西尼罗河病毒感染和干扰素 α 治疗改变了细胞外囊泡中分泌的编码和非编码宿主 RNA 的种类和水平。

West Nile virus infection and interferon alpha treatment alter the spectrum and the levels of coding and noncoding host RNAs secreted in extracellular vesicles.

机构信息

The Australian Infectious Diseases Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, MBS building 76, Cooper Rd, St Lucia, QLD, 4072, Australia.

The Pirbright Institute, Ash Rd, Pirbright, Surrey, GU24 GNF, UK.

出版信息

BMC Genomics. 2019 Jun 10;20(1):474. doi: 10.1186/s12864-019-5835-6.

DOI:10.1186/s12864-019-5835-6

PMID:31182021

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6558756/

Abstract

BACKGROUND

Extracellular vesicles (EVs) are small membrane vesicles secreted by the cells that mediate intercellular transfer of molecules and contribute to transduction of various signals. Viral infection and action of pro-inflammatory cytokines has been shown to alter molecular composition of EV content. Transfer of antiviral proteins by EVs is thought to contribute to the development of inflammation and antiviral state. Altered incorporation of selected host RNAs into EVs in response to infection has also been demonstrated for several viruses, but not for WNV. Considering the medical significance of flaviviruses and the importance of deeper knowledge about the mechanisms of flavivirus-host interactions we assessed the ability of West Nile virus (WNV) and type I interferon (IFN), the main cytokine regulating antiviral response to WNV, to alter the composition of EV RNA cargo.

RESULTS

We employed next generation sequencing to perform transcriptome-wide profiling of RNA cargo in EVs produced by cells infected with WNV or exposed to IFN-alpha. RNA profile of EVs secreted by uninfected cells was also determined and used as a reference. We found that WNV infection significantly changed the levels of certain host microRNAs (miRNAs), small noncoding RNAs (sncRNAs) and mRNAs incorporated into EVs. Treatment with IFN-alpha also altered miRNA and mRNA profiles in EV but had less profound effect on sncRNAs. Functional classification of RNAs differentially incorporated into EVs upon infection and in response to IFN-alpha treatment demonstrated association of enriched in EVs mRNAs and miRNAs with viral processes and pro-inflammatory pathways. Further analysis revealed that WNV infection and IFN-alpha treatment changed the levels of common and unique mRNAs and miRNAs in EVs and that IFN-dependent and IFN-independent processes are involved in regulation of RNA sorting into EVs during infection.

CONCLUSIONS

WNV infection and IFN-alpha treatment alter the spectrum and the levels of mRNAs, miRNAs and sncRNAs in EVs. Differentially incorporated mRNAs and miRNAs in EVs produced in response to WNV infection and to IFN-alpha treatment are associated with viral processes and host response to infection. WNV infection affects composition of RNA cargo in EVs via IFN-dependent and IFN-independent mechanisms.

摘要

背景

细胞外囊泡（EVs）是由细胞分泌的小膜囊泡，介导分子的细胞间转移，并有助于各种信号的转导。病毒感染和促炎细胞因子的作用已被证明会改变 EV 内容物的分子组成。EV 转移抗病毒蛋白被认为有助于炎症和抗病毒状态的发展。已证明，几种病毒在感染时会将选定的宿主 RNA 选择性纳入 EV，但WNV 除外。考虑到黄病毒的医学意义以及更深入了解黄病毒-宿主相互作用机制的重要性，我们评估了西尼罗河病毒（WNV）和 I 型干扰素（IFN）（调节 WNV 抗病毒反应的主要细胞因子）改变 EV RNA 货物组成的能力。

结果

我们采用下一代测序技术对感染 WNV 或暴露于 IFN-α的细胞产生的 EV 中的 RNA 货物进行全转录组谱分析。还确定了未感染细胞分泌的 EV 的 RNA 谱，并将其用作参考。我们发现 WNV 感染显着改变了某些宿主 microRNAs（miRNAs）、小非编码 RNA（sncRNA）和整合到 EV 中的 mRNAs 的水平。IFN-α处理也改变了 EV 中的 miRNA 和 mRNA 谱，但对 sncRNA 的影响较小。感染和 IFN-α处理后差异整合到 EV 中的 RNA 的功能分类表明，富集在 EV 中的 mRNAs 和 miRNAs 与病毒过程和促炎途径相关。进一步分析表明，WNV 感染和 IFN-α处理改变了 EV 中常见和独特的 mRNAs 和 miRNAs 的水平，并且 IFN 依赖和 IFN 非依赖过程参与了感染期间 RNA 分选到 EV 的调节。

结论

WNV 感染和 IFN-α处理改变了 EV 中 mRNAs、miRNAs 和 sncRNA 的谱和水平。响应 WNV 感染和 IFN-α处理产生的 EV 中差异整合的 mRNAs 和 miRNAs 与病毒过程和宿主对感染的反应相关。WNV 感染通过 IFN 依赖和 IFN 非依赖机制影响 EV 中 RNA 货物的组成。