7 Genomic Approaches in Aquaculture and Fisheries
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7.6.2 Transcriptomic Characterization of Host Immune Response
7.6.2.1 EST Analysis to Identify Genes Involved in Host Immune Response
EST analysis is one of the most rapid methods for gene discovery and identification, providing useful data for a first insight into gene expression profiles, alternative
splicing or differential polyadenylation analysis, as well as for identification of Type
I markers. Furthermore, ESTs are the basis for comparative mapping approaches and
development of microarrays. Most published data (e.g. Gong et al. 1994, Douglas
et al. 1999, Karsi et al. 2002, Sarropoulou et al. 2005a, Bai et al. 2007, Li et al.
2007; Marine Genomics Europe 2004–2008) resulted from EST projects using nonchallenged tissues in order to obtain a baseline unigene catalogue. However, to
identify transcripts of genes expressed during immune response, ESTs have to be
retrieved from cDNA libraries of infected tissues. Studies aiming to identify and
isolate transcripts involved in fish immune response have recently been performed
for common carp (Kono et al. 2003, Sakai et al. 2005) and European sea bass
(Sarropoulou et al. 2009). In the latter, levels of gene expression were analysed
using ESTs retrieved from six cDNA libraries derived from tissues infected with V.
anguillarum (liver, spleen, head kidney, peritoneal exudate, gill and intestine) and
from four cDNA libraries derived from tissues infected with nodavirus (head kidney,
spleen, brain and liver). Genes differentially expressed upon infection were isolated
and further analysed by real-time PCR, thus confirming some of them to be biomarkers for bacterial and viral infections in fish. Altogether, the increasing availability
of sequence information from various teleost species, as well as the corresponding
functional expression data, are of importance to better understand immunity-related
mechanisms of teleost and their evolution.
7.6.2.2 Microarray Analysis to Identify Genes Involved
in Host Immune Response
DNA microarrays, which allow high-throughput expression profiling (see Section
7.2.5 Functional genomics tools), have been only used in few studies to identify genes involved in the immune response of aquacultured fish species. One of
these studies aimed at profiling gene expression, using a cDNA microarray, during the acute immune response of catfish following infection with Gram-negative
bacteria (Peatman et al. 2007). Microarray analysis revealed that expression of the
majority of typical acute phase proteins was up-regulated in catfish, together with
a set of putative teleost acute phase reactants. A similar study performed in sea
bass (E. Sarropoulou, personal communication) showed that expression of several
genes involved in iron homeostasis was strongly induced during immune response,
suggesting that limitation of free iron may inhibit bacterial growth while avoiding metal-induced cellular damage. In a follow-up study by Peatman et al. (2008)
using an oligonucleotide microarray, a detailed analysis of transcripts involved in
the MHC I pathway was performed. The authors identified a total of 131 differentially expressed genes, of which 103 were believed to be unique genes. Interestingly,
241
7.6.2 Transcriptomic Characterization of Host Immune Response
7.6.2.1 EST Analysis to Identify Genes Involved in Host Immune Response
EST analysis is one of the most rapid methods for gene discovery and identification, providing useful data for a first insight into gene expression profiles, alternative
splicing or differential polyadenylation analysis, as well as for identification of Type
I markers. Furthermore, ESTs are the basis for comparative mapping approaches and
development of microarrays. Most published data (e.g. Gong et al. 1994, Douglas
et al. 1999, Karsi et al. 2002, Sarropoulou et al. 2005a, Bai et al. 2007, Li et al.
2007; Marine Genomics Europe 2004–2008) resulted from EST projects using nonchallenged tissues in order to obtain a baseline unigene catalogue. However, to
identify transcripts of genes expressed during immune response, ESTs have to be
retrieved from cDNA libraries of infected tissues. Studies aiming to identify and
isolate transcripts involved in fish immune response have recently been performed
for common carp (Kono et al. 2003, Sakai et al. 2005) and European sea bass
(Sarropoulou et al. 2009). In the latter, levels of gene expression were analysed
using ESTs retrieved from six cDNA libraries derived from tissues infected with V.
anguillarum (liver, spleen, head kidney, peritoneal exudate, gill and intestine) and
from four cDNA libraries derived from tissues infected with nodavirus (head kidney,
spleen, brain and liver). Genes differentially expressed upon infection were isolated
and further analysed by real-time PCR, thus confirming some of them to be biomarkers for bacterial and viral infections in fish. Altogether, the increasing availability
of sequence information from various teleost species, as well as the corresponding
functional expression data, are of importance to better understand immunity-related
mechanisms of teleost and their evolution.
7.6.2.2 Microarray Analysis to Identify Genes Involved
in Host Immune Response
DNA microarrays, which allow high-throughput expression profiling (see Section
7.2.5 Functional genomics tools), have been only used in few studies to identify genes involved in the immune response of aquacultured fish species. One of
these studies aimed at profiling gene expression, using a cDNA microarray, during the acute immune response of catfish following infection with Gram-negative
bacteria (Peatman et al. 2007). Microarray analysis revealed that expression of the
majority of typical acute phase proteins was up-regulated in catfish, together with
a set of putative teleost acute phase reactants. A similar study performed in sea
bass (E. Sarropoulou, personal communication) showed that expression of several
genes involved in iron homeostasis was strongly induced during immune response,
suggesting that limitation of free iron may inhibit bacterial growth while avoiding metal-induced cellular damage. In a follow-up study by Peatman et al. (2008)
using an oligonucleotide microarray, a detailed analysis of transcripts involved in
the MHC I pathway was performed. The authors identified a total of 131 differentially expressed genes, of which 103 were believed to be unique genes. Interestingly,