RNA-seq transcriptome analysis in flounder cells to compare innate immune responses to low- and high-virulence viral hem
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ORIGINAL ARTICLE
RNA‑seq transcriptome analysis in flounder cells to compare innate immune responses to low‑ and high‑virulence viral hemorrhagic septicemia virus Jee Youn Hwang1 · Unn Hwa Lee2 · Min Jin Heo3 · Ji Min Jeong1 · Mun Gyeong Kwon1 · Bo Young Jee1 · Chan‑Il Park3 · Jeong Woo Park2 Received: 23 June 2020 / Accepted: 21 September 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract Viral hemorrhagic septicemia virus (VHSV) is a rhabdovirus that causes high mortality in cultured flounder. Viral growth and virulence rely on the ability to inhibit the cellular innate immune response. In this study, we investigated differences in the modulation of innate immune responses of HINAE flounder cells infected with low- and high-virulence VHSV strains at a multiplicity of infection of 1 for 12 h and 24 h and performed RNA sequencing (RNA-seq)-based transcriptome analysis. A total of 193 and 170 innate immune response genes were differentially expressed by the two VHSV strains at 12 and 24 h postinfection (hpi), respectively. Of these, 73 and 77 genes showed more than a twofold change in their expression at 12 and 24 hpi, respectively. Of the genes with more than twofold changes, 22 and 11 genes showed high-virulence VHSV specificity at 12 and 24 hpi, respectively. In particular, IL-16 levels were more than two time higher and CCL20a.3, CCR6b, CCL36.1, Casp8L2, CCR7, and Trim46 levels were more than two times lower in high-virulence-VHSV-infected cells than in low-virulence-VHSV-infected cells at both 12 and 24 hpi. Quantitative PCR (qRT-PCR) confirmed the changes in expression of the ten mRNAs with the most significantly altered expression. This is the first study describing the genome-wide analysis of the innate immune response in VHSV-infected flounder cells, and we have identified innate immune response genes that are specific to a high-virulence VHSV strain. The data from this study can contribute to a greater understanding of the molecular basis of VHSV virulence in flounder.
Introduction Handling Editor: William G Dundon. Jee Youn Hwang, Unn Hwa Lee and Min Jin Heo contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04871-5) contains supplementary material, which is available to authorized users. * Chan‑Il Park [email protected] * Jeong Woo Park [email protected] 1
Aquatic Disease Control Division, National Institute Fisheries Science, Busan 46083, Korea
2
Department of Biological Sciences, University of Ulsan, Ulsan 44610, Korea
3
Department of Marine Biology and Aquaculture, Institute of Marine Industry, College of Marine Science, Gyeongsang National University, Gyeongnam 650‑160, Korea
Viral hemorrhagic septicemia virus (VHSV) is an enveloped negative-strand RNA virus belonging to the genus Novirhabdovirus of the family Rhabdoviridae [1]. VHSV is the etiological agent of viral hemorrhagic septicemia (VHS), which is one of the main threats to the fish culture industry, causin
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