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Functional genomics of host–pathogen interactions in species of veterinary importance
Veterinary Immunology and Immunopathology 105 (2005) 173–174 www.elsevier.com/locate/vetimm
Preface
Functional genomics of host–pathogen interactions in species of veterinary importance
This special issue of Veterinary Immunology and Immunopathology brings together a set of papers on transcriptional profiling of the main domestic animals of economic importance and their response to infectious challenge. Traditionally, scientists interested in gene expression have investigated one gene at a time, a slow and tedious process not readily amenable to investigation of outbred populations and complex systems. Now, thanks to an exponential increase in genomic information and technology over the past few years, opportunities to rapidly investigate thousands of gene expression events in more complex systems, and ask questions of a more global nature are a reality. Genomic information resources for cattle, chickens and pigs are increasing dramatically, with the chicken genome now sequenced, the cattle genome on the way to being sequenced and an international effort to sequence the pig genome getting organized and raising funds. In addition, for all three species there are highly informative genetic maps and large expressed sequence tag (EST) resources available (over 420,000, 280,000 and 480,000 EST sequences for cattle, swine and chickens, respectively, are reported in publicly available databases). Collections of these EST resources have been exploited to construct cDNA and oligonucleotide microarrays, facilitating large-scale gene expression analyses in domestic species. However, many available sequences and clones have been derived from cDNA libraries representing mainly non-immune tissue, and even the small contribution of immune-
related material present is derived from non-activated and non-infected tissues. Thus, to exploit the power of microarray technology to investigate immune responses in veterinary species, researchers have begun to construct and utilise immune-focused EST libraries and microarrays. In this issue, immune-focused microarrays are described for pigs (Dvorak et al.; Niebold et al.), chicken (Keeler) and cattle (Burton et al.; Coussens et al.; Everts et al.; Hill et al.; McGuire and Glass; Wilson et al.). Results from these studies have begun to shed considerable light on immune responses in domestic species, but will require considerable additional input from bioinformatics to fully realize their significance. Wilson et al. point out that annotation of genes represented on many microarrays needs to be improved, for example, by linking to their ENSEMBL gene names and ultimately their gene ontology; this will greatly aid interpretation of array results. An example of this type of annotation is utilized in Coussens et al. using a novel bioinformatics tool called GeneLink (http:// www.cafg.msu.edu/). Several authors in this special issue identify genes of unknown function or indeed apparently novel sequences that apparently play a role in host–pathogen interactions. In fact, the number of unknown or unannotated genes identified as differentially expressed in immune response to various pathogens underscores how much we have yet to learn about the immune system. Given the relatively high cost of microarray experiments, coupling experimental design and
0165-2427/$ – see front matter # 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.vetimm.2005.02.005
174
Preface / Veterinary Immunology and Immunopathology 105 (2005) 173–174
methods of statistical analysis is crucial to enhancing the power of any particular experiment, as discussed in this issue by Tempelman. Analysing results from mixed cell populations (such as peripheral blood mononuclear cells) is the subject of a paper by Bing et al., and although their model is based on embryos, is of relevance to samples of mixed cell types. Analysis methods discussed by Bing et al. also hold promise when an experiment destroys a sample and thus the final outcome cannot be known, although prior knowledge can be used to associate gene expression patterns with expected outcomes. As the veterinary research community is well aware, variability between animals is an issue, and nowhere more so than in microarray analysis. Use of cell lines and in vitro studies with tissues or cells can help, although the availability of appropriate cell lines is seriously limited for species of veterinary importance. However, the size of most veterinary species allows many studies to be effectively completed using primary cell cultures and isolates, as presented in Hill et al., Burton et al., Patel et al., and Coussens et al. Another promising area of functional genomics research is in the identification of host immune cell gene expression signature patterns, specific for various pathogens, or alternatively, common patterns of response to diverse pathogens may be discernable. These studies also have the potential to identify in vitro correlates of protection, which would be of great use in vaccine studies. Up-regulation of novel genes and pathways early in infection may also suggest candidates for new adjuvants. Transcriptome profiling of the in vivo response to pathogens promises to reveal much of relevance to host–pathogen interactions, though as with analysing ex vivo blood samples, considerations of the trafficking of inflammatory cells leading to changes in sub-populations must be taken into account. In many cases, only limited amounts of suitable material may be available for gene expression profiling, for example samples obtained from cell-
sorting or laser capture dissection. In this issue, Patel et al. discuss the use of amplified RNA from small samples, demonstrating that linear amplification of RNA yields results similar to those obtained with unamplified RNA. Disease resistance traits may be reflected by differences in expression of gene variants or components of pathways underlying resistance traits; this is the approach being taken by Hill et al., to try and determine the genes controlling trypanotolerance in some species of cattle. McGuire and Glass are taking a similar approach to identifying genes underlying resistance to tropical theileriosis using isolated primary bovine macrophages. Additionally de Koning et al. argues that linking microarray data with quantitative trait loci could provide a more powerful approach in the future to identifying candidate genes controlling complex traits, such as disease resistance or susceptibility. As more information is deposited in public databases, and with the establishment of suitable microarrays for veterinary species, we feel sure that the groundbreaking approaches presented in this issue will result in new paradigms and greater understanding of the interface between the immune system and invading pathogens. Finally, we would like to thank our many reviewers and contributors to this special issue. Elizabeth J. Glass* Department of Genetics and Genomics Roslin Institute, Roslin, Midlothian Edinburgh, EH25 9PS UK Paul M. Coussens Center for Animal Functional Genomics Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA * Corresponding author. Tel.: +44 131 527 4200 fax: +44 131 440 0434
Preface
Functional genomics of host–pathogen interactions in species of veterinary importance
This special issue of Veterinary Immunology and Immunopathology brings together a set of papers on transcriptional profiling of the main domestic animals of economic importance and their response to infectious challenge. Traditionally, scientists interested in gene expression have investigated one gene at a time, a slow and tedious process not readily amenable to investigation of outbred populations and complex systems. Now, thanks to an exponential increase in genomic information and technology over the past few years, opportunities to rapidly investigate thousands of gene expression events in more complex systems, and ask questions of a more global nature are a reality. Genomic information resources for cattle, chickens and pigs are increasing dramatically, with the chicken genome now sequenced, the cattle genome on the way to being sequenced and an international effort to sequence the pig genome getting organized and raising funds. In addition, for all three species there are highly informative genetic maps and large expressed sequence tag (EST) resources available (over 420,000, 280,000 and 480,000 EST sequences for cattle, swine and chickens, respectively, are reported in publicly available databases). Collections of these EST resources have been exploited to construct cDNA and oligonucleotide microarrays, facilitating large-scale gene expression analyses in domestic species. However, many available sequences and clones have been derived from cDNA libraries representing mainly non-immune tissue, and even the small contribution of immune-
related material present is derived from non-activated and non-infected tissues. Thus, to exploit the power of microarray technology to investigate immune responses in veterinary species, researchers have begun to construct and utilise immune-focused EST libraries and microarrays. In this issue, immune-focused microarrays are described for pigs (Dvorak et al.; Niebold et al.), chicken (Keeler) and cattle (Burton et al.; Coussens et al.; Everts et al.; Hill et al.; McGuire and Glass; Wilson et al.). Results from these studies have begun to shed considerable light on immune responses in domestic species, but will require considerable additional input from bioinformatics to fully realize their significance. Wilson et al. point out that annotation of genes represented on many microarrays needs to be improved, for example, by linking to their ENSEMBL gene names and ultimately their gene ontology; this will greatly aid interpretation of array results. An example of this type of annotation is utilized in Coussens et al. using a novel bioinformatics tool called GeneLink (http:// www.cafg.msu.edu/). Several authors in this special issue identify genes of unknown function or indeed apparently novel sequences that apparently play a role in host–pathogen interactions. In fact, the number of unknown or unannotated genes identified as differentially expressed in immune response to various pathogens underscores how much we have yet to learn about the immune system. Given the relatively high cost of microarray experiments, coupling experimental design and
0165-2427/$ – see front matter # 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.vetimm.2005.02.005
174
Preface / Veterinary Immunology and Immunopathology 105 (2005) 173–174
methods of statistical analysis is crucial to enhancing the power of any particular experiment, as discussed in this issue by Tempelman. Analysing results from mixed cell populations (such as peripheral blood mononuclear cells) is the subject of a paper by Bing et al., and although their model is based on embryos, is of relevance to samples of mixed cell types. Analysis methods discussed by Bing et al. also hold promise when an experiment destroys a sample and thus the final outcome cannot be known, although prior knowledge can be used to associate gene expression patterns with expected outcomes. As the veterinary research community is well aware, variability between animals is an issue, and nowhere more so than in microarray analysis. Use of cell lines and in vitro studies with tissues or cells can help, although the availability of appropriate cell lines is seriously limited for species of veterinary importance. However, the size of most veterinary species allows many studies to be effectively completed using primary cell cultures and isolates, as presented in Hill et al., Burton et al., Patel et al., and Coussens et al. Another promising area of functional genomics research is in the identification of host immune cell gene expression signature patterns, specific for various pathogens, or alternatively, common patterns of response to diverse pathogens may be discernable. These studies also have the potential to identify in vitro correlates of protection, which would be of great use in vaccine studies. Up-regulation of novel genes and pathways early in infection may also suggest candidates for new adjuvants. Transcriptome profiling of the in vivo response to pathogens promises to reveal much of relevance to host–pathogen interactions, though as with analysing ex vivo blood samples, considerations of the trafficking of inflammatory cells leading to changes in sub-populations must be taken into account. In many cases, only limited amounts of suitable material may be available for gene expression profiling, for example samples obtained from cell-
sorting or laser capture dissection. In this issue, Patel et al. discuss the use of amplified RNA from small samples, demonstrating that linear amplification of RNA yields results similar to those obtained with unamplified RNA. Disease resistance traits may be reflected by differences in expression of gene variants or components of pathways underlying resistance traits; this is the approach being taken by Hill et al., to try and determine the genes controlling trypanotolerance in some species of cattle. McGuire and Glass are taking a similar approach to identifying genes underlying resistance to tropical theileriosis using isolated primary bovine macrophages. Additionally de Koning et al. argues that linking microarray data with quantitative trait loci could provide a more powerful approach in the future to identifying candidate genes controlling complex traits, such as disease resistance or susceptibility. As more information is deposited in public databases, and with the establishment of suitable microarrays for veterinary species, we feel sure that the groundbreaking approaches presented in this issue will result in new paradigms and greater understanding of the interface between the immune system and invading pathogens. Finally, we would like to thank our many reviewers and contributors to this special issue. Elizabeth J. Glass* Department of Genetics and Genomics Roslin Institute, Roslin, Midlothian Edinburgh, EH25 9PS UK Paul M. Coussens Center for Animal Functional Genomics Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA * Corresponding author. Tel.: +44 131 527 4200 fax: +44 131 440 0434