Specific gene expression responses to parasite genotypes reveal redundancy of innate immunity in vertebrates

Abstract

Vertebrate innate immunity is the first line of defense against an invading pathogen and has long been assumed to be largely unspecific with respect to parasite/pathogen species. However, recent phenotypic evidence suggests that immunogenetic variation, i.e. allelic variability in genes associated with the immune system, results in host-parasite genotype-by-genotype interactions and thus specific innate immune responses. Immunogenetic variation is common in all vertebrate taxa and this reflects an effective immunological function in complex environments. However, the underlying variability in host gene expression patterns as response of innate immunity to within-species genetic diversity of macroparasites in vertebrates is unknown. We hypothesized that intra-specific variation among parasite genotypes must be reflected in host gene expression patterns. Here we used high-throughput RNA-sequencing to examine the effect of parasite genotypes on gene expression patterns of a vertebrate host, the three-spined stickleback (Gasterosteus aculeatus). By infecting naïve fish with distinct trematode genotypes of the species Diplostomum pseudospathaceum we show that gene activity of innate immunity in three-spined sticklebacks depended on the identity of an infecting macroparasite genotype. In addition to a suite of genes indicative for a general response against the trematode we also find parasite-strain specific gene expression, in particular in the complement system genes, despite similar infection rates of single clone treatments. The observed discrepancy between infection rates and gene expression indicates the presence of alternative pathways which execute similar functions. This suggests that the innate immune system can induce redundant responses specific to parasite genotypes.

Figure 1. Effects of parasite exposure to parasite load in sticklebacks.

Shown is parasite load of three-spined sticklebacks, exposed to three different treatments of Diplostomum pseudospathaceum cercariae; clone I, clone XII and clone mix. The box plots show distribution of total number of cercaria per fish in each infection treatment.

Figure 2. Treatment specific pairwise comparisons of host gene expression.

(a) Exemplary comparison of log2-fold change values of genes differentially expressed in head kidney tissue of the clone I and XII treatments. Genes with fold changes only significant in one of two treatments are set to zero in the other treatment, thus genes can be either identified as unique to a certain treatment (yellow, blue), similar in both treatments (red) or up-regulated in one treatment while down-regulated in the other (green). (b) Figure 2b shows comparison of log2-fold changes for all pairwise treatment comparisons. From top to bottom, clone I vs. mix, clone XII vs. mix and clone I vs. XII, with gill tissue samples in the left column and head kidney samples in the right column. Differential expression is defined a statistical significance in differences of gene expression between exposed and control fish.

Figure 3. Venn diagrams for clone-wise distribution of differentially expressed genes in three-spined sticklebacks.

Differential expression is defined as statistical significance in differences of gene expression between exposed and control fish. The first row of numbers shows up-regulated, the second row down-regulated genes. (a, b) Displayed are all genes with significantly different expression values in head kidney (a) and gills (b). (c, d) Venn diagrams show genes significantly different and associated to putative immune functions in head kidney (c) and gills (d).

Figure 4. Heat map of genes attributed to the complement system.

Shown are transformed FPKM values indicating high (bright) and low (dark) expression of genes for both mono-clonal, clone I (I) and clone XII (XII), and the clone mix (M) treatment as well as for the control in (a) head kidney tissue and (b) gills.