Seasonal Immunoregulation in a Naturally-Occurring Vertebrate

Brown et al. BMC Genomics (2016) 17:369 DOI 10.1186/s12864-016-2701-7 RESEARCH ARTICLE Open Access Seasonal immunoregulation in a naturally- occurring vertebrate Martha Brown1, Pascal Hablützel1, Ida M. Friberg2, Anna G. Thomason2, Alexander Stewart3, Justin A. Pachebat1 and Joseph A. Jackson2* Abstract Background: Fishes show seasonal patterns of immunity, but such phenomena are imperfectly understood in vertebrates generally, even in humans and mice. As these seasonal patterns may link to infectious disease risk and individual condition, the nature of their control has real practical implications. Here we characterize seasonal dynamics in the expression of conserved vertebrate immunity genes in a naturally-occurring piscine model, the three-spined stickleback. Results: We made genome-wide measurements (RNAseq) of whole-fish mRNA pools (n = 36) at the end of summer and winter in contrasting habitats (riverine and lacustrine) and focussed on common trends to filter habitat-specific from overarching temporal responses. We corroborated this analysis with targeted year-round whole-fish gene expression (Q-PCR) studies in a different year (n = 478). We also considered seasonal tissue-specific expression (6 tissues) (n = 15) at a third contrasting (euryhaline) locality by Q-PCR, further validating the generality of the patterns seen in whole fish analyses. Extremes of season were the dominant predictor of immune expression (compared to sex, ontogeny or habitat). Signatures of adaptive immunity were elevated in late summer. In contrast, late winter was accompanied by signatures of innate immunity (including IL-1 signalling and non-classical complement activity) and modulated toll-like receptor signalling. Negative regulators of T-cell activity were prominent amongst winter-biased genes, suggesting that adaptive immunity is actively down-regulated during winter rather than passively tracking ambient temperature. Network analyses identified a small set of immune genes that might lie close to a regulatory axis. These genes acted as hubs linking summer-biased adaptive pathways, winter-biased innate pathways and other organismal processes, including growth, metabolic dynamics and responses to stress and temperature. Seasonal change was most pronounced in the gill, which contains a considerable concentration of T-cell activity in the stickleback. Conclusions: Our results suggest major and predictable seasonal re-adjustments of immunity. Further consideration should be given to the effects of such responses in seasonally-occurring disease. Keywords: Seasonality, RNAseq, Teleost, Three-spined stickleback, Immunity, Immunoregulation, Ecoimmunology, Wildlife Background vertebrate immune system, here we use transcriptomic Seasonal immune function has often been observed in measurements to reveal seasonal re-adjustments of im- vertebrates [1], including humans [2, 3], but is relatively munity in a naturally-occurring teleost model. Crucially, poorly understood. As with more studied circadian through focussing on wild organisms exposed to real- rhythms, though, there are fundamental implications for world environmental extremes, we expected to discover health [4, 5] (e.g., effects on vaccination and diseases more measurable variation than would be the case in a linked to immune function). Taking a comparative ap- study of domesticated animals, where seasonal variation proach [6] and considering the conserved genes of the may be muted by anthropogenic influences. We chose the three-spined stickleback (Gasterosteus * Correspondence: [email protected] aculeatus) as a subject because it has an annotated 2School of Environment and Life sciences, University of Salford, Salford M5 4WT, UK whole genome sequence [7] and occurs accessibly in Full list of author information is available at the end of the article highly seasonal natural habitats. Also, a considerable © 2016 Brown et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Brown et al. BMC Genomics (2016) 17:369 Page 2 of 18 knowledge base exists for this species: it is a highly stud- both sites at the individual error rate (in practice a more ied model organism [8, 9], and there are particularly de- stringent cut-off than an FDR-adjusted P = 0.05 for one tailed ecological studies relating to our main study area, locality). Following this criterion, 1263 genes were differ- mid Wales [10, 11]. We compared the transcriptomes of entially expressed in a consistent direction (Additional populations in late winter and late summer (outside of file 1: Table S1 shows those with Ensembl annotations), the breeding season, to reduce complexity) in ecologic- 850 increasing expression during winter (winter-biased) ally divergent natural populations, reasoning that a focus and 413 increasing expression during summer (summer- on common responses would provide a way to filter biased). overriding seasonal trends from locality-specific vari- We then considered genome-wide winter-summer ex- ation. We chose to primarily use global mRNA extracts pression changes in functional gene sets using gene set from individual whole fishes rather than from isolated enrichment analyses (GSEA) (Fig. 1), focussing on pre- cell populations or tissues. This was because a fully re- dicted orthologues of human genes (n = 11455 genes). ductionist approach to cell populations would be im- We compared ranked gene expression to KEGG and practical, and because the majority of the teleost REACTOME pathways, globally (Fig. 1a, Additional immune system is likely to be diffusely distributed in the file 2: Table S2). We also compared the ranked genes gut, under the skin and mucosal surfaces and in associ- to a selected group of gene sets reflecting different ation with the gills and liver (where, for example, com- organismal processes and immunological pathways plement proteins are mostly synthesized) [12–16]. (Fig. 1b, Additional file 3: Table S3). Finally, we con- By considering global (whole-fish) samples, we were sidered hypergeometric overlap of the selected gene thus able to take a holistic view of which immune sys- sets with the summer- and winter-biased genes de- tem pathways are differentially expressed at seasonal ex- fined above (Fig. 1b). Taken together, these analyses tremes. We corroborated our transcriptomic analyses by (Fig. 1) indicated signatures of growth in summer targeted gene expression measurements in year-round (summer bias of pathways reflecting mitotic activity, samples of fishes from the original sites in a new annual ECM processes, neural development, developmental cycle, and by tissue-specific analyses at a further site. biology) and physiological challenge in winter (winter Moreover, using network analyses we were able to ask bias of pathways reflecting autophagy, metabolism, what genes are important in regulating seasonal immune biological oxidation and the transport of a wide range function and how do seasonally-biased immune net- of biomolecules). In all analyses, some immune path- works interact with other seasonally-biased organismal ways were seasonally-biased, with innate processes processes? (complement cascade) emphasised in winter and adaptive (lymphocyte) processes in summer (Fig. 1). Results The above analyses were carried out on expression Seasonal expression bias of immune system genes occurs data un-adjusted for individual size, as this variable was against a well-defined genome-wide seasonal signature (intentionally) approximately balanced across winter and We analyzed the global (whole fish) transcriptomes of G. summer samples. However, as our sampling points aculeatus from two contrasting habitats in mid Wales, bounded a non-recruiting population ageing in the inter- River (Afon) Rheidol (RHD) and Lake (Llyn) Frongoch val between breeding seasons, we considered in more (FRN), in September 2012 and March 2013. To begin detail the potential influence of ontogenetic stage. It is our analysis we considered, genome-wide, which genes likely, given the months (March to September) in which were associated with seasonal expression bias. At FRN, we recorded reproductive activity in the field, and taking 4464 genes were significantly differentially expressed into account slower biological ageing at lower tempera- from summer to winter with an individual cut-off (P = tures (through measuring age in growing degree days), 0.05) and 1678 with a false discovery rate (FDR)-adjusted that the 0+ cohort in our approximately size-matched cut-off. At RHD, 4383 genes were significantly differen- summer and winter samples would have included tially expressed with an individual cut-off and 2067 with individuals widely overlapping in effective age (see an FDR-adjusted cut-off. Genes that were seasonally dif- Additional file 4: Figures S1-S2). Furthermore, as our ferentially expressed at both localities tended, over- sampling deliberately selected a wide range of fish sizes, whelmingly, to show synchronous expression (in the it is probable that 0+ and 1+ cohorts [11] were repre- same

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