Extracellular RNA in viral-host interactions: Thinking outside the cell

Abstract

Small RNAs and their associated RNA interference (RNAi) pathways underpin diverse mechanisms of gene regulation and genome defense across all three kingdoms of life and are integral to virus-host interactions. In plants, fungi and many animals, an ancestral RNAi pathway exists as a host defense mechanism whereby viral double-stranded RNA is processed to small RNAs that enable recognition and degradation of the virus. While this antiviral RNAi pathway is not generally thought to be present in mammals, other RNAi mechanisms can influence infection through both viral- and host-derived small RNAs. Furthermore, a burgeoning body of data suggests that small RNAs in mammals can function in a non-cell autonomous manner to play various roles in cell-to-cell communication and disease through their transport in extracellular vesicles. While vesicular small RNAs have not been proposed as an antiviral defense pathway per se, there is increasing evidence that the export of host- or viral-derived RNAs from infected cells can influence various aspects of the infection process. This review discusses the current knowledge of extracellular RNA functions in viral infection and the technical challenges surrounding this field of research. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.

Keywords: RNA interference; extracellular RNA; extracellular vesicle; host-pathogen; microRNA.

Figure 1

Functions of microRNA (miRNA)–target interactions inside an infected cell. Viruses encode miRNAs which can regulate host messenger RNAs (mRNAs), viral mRNAs, and host miRNAs to promote infection. At the same time infections lead to changes in host miRNA expression which influences immune responses

Figure 2

Functional modes of secreted (viral) microRNAs (miRNAs). Host‐ and viral‐encoded miRNAs which are transcribed in the nucleus and processed in the nucleus and cytoplasm can be exported from the cell in extracellular vesicles (EVs). Export pathways involve multivesicular endosomes (MVEs) or budding from the plasma membrane. Viral miRNAs when transferred to recipient cells can promote/inhibit infection by regulating gene transcripts. Examples are shown involving viral miRNA transfer to dendritic cells (DCs) or macrophages (MΦ) that can lead to chronic inflammation through the activation of toll‐like receptors (TLRs). Host miRNAs transmitted from infected to uninfected cells can either enhance or suppress viral infections and/or contribute to chronic inflammation. Antiviral immune responses can be suppressed by host miRNAs that target the interferon (IFN) pathway in epithelial cells (Epi) or through inhibition of macrophage activation. On the other hand, host miRNAs can activate the IFN response by suppressing negative regulators of the retinoic acid‐inducible gene I (RIG‐I). Other mechanisms of host defense include the activation of autophagy

Figure 3

Proposed mechanism for transmission of hepatitis C virus (HCV) in extracellular vesicles (EVs) in complex with miR‐122. HCV genomic RNA is exported from infected cells in EVs in a complex with miR‐122 and Argonaute 2 (AGO2) protein. The absence of viral surface protein prevents immune recognition and allows the transfer to uninfected cells where the virus replicates. EVs harboring viral proteins on their surface are recognized by the immune system and fail to establish viral infection in uninfected cells

Figure 4

Release and uptake mechanisms of RNA via extracellular vesicles (EVs). EVs containing RNAs can be released from cells either through budding from the plasma membrane or through endosomal pathways involving the multivesicular endosomes (MVEs). Uptake mechanisms in the target cells include fusion with the plasma membrane, phagocytosis or macropinocytosis, (receptor‐mediated) endocytosis, clathrin‐dependent endocytosis, caveolin‐mediated endocytosis, and endocytosis involving filopodia. The mechanism for secretion of small RNAs independent of EVs but in association with RNA‐binding proteins (RBPs) is still unknown (black box)