DahariLAB
Mathematical/Computational Virology & Medicine
HBV Translational Science
Despite an effective vaccine, hepatitis B virus (HBV) remains a growing health concern and burden on systems. Hundreds of millions globally are infected. The virus in adults will typically be an acute infection but for children and infants, the rate of HBV as a chronic infection can be as high as 90%. This presents a serious health issue for the patient and strains healthcare resources. Additionally, HBV carries are at risk of co-infection with hepatitis D which is more aggressive in its attack on the liver. Previous research was limited by lack of in vitro cultures and small animal models to study both the infection and treatment. Now we are able to observe the HBV lifecycle and treatment response in cell cultures as well as mice. This will lead to a better understanding of the virus at the molecular level and is critical to developing more effective treatment strategies. Mathematical modelling has played a key role in filling previous clinical gaps and will deepen our understanding as the research evolves. The goal is to map and understand the detailed molecular biological processes that regulate HBV infection. In Dahari Lab we work with a cross disciplinary team of virologists, animal modeling experts, computational scientists, clinicians and pharmaceutical companies, we aim to better understand the virus-host interplay, the mode of actions of current and new antivirals, and treatment strategies. All of this is possible with more sophisticated models and is key to achieving a cure.
Research Topics
New drug research for improved treatments for HBV: RNAi-based therapy in patients
Current drugs are effective in suppressing the virus but do not lead to cure. Achieving HBV cure is early stages for hepatitis B since current treatment options focus on removing circulating HBV DNA but are not effective in removing the HBV surface- and e- antigens that allow patients’ immune response to fight the virus.
Why does this matter? What are their functions?
Recent clinical studies showed promising results in the use of an RNA interference-based (RNAi) treatment to address this short coming of the existing treatment. By mathematically modeling available HBV kinetic data under RNAi treatment, we were able to provide insights into HBV-host dynamics and estimate RNAi efficacy in reducing circulating virus, s and e antigens (Scientific Reports). Further research in this area could aid in the development of 2nd generation RNAi-based therapies.
Research in chimeric mice with humanized livers provides insights into the early dynamics of acute HBV infection
Two significant pieces of collaborative research with Prof. Chayama at Hiroshima University, revealed, and further explored the multiphasic nature of HBV. The first piece of research (Hepatology) uncovered and characterized the surprising multiphasic nature of HBV infection. This finding is especially significant when it was revealed that the virus moves through these phases without the host producing a specific anti-HBV adaptive immune response.
The second study is more theoretical and builds on this knowledge. It describes in greater detail the multiphasic viral host dynamics (Journal of Hepatology 2018, V. 68). The humanized chimeric mice allow for researchers to track from the exact moment of infection which allows for more accurate HBV infection patterns to be studied. The combined efforts of observational study and the ongoing theoretical modeling allow for a better understanding of the release of virions (infective form of the virus) over time from the moment of infection.
Understanding HBV dynamics and the antiviral effect of interferon-α treatment in humanized chimeric mice Tracking virus kinetics via the blood/serum is very common and data is abundant from patients, whereas the dynamics of the virus at the cellular level (in the liver) is still in the early stages of data collection. Collaboration with Prof. Chayama of Hiroshima University resulted in a deeper understanding of the mode of action of interferon-α-based treatments. However, this research is important beyond showing differences in the efficacy of these treatments (Journal of Virology). The ability to compare the results simultaneously of the viral kinetics in the blood as well as “inside” the liver at the cellular level is an important contribution to the study of HBV. The richer data gathered through chimeric mice with humanized livers results in a more accurate model. This liver-based cellular data is necessary to build a strong foundational knowledge for more advanced research.
Understanding HBV pre-genomic RNA (pgRNA) dynamics in patients
In two letters published in Hepatology and Journal of Viral Hepatitis, Dahari Lab and partners underscored some interesting data in the search for better treatments and ultimately a cure for HBV. Specifically, the Lab identified two areas of interest.
One is HBV pgRNA as additional new marker in the blood when trying to understand the status of HBV infection in patients (Hepatology). Current markers such as HBV DNA in the blood stream, have proven to be limited in their indication of covalently closed circular DNA (cccDNA) clearance for HBV. The research on HBV RNA kinetics suggests this marker may be more reliable in understanding the viral levels present.
The second is nucleos(t)ide analogue (NA) therapy (Journal of Viral Hepatitis). Using mathematical modeling it is possible to gain a clearer understanding of the NA mode of actions, especially as it relates to the interplay with pgRNA kinetics. Further study of HBV pgRNA kinetics during NA treatment in patients could yield significant data that informs more effective therapies for clearing the virus.
A third research study (submitted) with a broader scope, characterizes pgRNA as well as a broader set of variables and markers during 24-week monotherapy with tenofovir disoproxil fumarate (TDF). The HBV life cycle is complicated and the marker pgRNA as well as the other HBV markers included in this study, may give us a greater insight into how to potentially interrupt this cycle and develop better therapies. Our research in this area is ongoing as we collect richer data sets to build more detailed mathematical models on the molecular level to examine the HBV-host dynamics during NA monotherapy.
Understanding early HBV kinetics in primary human hepatocytes (PHH) through mathematical modeling Data and insights on HBV kinetics at the molecular (cellular) level is still in the early stages but is essential to building strong foundational science in the treatment of HBV. There are no data-driven mathematical models for understanding extracellular and intracellular HBV kinetics in cell cultures (PHHs) during early infection and treatment. This research developed and utilized a tri-compartment mathematical model to better understand HBV dynamics during infection and treatment in PHHs. This model provides novel insights into the interrelationships and dynamics of three variables. These include: cccDNA accumulation in the nucleus, intracellular HBV DNA production from the cell cytoplasm, and the kinetics of HBV DNA extracellularly. PHH-based research (using a combination of human cells + modeling data) is an effective complement without the cost and complexities of patient- and chimeric mice-based research. These insights were presented in late 2019 at The Annual AASLD and is ongoing. (Hepatology 2019; Vol 70. Suppl1:178A)
Treating chronic HBV infection with nucleic acid polymer (NAPs) monotherapy
Early research findings have been very promising in the use of NAPs. Our previous and upcoming EASL presentations (Journal of Hepatology 2019) contribute to the already strong foundational science in the fight against HBV. Two specific areas show promise in the research for a functional cure*: new knowledge of HBV surface antigen (HBsAg) turnover in the blood and the effective use of NAPs in treatment of patients (Scientific Reports 2020)
Not much is known about HBsAg clearance and production (turnover). The partnership with Replicor allowed us, through mathematical modeling, to better estimate/understand this phenomenon. Current approved treatments for HBV mainly suppress the virus, while the Replicor treatment uses NAPs to directly suppress HBsAg production. This suppression exposes the antigen turnover for deeper study for the first time.
Of particular interest in this research is the effects of the NAPs drug on the immune response (anti-HBs antibody in the blood). Of all the current treatments for HBV, only this one directly suppresses HBsAg. What happens to the immune system once the HBsAg are greatly reduced? What is the body’s response? The indirect effects of this suppression provide a rich area of exploration through modeling to better understand the viral kinetics. Without suppression of surface antigen, a functional cure is difficult to achieve.
The current research suggests that this treatment results in rapid viral and HBsAg clearance as well as the appearance of anti-HBs (immune response) restoring and supporting the patient’s own immune response. Further modeling efforts to refine the understanding of the modes of action of NAPs against HBV is ongoing.
*Defined as suppression of the virus (HBV DNA + HBsAg) in the blood.
NAP-Based combination therapy in treating HBV infection Characterizing the kinetics of hepatitis B surface Antigen (HBsAg) and other markers of HBV is an important step in the development of more effective multi-therapy approaches to treating HBV. Building on the research and data (Bazinet et al., Gastroenterology) from previous nucleic acid polymers (NAPs) monotherapy studies, a detailed analysis was applied to measured HBV serum samples (Hershkovich et al., EASL). The aim of this research was to characterize the kinetic patterns of a triple therapy treatment in treating HBV. NAP (REP 2139-Mg or REP 2165-Mg) was combined with pegylated interferon alpha-2a (IFN) and tenofovir disoproxil fumarate (TDF). The analysis identified early HBsAg kinetic markers that are associated with favorable clinical outcome (such as a functional cure). This analysis is useful in the development of data-driven mathematical models as well as contributing to foundational HBV science. A more practical application is the potential ability to predict duration and successful outcomes leading to improved therapies.
Characterization of serum HBV kinetics in mice engrafted with components of a human immune system (HIS) and/or human hepatocytes (HEP) Currently the most important phase of HBV research is the collection of basic science data to build more robust models and truly understand the nature of HBV in order to achieve the same level of treatment options as HCV. This research aimed to replicate a human-like immunological response in mice to better understand mechanisms of HBV-host interplay during infection. Three groups of mice were engineered in Ploss Lab at Princeton University, for this purpose: HIS, HEP and HIS-HEP. The current preliminary results demonstrate that the mice dually engrafted with components of HIS and HEP are susceptible to HBV infection and mount HBV-specific immune responses that we plan together to be further experimentally and theoretically investigated.
HBV Translational Science
Despite an effective vaccine, hepatitis B virus (HBV) remains a growing health concern and burden on systems. Hundreds of millions globally are infected. The virus in adults will typically be an acute infection but for children and infants, the rate of HBV as a chronic infection can be as high as 90%. This presents a serious health issue for the patient and strains healthcare resources. Additionally, HBV carries are at risk of co-infection with hepatitis D which is more aggressive in its attack ...
Despite an effective vaccine, hepatitis B virus (HBV) remains a growing health concern and burden on systems. Hundreds of millions globally are infected. The virus in adults will typically be an acute infection but for children and infants, the rate of HBV as a chronic infection can be as high as 90%.