Abstract
BackgroundInterferons (IFN) are cytokines secreted by vertebrate cells involved in activation of signaling pathways that direct the synthesis of antiviral genes. To gain a global understanding of antiviral genes induced by type I IFNs in salmonids, we used RNA-seq to characterize the transcriptomic changes induced by type I IFN treatment and salmon alphavirus subtype 3 (SAV-3) infection in TO-cells, a macrophage/dendritic like cell-line derived from Atlantic salmon (Salmo salar L) head kidney leukocytes.ResultsMore than 23 million reads generated by RNA-seq were de novo assembled into 58098 unigenes used to generate a total of 3149 and 23289 differentially expressed genes (DEGs) from TO-cells exposed to type I IFN treatment and SAV-3 infection, respectively. Although the DEGs were classified into genes associated with biological processes, cellular components and molecular function based on gene ontology classification, transcriptomic changes reported here show upregulation of genes belonging to the canonical type I IFN signaling pathways together with a broad spectrum of antiviral genes that block virus replication in host cells. In addition, the transcriptome shows a profile of genes associated with apoptosis as well as genes that activate adaptive immunity. Further, our findings show that the profile of genes expressed by TO-cells is comparable to orthologous genes expressed by mammalian macrophages and dendritic cells in response to type I IFNs. Twenty DEGs randomly selected for qRT-PCR confirmed the validity of the transcriptomic changes detected by RNA-seq by showing that the genes upregulated by RNA-seq were also upregulated by qRT-PCR and that genes downregulated by RNA-seq were also downregulated by qRT-PCR.ConclusionsThe de novo assembled transcriptome presented here provides a global description of genes induced by type I IFNs in TO-cells that could serve as a repository for future studies in fish cells. Transcriptome analysis shows that a large proportion of IFN genes expressed in this study are comparable to IFNs genes expressed in mammalia. In addition, the study shows that SAV-3 is a potent inducer of type I IFNs and that the responses it induces in TO-cells could serve as a model for studying IFN responses in salmonids.
Highlights
Interferons (IFN) are cytokines secreted by vertebrate cells involved in activation of signaling pathways that direct the synthesis of antiviral genes
Several computer based de novo assembly tools (e.g. Trans-AbySS, Oasis, SOAP2denovo and Trinity) have been developed, only the trinity program was used for sequence assembly in this study given that several studies have shown that Trinity is a powerful tool that has proved to be useful for annotating transcriptomes for different vertebrate species across taxa [12,13]
Compared to other de novo transcriptome assemblers, Trinity recovers more full length transcripts from RNA-seq data without a reference genome with a sensitivity similar to methods that rely on genome alignments [12] and as such Trinity was considered to be a better tool for use in TO-cells given the limited number of annotated genes that would serve as reference genes in salmonids
Summary
Interferons (IFN) are cytokines secreted by vertebrate cells involved in activation of signaling pathways that direct the synthesis of antiviral genes. To gain a global understanding of antiviral genes induced by type I IFNs in salmonids, we used RNA-seq to characterize the transcriptomic changes induced by type I IFN treatment and salmon alphavirus subtype 3 (SAV-3) infection in TO-cells, a macrophage/dendritic like cell-line derived from Atlantic salmon (Salmo salar L) head kidney leukocytes. Salmonid alphavirus (SAV) causes pancreas disease (PD) in Atlantic salmon (Salmo salar L) and rainbow trout (Oncorhynchus mykiss) characterized by necrosis of the exocrine pancreas, cardiomyopathy and skeletal myopathy [1]. It was first reported in 1984 [2] and later characterized as a member of the family Togaviridae [3]. Our previous studies have shown that type I interferon (IFN) inhibits the replication of SAV-3 in TO-cells [6] which has stimulated further interest to elucidate the transcriptomic changes induced by type I IFNs in salmonids
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