title: High-throughput transcriptome analysis of ISAV-infected Atlantic salmon Salmo salar unravels divergent immune responses associated to head-kidney, liver and gills tissues.
abstract: Infectious salmon anaemia virus (ISAV) is an orthomyxovirus causing high mortality in farmed Atlantic salmon (Salmo salar). The collective data from the Atlantic salmon-ISAV interactions, performed "in vitro" using various salmon cell lines and "in vivo" fish infected with different ISAV isolates, have shown a strong regulation of immune related transcripts during the infection. Despite this strong defence response, the majority of fish succumb to infections with ISAV. The deficient protection of the host against ISAV is in part due to virulence factors of the virus, which allow evade the host-defence machinery. As such, the viral replication is uninhibited and viral loads quickly spread to several tissues causing massive cellular damage before the host can develop an effective cell-mediated and humoral outcome. To interrogate the correlation of the viral replication with the host defence response, we used fish that have been infected by cohabitation with ISAV-injected salmons. Whole gene expression patterns were measured with RNA-seq using RNA extracted from Head-kidney, Liver and Gills. The results show divergent mRNA abundance of functional modules related to interferon pathway, adaptive/innate immune response and cellular proliferation/differentiation. Furthermore, gene regulation in distinct tissues during the infection process was independently controlled within the each tissue and the observed mRNA expression suggests high modulation of the ISAV-segment transcription. Importantly this is the first time that strong correlations between functional modules containing significant immune process with protein-protein affinities and viral-segment transcription have been made between different tissues of ISAV-infected fish.
authors.affiliation: Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile.
authors.forename: Diego
authors.initials: D
authors.lastname: Valenzuela-Miranda
authors.affiliation: Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Boltaña
authors.affiliation: Facultad de Ciencias Agronómicas, Universidad de Chile, Av Santa Rosa 11315, La Pintana, Santiago 8820808, Chile.
authors.forename: Maria E
authors.initials: ME
authors.lastname: Cabrejos
authors.affiliation: Aquainnovo, Talca 60, P.O. Box 30B, Puerto Montt 5503032, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago 8820808, Chile.
authors.forename: José M
authors.initials: JM
authors.lastname: Yáñez
authors.affiliation: Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile. Electronic address: crisgallardo@udec.cl.
authors.forename: Cristian
authors.initials: C
authors.lastname: Gallardo-Escárate
mesh_terms: D056704:Adaptive Immunity; D000818:Animals; D005393:Fish Diseases / Q000235:genetics / Q000276:immunology* / Q000821:virology; D020869:Gene Expression Profiling / Q000662:veterinary; D005786:Gene Expression Regulation; D005880:Gills / Q000276:immunology; D060226:Head Kidney / Q000276:immunology; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary; D007113:Immunity, Innate; D046829:Isavirus / Q000502:physiology*; D008099:Liver / Q000276:immunology; D009928:Organ Specificity; D009976:Orthomyxoviridae Infections / Q000235:genetics / Q000276:immunology / Q000662:veterinary* / Q000821:virology; D020317:Salmo salar
keywords: ISAV; RNA-seq; Salmo salar; Viral segments; rt-qPCR