A circadian model for viral persistence

Significant Unresolved Questions and Opportunities for Bioengineering in Understanding and Treating COVID-19 Disease Progression

COVID-19 is a disease that manifests itself in a multitude of ways across a wide range of tissues. Many factors are involved, and though impressive strides have been made in studying this novel disease in a very short time, there is still a great deal that is unknown about how the virus functions. Clinical data has been crucial for providing information on COVID-19 progression and determining risk factors. However, the mechanisms leading to the multi-tissue pathology are yet to be fully established. Although insights from SARS-CoV-1 and MERS-CoV have been valuable, it is clear that SARS-CoV-2 is different and merits its own extensive studies. In this review, we highlight unresolved questions surrounding this virus including the temporal immune dynamics, infection of non-pulmonary tissue, early life exposure, and the role of circadian rhythms. Risk factors such as sex and exposure to pollutants are also explored followed by a discussion of ways in which bioengineering approaches can be employed to help understand COVID-19. The use of sophisticated in vitro models can be employed to interrogate intercellular interactions and also to tease apart effects of the virus itself from the resulting immune response. Additionally, spatiotemporal information can be gleaned from these models to learn more about the dynamics of the virus and COVID-19 progression. Application of advanced tissue and organ system models into COVID-19 research can result in more nuanced insight into the mechanisms underlying this condition and elucidate strategies to combat its effects.

Exploitation of host clock gene machinery by hepatitis viruses B and C

Many aspects of cellular physiology display circadian (approximately 24-h) rhythms. Dysfunction of the circadian clock molecular circuitry is associated with human health derangements, including neurodegeneration, increased risk of cancer, cardiovascular diseases and the metabolic syndrome. Viruses triggering hepatitis depend tightly on the host cell synthesis machinery for their own replication, survival and spreading. Recent evidences support a link between the circadian clock circuitry and viruses’ biological cycle within host cells. Currently, in vitro models for chronobiological studies of cells infected with viruses need to be implemented. The establishment of such in vitro models would be helpful to better understand the link between the clock gene machinery and viral replication/viral persistence in order to develop specifically targeted therapeutic regimens. Here we review the recent literature dealing with the interplay between hepatitis B and C viruses and clock genes.

Mutual antagonism between circadian protein period 2 and hepatitis C virus replication in hepatocytes

BACKGROUND

Hepatitis C virus (HCV) infects approximately 3% of the world population and is the leading cause of liver disease, impacting hepatocyte metabolism, depending on virus genotype. Hepatic metabolic functions show rhythmic fluctuations with 24-h periodicity (circadian), driven by molecular clockworks ticking through translational-transcriptional feedback loops, operated by a set of genes, called clock genes, encoding circadian proteins. Disruption of biologic clocks is implicated in a variety of disorders including fatty liver disease, obesity and diabetes. The relation between HCV replication and the circadian clock is unknown.

METHODS

We investigated the relationship between HCV core infection and viral replication and the expression of clock genes (Rev-Erbα, Rorα, ARNTL, ARNTL2, CLOCK, PER1, PER2, PER3, CRY1 and CRY2) in two cellular models, the Huh-7 cells transiently expressing the HCV core protein genotypes 1b or 3a, and the OR6 cells stably harboring the full-length hepatitis C genotype 1b replicon, and in human liver biopsies, using qRT-PCR, immunoblotting, luciferase assays and immunohistochemistry.

RESULTS

In Huh-7 cells expressing the HCV core protein genotype 1b, but not 3a, and in OR6 cells, transcript and protein levels of PER2 and CRY2 were downregulated. Overexpression of PER2 led to a consistent decrease in HCV RNA replicating levels and restoration of altered expression pattern of a subset of interferon stimulated genes (ISGs) in OR6 cells. Furthermore, in liver biopsies from HCV genotype 1b infected patients, PER2 was markedly localized to the nucleus, consistent with an auto-inhibitory transcriptional feedback loop.

CONCLUSIONS

HCV can modulate hepatic clock gene machinery, and the circadian protein PER2 counteracts viral replication. Further understanding of circadian regulation of HCV replication and rhythmic patterns of host-hosted relationship may improve the effectiveness of HCV antiviral therapy. This would extend to hepatic viral infections the current spectrum of chronotherapies, implemented to treat metabolic, immune related and neoplastic disease.

The "metabolovirus" model of hepatitis B virus suggests nutritional therapy as an effective anti-viral weapon

Hepatitis B virus (HBV) is a small DNA virus that targets the liver almost exclusively. Chronic infection with HBV might lead to severe liver-related pathologies including chronic hepatitis, cirrhosis and hepatocellular carcinoma. Based on its enhancer composition, which links nutritional signals that control hepatic glucose and fat metabolism in the liver to HBV gene expression and replication, it appears that the virus has adopted a regulatory system that is unique to the major hepatic metabolic genes. This unique virus-host interaction, mediated by metabolic events in the liver, is designated by us the "metabolovirus model". We hypothesize that by mimicking the expression of key genes implicated in glucose homeostasis, HBV sophisticatedly exploits the host resources to ensure its persistence. Specifically, by recruiting transcription factors and coactivators common to essential hepatic metabolic genes the virus avoids a possible resistance by its host, on the one hand, and ensures a timely and proper response to changes in its environment in terms of metabolic milieu, on the other hand. Furthermore, by coupling its gene expression to the expression of hepatic metabolic genes that fluctuate during the day, we predict a fluctuating nature of HBV gene expression. This can serve the virus in its attempts to escape the host immune system in addition to other immune evading strategies adopted by the virus, such as the secretion of the e antigen. Based on our "metabolovirus model", we suggest new mechanisms to previously unexplained clinical phenomena, such as the observed diversity in disease severity between different geographical areas that differ in nutritional habits. Furthermore, given the up-regulatory effect of food deprivation on HBV gene expression and replication, we suggest that conditions of short-term starvation should be completely avoided by HBV-infected individuals, and dietary recommendations such as the ingestion of complex carbohydrates before sleep should be adopted. Thus, our hypothesis sets the stage for viral manipulation by controlling food intake, and opens additional avenues towards food or nutritional therapy as an effective anti-HBV weapon.