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RNA-seq transcriptome analysis in flounder cells to compare innate immune responses to low- and high-virulence viral hemorrhagic septicemia virus

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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.

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Acknowledgements

This work was supported by a grant from the National Institute of Fisheries Science in the Republic of Korea (Grant Number: R2019058) and the National Research Foundation of the Republic of Korea (2019R1A2C1006721).

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  1. Jee Youn Hwang, Unn Hwa Lee and Min Jin Heo contributed equally to this work.

Authors and Affiliations

  1. Aquatic Disease Control Division, National Institute Fisheries Science, Busan, 46083, Korea

    Jee Youn Hwang, Ji Min Jeong, Mun Gyeong Kwon & Bo Young Jee

  2. Department of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea

    Unn Hwa Lee & Jeong Woo Park

  3. Department of Marine Biology and Aquaculture, Institute of Marine Industry, College of Marine Science, Gyeongsang National University, Gyeongnam, 650-160, Korea

    Min Jin Heo & Chan-Il Park

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Contributions

JYH collected VHSV strains and performed the in vivo infection experiment. UHL performed the in vitro VHSV growth experiment. JYH and UHL analyzed RNA-seq data. MJH and JMJ performed the in vivo infection experiment and analyzed RNA-seq data. MGK and BYJ designed the experiments and discussed the results. CIP and JWP designed the experiments, wrote the manuscript, and analyzed the results.

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Correspondence to Chan-Il Park or Jeong Woo Park.

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705_2020_4871_MOESM1_ESM.xlsx

Supplementary file1 Supplemental Table S1 List of DEGs between mock-infected control and VHS2012-6-infected HINAE cells at 12 h postinfection (XLSX 6674 KB)

705_2020_4871_MOESM2_ESM.xlsx

Supplementary file2 Supplemental Table S2 List of DEGs between mock-infected control and VHS2015-5-infected HINAE cells at 12 h postinfection (XLSX 6730 KB)

705_2020_4871_MOESM3_ESM.xlsx

Supplementary file3 Supplemental Table S3 List of DEGs between mock-infected control and VHS2012-6-infected HINAE cells at 24 h postinfection (XLSX 6636 KB)

705_2020_4871_MOESM4_ESM.xlsx

Supplementary file4 Supplemental Table S4 List of DEGs between mock-infected control and VHS2015-5-infected HINAE cells at 24 h postinfection (XLSX 6571 KB)

705_2020_4871_MOESM5_ESM.xlsx

Supplementary file5 Supplemental Table S5 List of innate immune response genes differentially expressed in VHS2015-5-infected and VHS2012-6-infected HINAE cells compared to mock-infected control HINAE cells at 12 h postinfection (XLSX 19 KB)

705_2020_4871_MOESM6_ESM.xlsx

Supplementary file6 Supplemental Table S6 List of innate immune response genes differentially expressed in VHS2015-5-infected and VHS2012-6-infected HINAE cells compared to mock-infected control HINAE cells at 24 h postinfection (XLSX 18 KB)

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Hwang, J.Y., Lee, U.H., Heo, M.J. et al. RNA-seq transcriptome analysis in flounder cells to compare innate immune responses to low- and high-virulence viral hemorrhagic septicemia virus. Arch Virol 166, 191–206 (2021). https://doi.org/10.1007/s00705-020-04871-5

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