genes permitem a expressão de antígenos de patógenos em larga escala, com a potencial utilização como reagentes para diagnóstico ou imunógenos. Adicionalmente, essas técnicas poderão levar à obtenção de novas vacinas vivas atenuadas. Por outro lado, a determinação da seqüência dos genomas de patógenos poderá levar a novos alvos para o desenho racional de drogas com potencial quimioterápico. Entretanto, esses avanços só estarão à disposição dos países em desenvolvimento se houver um programa contínuo de investimento e de formação e valorização de recursos humanos competentes nessas novas tecnologias.

Gene array technology to determine host responses to Salmonella

Gene expression array technology is a powerful new tool that has already been used to expand our understanding of host-pathogen interactions. There has been a rapid increase in published reports describing use of this approach to profile host responses to pathogenic bacteria and viruses. The large number of array studies currently in progress coupled with increasing accessibility of this new technology promises a plethora of gene expression data on host response to infection in the near future. Recent insights into macrophage and epithelial cell responses to Salmonella infection garnered from array studies are outlined and used as a basis to discuss various future research directions using gene arrays that will advance the field of cellular microbiology. There is an exciting potential for the gene expression data generated in such studies to provide insights into host physiology, the pathophysiology of disease and novel therapeutics.

Genomics and future biological weapons: the need for preventive action by the biomedical community

There is an increasing concern within both the scientific and security communities that the ongoing revolution in biology has great potential to be misused in offensive biological weapons programs. In light of the 11 September tragedy, we can no longer afford to be complacent about the possibility of biological terrorism. Here we review the major relevant trends in genomics research and development, and discuss how these capabilities might be misused in the design of new bioweapons. We also discuss how the breakthroughs that have come from the genomics revolution may be used to enhance detection, protection and treatment so that biological warfare agents are never used.

Biomarker identification by feature wrappers

Gene expression studies bridge the gap between DNA information and trait information by dissecting biochemical pathways into intermediate components between genotype and phenotype. These studies open new avenues for identifying complex disease genes and biomarkers for disease diagnosis and for assessing drug efficacy and toxicity. However, the majority of analytical methods applied to gene expression data are not efficient for biomarker identification and disease diagnosis. In this paper, we propose a general framework to incorporate feature (gene) selection into pattern recognition in the process to identify biomarkers. Using this framework, we develop three feature wrappers that search through the space of feature subsets using the classification error as measure of goodness for a particular feature subset being "wrapped around": linear discriminant analysis, logistic regression, and support vector machines. To effectively carry out this computationally intensive search process, we employ sequential forward search and sequential forward floating search algorithms. To evaluate the performance of feature selection for biomarker identification we have applied the proposed methods to three data sets. The preliminary results demonstrate that very high classification accuracy can be attained by identified composite classifiers with several biomarkers.

Microarray analysis of pathogens and their interaction with hosts

Microarrays are a promising technique for elucidating and interpreting the mechanistic roles of genes in the pathogenesis of infectious disease. Microarrays have been used to analyse the genetic polymorphisms of specific loci associated with resistance to antimicrobial agents, to explore the distribution of genes among isolates from the same and similar species, to understand the evolutionary relationship between closely related species and to integrate the clinical and genomic data. This technique has also been used to study host-pathogen interactions, mainly by identifying genes from pathogens that may be involved in pathogenicity and by surveying the scope of the host response to infection. The RNA expression profile of pathogens has been used to identify regulatory mechanisms that ensure gene expression in the appropriate environment, to hypothesize functions of hundreds of uncharacterized genes and to identify virulence genes that promote colonization or tissue damage. This information also has the potential to identify targets for drug design. Furthermore, microarrays have been used to investigate the mechanism of drug action and to delineate and predict adverse effects of new drugs. In this paper, we review the use of spotted and high-density oligonucleotide arrays to study the genetic polymorphisms of pathogens, host-pathogen interactions and whole-genome expression profiles of pathogens, as well as their use for drug discovery.

Gene expression microarrays: a 21st century tool for directed vaccine design

DNA microarray technology is a new and powerful tool that allows the simultaneous analysis of a large number of nucleic acid hybridization experiments in a rapid and efficient fashion. The development of the DNA microarray chip has been driven by modern techniques of microelectronic fabrication, miniaturization and integration to produce what is referred to as "laboratory-on-chip" devices. The application of DNA chip technology includes the comprehensive analysis of multiple gene mutations and expressed sequences with regard to newer drug designs, host-pathogen interactions and the design of new vaccines. An advantage of microarray technology is that it can assist researchers to better define and understand the expression profile of a given genotype associated with disease, adverse effects from exposure to certain stimuli, or the ability to understand or predict immune responses to specific antigens. This paper briefly reviews DNA microarray technology and its implications with special reference to vaccine design. The technical aspects comprising array manufacturing and design, array hybridization, formatting, scanning and data handling are also briefly discussed.

Post-genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions

Post-genomic research encompasses many diverse aspects of modern science. These include the two broad subject areas of computational biology (bioinformatics) and functional genomics. Laboratory based functional genomics aims to measure and assess either the messenger RNA (mRNA) levels (transcriptome studies) or the protein content (proteome studies) of cells and tissues. All of these methods have been applied recently to the study of host and pathogen interactions for both bacteria and viruses. A basic overview of the technology is given in this review together with approaches to data analysis. The wealth of information produced from even these preliminary studies has shown the generalities, subtleties and specificities of host-pathogen interactions. Such research should ultimately result in new methods for diagnosing and treating infectious diseases.

Microarrays for studying the host transcriptional response to microbial infection and for the identification of host drug targets

It is essential to understand the molecular basis of a host's response to microbial infection so that disease and tissue damage can be prevented. Modulation of host RNA expression is a critical set of molecular changes that occur upon infection. Global analysis of gene expression should provide an understanding of host RNA transcriptional changes that occur upon host-pathogen interaction. This series of articles focuses on the use of microarrays for analyzing the transcriptional response of a host to microbial infection and for drug target identification.

Prospects offered by genome studies for combating meningococcal disease by vaccination

Meningococcal disease was first recognised and Neisseria meningitidis isolated as the causative agent over 100 years ago, but despite more than a century of research, attempts to eliminate this distressing illness have so far been thwarted. The main problem lies in the fact that N. meningitidis usually exists as a harmless commensal inhabitant of the human nasopharynx, the pathogenic state being the exception rather than the norm. As man is its only host, the meningococcus is uniquely adapted to this ecological niche and has evolved an array of mechanisms for evading clearance by the human immune response. Progress has been made in combating the disease by developing vaccines that target specific pathogenic serogroups of meningococci. However, a fully comprehensive vaccine that protects against all pathogenic strains is still just beyond reach. The publication of the genome sequences of two meningococcal strains, one each from serogroups A and B and the imminent completion of a third illustrates the extent of the problems to be overcome, namely the vast array of genetic mechanisms for the generation of meningococcal diversity. Fortunately, genome studies also provide new hope for solutions to these problems in the potential for a greater understanding of meningococcal pathogenesis and possibilities for the identification of new vaccine candidates. This review describes some of the approaches that are currently being used to exploit the information from meningococcal genome sequences and seeks to identify future prospects for combating meningococcal disease.

Analysis of host responses to microbial infection using gene expression profiling

Gene expression profiling offers new opportunities for understanding host-cell responses to microbial pathogens and their products. Current strategies involve either first identifying mRNAs that differ in their expression status under different experimental conditions and later defining the identity of the respective genes (for example, differential display or serial analysis of gene expression), or alternatively assessing changes in the expression of already defined genes (for example, cDNA or oligonucleotide microarrays). Early studies indicate the power of gene expression profiling for providing new insights into groups of genes whose expression is altered during the course of host-microbe interactions, and for the discovery of cellular genes that were not previously recognized to be regulated by infection.

Molecular typing methods for the epidemiological identification of Clostridium difficile strains

Toxigenic Clostridium difficile is the etiologic agent of C. difficile-associated diarrhea (CDAD), the most common cause of nosocomial diarrhea. Cross-infection between patients and transmission through the environment and medical personnel are important factors in the acquisition of CDAD. In order to understand differences in epidemiology and pathogenesis, a number of typing schemes have been developed. We will review the typing methods used to study the epidemiology of C. difficile infections and how they have evolved from a phenotypic identification to state of the art molecular methods, detecting genetic polymorphisms among strains. These molecular methods include PCR-based methods (arbitrarily primed-PCR [AP-PCR] and PCR ribotyping), restriction endonuclease analysis (REA) and pulse field gel electrophoresis (PFGE). The application, usefulness and feasibility of these methods are compared and discussed. Finally, the role of genomics as a tool to investigate CDAD is introduced.

Global impact of influenza virus on cellular pathways is mediated by both replication-dependent and -independent events

Influenza virus, the causative agent of the common flu, is a worldwide health problem with significant economic consequences. Studies of influenza virus biology have revealed elaborate mechanisms by which the virus interacts with its host cell as it inhibits the synthesis of cellular proteins, evades the innate antiviral response, and facilitates production of viral RNAs and proteins. With the advent of DNA array technology it is now possible to obtain a large-scale view of how viruses alter the environment within the host cell. In this study, the cellular response to influenza virus infection was examined by monitoring the steady-state mRNA levels for over 4,600 cellular genes. Infections with active and inactivated influenza viruses identified changes in cellular gene expression that were dependent on or independent of viral replication, respectively. Viral replication resulted in the downregulation of many cellular mRNAs, and the effect was enhanced with time postinfection. Interestingly, several genes involved in protein synthesis, transcriptional regulation, and cytokine signaling were induced by influenza virus replication, suggesting that some may play essential or accessory roles in the viral life cycle or the host cell's stress response. The gene expression pattern induced by inactivated viruses revealed induction of the cellular metallothionein genes that may represent a protective response to virus-induced oxidative stress. Genome-scale analyses of virus infections will help us to understand the complexities of virus-host interactions and may lead to the discovery of novel drug targets or antiviral therapies.

Regulation of virulence genes in Mycobacterium tuberculosis

Mycobacterium tuberculosis has demonstrated remarkable ability to survive in diverse conditions encountered during the infection process. These involve surviving the bactericidal stresses within the macrophage, the anaerobic and nutritionally altered environment of the granuloma, and the metabolically inactive latent state. Understanding the molecular basis of this adaptive behavior lies in the identification of genes (or virulence determinants) specifically expressed under these varied conditions. Transcriptional control plays a key role in regulating gene expression in response to environmental signals. However, even after decades of investigation our knowledge about the function of these regulatory mechanisms in mycobacteria remains meagre. But the elucidation of the genome sequence and implementation of sophisticated molecular genetic approaches to this organism have made a revolutionary impact on the study of mycobacterial pathogenesis. Deletion and complementation of individual genes can be done at will facilitating the comparative analysis of mutants and wild-type strains. Novel and powerful technologies such as DNA microarrays, fluorescent beacons and proteomics have made possible the analysis of the expression levels of multiple genes in in vitro systems. More technically challenging uses of these techniques is being undertaken to explore pathogen gene expression within the host. This will lead to the identification of virulence factors and give definitive insight into their regulatory signals.

Antibacterial vaccine design using genomics and proteomics

After 200 years of practice, vaccinology has proved to be very effective in preventing infectious diseases. However, several human and animal pathogens exist for which vaccines have not yet been discovered. As for other fields of medical sciences, it is expected that vaccinology will greatly benefit from the emerging genomics technologies such as bioinformatics, proteomics and DNA microarrays. In this article the potential of these technologies applied to bacterial pathogens is analyzed, taking into account the few existing examples of their application in vaccine discovery.

Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions

Functional genomic technologies such as high density DNA microarrays allow biologists to study the structure and behavior of thousands of genes in a single experiment. One of the fields in which microarrays have had an increasingly important impact is host-pathogen interactions. Early investigations in this area over the past two years not only emphasize the utility of this approach, but also highlight the stereotyped gene expression responses of different host cells to diverse infectious stimuli, and the potential value of broad dataset comparisons in revealing fundamental features of innate immunity. The comparative analysis of recently published datasets involving human gene expression responses to two bacterial respiratory pathogens illustrates many of these points. Comparisons between these large, highly parallel sets of experimental observations also emphasize important technical and experimental design issues as future challenges.

New (and used) approaches to the study of fungal pathogenicity

The fungi are the most economically important plant pathogens and continue to be the focus of extensive research with a wide variety of methodologies. Enhancements in microscopy techniques have increased our ability to visualize the intimate interaction of fungi and their host plants. Improving methods allow pharmacological inhibition and genetic dissection of the determinants of fungal pathogenicity in a gene-by-gene approach. Identification and analysis of genes differentially transcribed in ways pertinent to pathogenicity continues to be a frequent research approach. Genome-wide analysis is gaining favor in biological research and fungal plant pathogens are no exception. Several industrial research groups are exploring fungal plant pathogenesis based on genomic sequence data and genome-wide mutagenesis. In March 2001 the first publicly available complete genome of a filamentous fungus (Neurospora crassa) was released. N. crassa is of course a saprophyte and there is no complete sequence available for a plant pathogenic fungus in public databases. However, freely accessible entire genome sequences for both plant pathogenic fungi and their hosts are on the horizon. Sequence availability promises to revolutionize the rate at which data relevant to disease processes will be accrued. In this review we describe approaches currently applied to the study of plant pathogenic fungi and explore developments of potential future benefit with existing technologies not yet applied to this group of important organisms.