HHV-6 encoded small non-coding RNAs define an intermediate and early stage in viral reactivation, 2018, Prusty et al

[SNT Gatchaman]

HHV-6 encoded small non-coding RNAs define an intermediate and early stage in viral reactivation
Prusty BK, Gulve N, Chowdhury SR, Schuster M, Strempel S, Descamps V, Rudel T

Human herpesvirus 6A and 6B frequently acquires latency. HHV-6 activation has been associated with various human diseases. Germ line inheritance of chromosomally integrated HHV-6 makes viral DNA-based analysis difficult for determination of early stages of viral activation.

We characterized early stages of HHV-6 activation using high throughput transcriptomics studies and applied the results to understand virus activation under clinical conditions. Using a latent HHV-6A cell culture model in U2OS cells, we identified an early stage of viral reactivation, which we define as transactivation that is marked by transcription of several viral small non-coding RNAs (sncRNAs) in the absence of detectable increase in viral replication and proteome. Using deep sequencing approaches, we detected previously known as well as a new viral sncRNAs that characterized viral transactivation and differentiated it from latency.

Here we show changes in human transcriptome upon viral transactivation that reflect multiple alterations in mitochondria-associated pathways, which was supported by observation of increased mitochondrial fragmentation in virus reactivated cells. Furthermore, we present here a unique clinical case of DIHS/DRESS associated death where HHV-6 sncRNA-U14 was abundantly detected throughout the body of the patient in the presence of low viral DNA.

In this study, we have identified a unique and early stage of viral activation that is characterized by abundant transcription of viral sncRNAs, which can serve as an ideal biomarker under clinical conditions.

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[SNT Gatchaman]

Selected quotes (my bolding) —

Similar to viral latency, initiation of viral reactivation from latency that lays the foundation for further changes in viral and host cell fate is fairly unknown. An intermediate stage in viral latency that marks the beginning of viral reactivation was previously postulated.

Virus encoded small non-coding RNAs (sncRNAs) including microRNAs (miRNAs) play crucial role in establishment of viral infection, immune evasion as well as disease development.

In this study we have identi!ed a unique expression pattern of virus-encoded small non-coding RNAs (sncRNAs) that clearly differentiates viral latency from reactivation.

Viral transactivation in U2OS cells was associated with upregulation and downregulation of several human transcripts.

Analysis of GO biological processes and KEGG pathway, suggested major changes in mitochondria associated pathways upon HHV- 6A transactivation. Careful analysis of virus transactivated cells also revealed major changes in mitochondrial morphology.

HHV-6 latency and activation is a heterogeneous process. At any point of time only a fraction of infected cells carry the integrated or reactivated viral genome.

Our studies show lack of complete and productive viral reactivation in U2OS cells that are possibly non-permissive for HHV-6 replication. However we show that viral genome excision in these cells and gain of partial function by viral genome (transactivation) might be clinically signi!cant. Through high throughput transcriptomics, we showed here that transactivation of HHV-6 is capable of bringing in major changes in host cell transcriptome.

Furthermore, we observed increased mitochondrial fission in HHV-6A transactivated cell, which provides possible explanation for changes in various mitochondria-associated metabolic pathways.

Our deep sequencing approach revealed major changes in expression pattern of a large panel of human miRNAs that hints to a broad range of effect on mitochondria and associated metabolic functions upon viral activation. We detected signi!cant changes in the expression pattern of miR-33 and miR-24-2-5p upon viral transactivation. miR- 33 plays crucial role in cholesterol metabolism whereas miR-24- 2-5p plays key role in fatty acid metabolism.

Similarly, miR-195, which has been reported to induce mitochondrial degeneration and ATP reduction in cardiomyocytes was altered upon viral activation. Several studies have reported the regulation of OXPHOS by miRNAs, particularly miR-210 down-regulating Complex III in mitochondria; miR-181c, miR-210 and miR-338 downregulating Complex IV; miR-141 downregulating Complex V; miR-338 regulating COX IV and miR-210 regulating COX 10 in the mitochondrial electron transport chain. Our results show significant changes in all these miRNAs suggesting an effective modulation of electron transport chain upon viral activation.

We observed an intermediate stage in viral reactivation that is characterized by increased transcription from a very few selected viral loci [...] This points towards a possible need for the virus reactivation machinery to modulate both host and/or viral DNA for further viral DNA replication.

Our study hints to a unique stage in viral life cycle, which is not yet being understood completely. PCR-based DNA studies would not identify this stage in viral life cycle as a clinically important stage in virus activation. However, molecular impact of this stage of HHV-6 on host cell should not be ignored from clinical point of view. Moreover, we show several small non-coding RNAs being transcribed upon viral transactivation making them suitable candidate to be used as biomarkers for HHV-6 studies.

 

[Tia]

I'd be interested to know if/how Prusty's research might fit with @Manuel 's work (thread here: https://www.s4me.info/threads/cd4-c...-diseases-2022-ruiz-pablos.28782/#post-430450)