背景:传染性鲑鱼贫血病毒(ISAV)是一种正多米病毒,对全世界的鲑鱼水产养殖来说是一个大问题。目前的预防和治疗方法仅部分有效。遗传选择和基因组工程具有开发ISAV抗性鲑鱼种群的潜力。两种策略都可以受益于对ISAV发病机理的基因组调控的改进理解。这里,我们使用大西洋鲑鱼细胞系的单细胞RNA测序,首次对ISAV感染早期宿主-病毒相互作用的基础转录景观进行了高维分析.
结果:在ISAV攻击后24、48和96小时对鲑鱼头肾(SHK-1)细胞进行单细胞RNA测序。感染后24小时,细胞显示与病毒进入一致的表达特征,有PI3K等基因,FAK或JNK相对于未感染的细胞上调。在48和96小时,感染的细胞表现出明显的抗病毒反应,其特征在于IFNA2或IRF2的表达。未感染的旁观者细胞在48和96小时也显示出明显的转录差异,可能提示来自受感染细胞的旁分泌信号。这些旁观者细胞表达的途径,如mRNA传感,RNA降解,泛素化或蛋白酶体;线粒体核糖体基因的上调似乎也在宿主对感染的反应中起作用。病毒和宿主基因之间的相关性揭示了这种鱼-病毒相互作用的潜在关键基因。
结论:这项研究增加了我们对ISAV感染过程中大西洋鲑鱼的细胞反应的理解,并揭示了细胞水平上的宿主病毒相互作用。我们的结果突出了这种宿主病毒相互作用中的各种潜在关键基因,可以在未来的功能研究中进行操作,以增加大西洋鲑鱼对ISAV的抗性。
BACKGROUND: Infectious Salmon Anaemia Virus (ISAV) is an Orthomixovirus that represents a large problem for salmonid aquaculture worldwide. Current prevention and treatment methods are only partially effective. Genetic selection and genome engineering have the potential to develop ISAV resistant salmon stocks. Both strategies can benefit from an improved understanding of the genomic regulation of ISAV pathogenesis. Here, we used single-cell RNA sequencing of an Atlantic salmon cell line to provide the first high dimensional insight into the transcriptional landscape that underpins host-virus interaction during early ISAV infection.
RESULTS: Salmon head kidney (SHK-1) cells were single-cell RNA sequenced at 24, 48 and 96 h post-ISAV challenge. At 24 h post infection, cells showed expression signatures consistent with viral entry, with genes such as PI3K, FAK or JNK being upregulated relative to uninfected cells. At 48 and 96 h, infected cells showed a clear anti-viral response, characterised by the expression of IFNA2 or IRF2. Uninfected bystander cells at 48 and 96 h also showed clear transcriptional differences, potentially suggesting paracrine signalling from infected cells. These bystander cells expressed pathways such as mRNA sensing, RNA degradation, ubiquitination or proteasome; and up-regulation of mitochondrial ribosome genes also seemed to play a role in the host response to the infection. Correlation between viral and host genes revealed novel genes potentially key for this fish-virus interaction.
CONCLUSIONS: This study has increased our understanding of the cellular response of Atlantic salmon during ISAV infection and revealed host-virus interactions at the cellular level. Our results highlight various potential key genes in this host-virus interaction, which can be manipulated in future functional studies to increase the resistance of Atlantic salmon to ISAV.