Review Viral miRNA regulation of host gene expression, 2023, Diggins and Hancock

[SNT Gatchaman]

Viral miRNA regulation of host gene expression
Diggins; Hancock

Viruses have evolved a multitude of mechanisms to combat barriers to productive infection in the host cell. Virally-encoded miRNAs are one such means to regulate host gene expression in ways that benefit the virus lifecycle. miRNAs are small non-coding RNAs that regulate protein expression but do not trigger the adaptive immune response, making them powerful tools encoded by viruses to regulate cellular processes. Diverse viruses encode for miRNAs but little sequence homology exists between miRNAs of different viral species. Despite this, common cellular pathways are targeted for regulation, including apoptosis, immune evasion, cell growth and differentiation.

Herein we will highlight the viruses that encode miRNAs and provide mechanistic insight into how viral miRNAs aid in lytic and latent infection by targeting common cellular processes. We also highlight how viral miRNAs can mimic host cell miRNAs as well as how viral miRNAs have evolved to regulate host miRNA expression. These studies dispel the myth that viral miRNAs are subtle regulators of gene expression, and highlight the critical importance of viral miRNAs to the virus lifecycle.

Link (Seminars in Cell & Developmental Biology) Paywall

 

[Hutan]

Interesting.

Having got my head around micro-RNAs made by the host in order to adjust gene expression, here we have viruses making micro-RNAs that can hijack the host's gene expression, in order to help the viruses survive and/or replicate.

And we've seen elsewhere where a cell infected with HSV seems to be protected against infection from other viruses, so things are, no doubt, even more complicated and finely tuned.

 

[SNT Gatchaman]

A successful viral infection necessitates that viral gene products reengineer the infected cell to support the viral lifecycle. This includes preventing apoptosis and other antiviral responses as well as altering host metabolism to support viral gene expression, DNA replication and the production of new virions. [...] until recently the importance and functions of viral non-coding RNAs has not been as well appreciated. Virus-encoded long non-coding RNAs (lncRNA), circular RNAs (circRNAs) and microRNAs (miRNAs) as well as many other small non-coding RNAs have critical roles

We describe [...] how viral miRNAs regulate (i) apoptosis, (ii) innate and adaptive immunity and (iii) cellular signaling pathways regulating cell growth and differentiation. Furthermore, we discuss how viral miRNAs regulate transcription factor and cytokine expression, mimic cellular miRNAs and regulate cellular miRNA expression and function.

Finally, we discuss viral miRNA packaging into exosomes and their use as biomarkers of infection and disease states and how viral miRNA targeting of viral genes plays an essential role in latency and reactivation.

 

[SNT Gatchaman]

While an individual miRNA rarely reduces protein expression greater than 50%, multiple sites for the same miRNA, or sites for additional miRNAs within the transcript can have both additive and cooperative effects. Furthermore, miRNAs are very stable, with a half-life of days

Host and virus-encoded miRNAs have substantial regulatory potential, with some estimates suggesting that individual miRNAs could target upwards of 100 different transcripts. This implies that miRNAs could regulate essentially all cellular processes and disease states.

High-throughput approaches such as [...] have identified many thousands of cellular targets of viral miRNAs and revealed extensive gene networks regulated by herpesvirus miRNAs

These findings are contrary to the idea that miRNAs have redundant or only subtle effects on gene expression.

 

[SNT Gatchaman]

Why herpesviruses have evolved to express miRNAs is likely due to the life-long nature of herpesvirus infection. The hallmark of herpesviruses is their ability to establish a latent infection[...]. During latency, expression from the viral genome is reduced, but not completely silenced, as the virus retains a need to manipulate the cell to maintain the viral genome and dampen extracellular signals. This leads to some exposure to the host immune system, necessitating an immune evasion strategy which is at least partially achieved by expression of viral miRNAs.

miRNA sequences across herpesviruses are highly divergent. Despite this lack of sequence conservation, many similar proteins and pathways are targeted by herpesvirus miRNAs, indicating that viral miRNAs have undergone convergent evolution to overcome common obstacles

 

[SNT Gatchaman]

it is clear that suppression of apoptosis is an important function of viral miRNAs, especially during latency. Given the multiple signaling pathways that contribute to the induction of apoptosis, viruses have evolved redundant methods to inhibit apoptosis using viral proteins and non-coding RNAs.

Even within the spectrum of viral miRNAs, redundant functions exist, likely due to the modulatory nature of miRNA function. In this case, viruses use multiple miRNAs and target multiple components of the pathway [...]. Caspase-3 sits at the convergence point of all apoptosis pathways and is key in regulating the downstream effects of apoptosis and as such is highly targeted by many herpesviruses using multiple miRNAs.

 

[SNT Gatchaman]

viruses are recognized by cellular sensors which act to signal the infection to neighboring cells using the production and secretion of type I IFNs and pro-inflammatory cytokines. Innate immune cells, such as natural killer (NK) cells [and] specific lymphocytes direct killing of infected cells and ultimately provide long-term immunity against pathogens. Thus, long-term persisting viruses devote significant effort to evading the intrinsic, innate and adaptive immune responses elicited by the host, including encoding miRNAs that target components of these pathways

Another critical PRR is RIG-I, which detects viral dsRNA in the cytoplasm. Viral miRNAs themselves can be recognized by RIG-I since miRNAs are exported to the cytoplasm as double-stranded pre-miRNAs. Indeed, EBV-encoded small noncoding RNAs are recognized by RIG-I and induce expression of type I interferon (IFN) as well as IFN stimulated gene (ISG) induction

Viruses devote considerable efforts to subverting the production and signaling of IFNs using proteins and non-coding RNAs.

Collectively, herpesvirus miRNAs commonly target the TLR/IKK/NFκB signaling pathways, albeit by interfering with different parts of the pathway, with the ultimate goal of supporting virus infection.

NK cells are potent cytotoxic lymphocytes that can recognize and kill pathogen-infected cells. Patients with NK cell deficiencies are more susceptible to herpesvirus infections, highlighting these cells an important contributor to controlling infections. Upon infection or other stresses, cells can express so-called ‘kill me’ ligands, which are recognized by activating receptors such as NKG2D, expressed on NK cells.

EBV miR-BART2–5p, KSHV miR-K12–7, and HCMV miR-UL112–3p all bind MICB mRNA via different target sites in the 3’UTR. Ectopic expression of any of these miRNAs reduces NK cell cytotoxicity

NK cell killing is a powerful tool used by the host to respond to viral infection, and viruses that encode miRNAs have evolved ways to target proteins that contribute to recognition of the infected cell as a potent means of immune evasion.

In order to prevent the recognition of virally infected cells, many viruses affect the processing and presentation of antigens on the cell surface using a variety of methods. EBV miRNAs have been implicated in preventing antigen processing and presentation [...] thus reducing the ability of virus-specific CD8 + T cell to recognize infected cells. Surface levels of HLA class I and II proteins and co-receptors were also downregulated as a result of miRNA targeting of the EBV latent membrane protein 1 (LMP1).

 

[SNT Gatchaman]

TGFβ signaling regulates multiple different cellular processes including apoptosis, proliferation, [Epithelial-Mesenchymal Transition] and differentiation. TGFβ signaling is normally anti-proliferative and can suppress growth of premalignant cells. [...] In B cells, TGFβ can induce cell cycle arrest and apoptosis, and hence EBV and KSHV invest heavily in viral proteins and miRNAs to affect this pathway.

like with the other signaling pathways highlighted here, TGFβ signaling is carefully regulated by DNA virus miRNAs through targeting multiple components of the signaling pathway to limit the detrimental effects on viral replication.

EBV miR-BHRF1–3 inhibits both basal levels and IFNγ induction of the T cell chemoattractant CXCL-11 either directly, or indirectly

Blocking the secretion of cytokines can also be accomplished by altering the vesicular trafficking pathways needed for cytokine release.

 

[SNT Gatchaman]

Another mechanism used by viruses to alter the host gene expression landscape is to alter the production or function of cellular miRNAs.

HHV-6A-encoded miRNA miR-aU14 inhibits the processing of multiple miR-30 family members through direct interaction with miR-30 hairpin loops within the pri-miRNA. By affecting the cellular miR-30 regulatory network, miR-aU14 affects mitrochondrial architecture and type I IFN responses

This is an intriguing example of a new method of regulation by a viral miRNA

virus-encoded circular RNAs (circRNAs) can act as miRNA ‘sponges’ to reduce the levels of available miRNA in the infected cell. [...] In the context of EBV and KSHV infection, virus-encoded circRNAs modulate the levels of cellular miRNAs and alter gene regulation networks.

 

[SNT Gatchaman]

The life-long nature of most herpesvirus infections and the limited coding capacity of viral genomes has resulted in numerous examples of convergent evolution of viral molecules that are functionally similar to host molecules. Within the context of viral miRNAs, numerous examples exist of viral miRNAs which share identical or highly similar seed sequences to host miRNAs, thus allowing the virus to tap into finely tuned and extensive host regulatory networks.

emerging evidence suggests that viral miRNAs are themselves loaded into exosomes as a way of influencing bystander cells without direct infection

For human miRNAs, the majority of circulating miRNAs are associated with proteins, not exosomes. Furthermore, copy numbers of a given miRNA are less than 1 per 100 exosomes, bringing into question the functional relevance of viral miRNAs packaged in exosomes.

how exosomal transfer of viral miRNAs to uninfected cells can benefit the viral life cycle is still poorly understood.

Viral proteins are inherently immunogenic, and one means to limit immune recognition is to regulate viral gene expression.

While it was initially theorized that herpesviruses targeted viral genes to promote the establishment of latency, there is evidence to suggest that herpesviruses also utilize miRNAs to target highly expressed viral genes that evoke an immune response.

 

[Hutan]

Another critical PRR is RIG-I, which detects viral dsRNA in the cytoplasm. Viral miRNAs themselves can be recognized by RIG-I since miRNAs are exported to the cytoplasm as double-stranded pre-miRNAs. Indeed, EBV-encoded small noncoding RNAs are recognized by RIG-I and induce expression of type I interferon (IFN) as well as IFN stimulated gene (ISG) induction

I was wondering whether it's possible to easily differentiate viral miRNA from host miRNA, even if a particular viral miRNA is doing the same job as the host miRNA. It sounds as though it might be possible.?