Research Projects

Herpes simplex viruses type 1 and type 2 are significant human pathogens. Approximately 67% of the US population are infected with HSV-1 and 20% with HSV-2. The viruses persist in the body for life in the form of a latent, or silent, infection of neurons. Periodically, the viruses reactivate from latency to allow transmission to a new host, which can be associated with disease including cold sores, kerato-conjunctivitis, genital lesions and encephalitis. The Cliffe lab investigates the mechanisms of herpes simplex virus (HSV) latency and reactivation in neurons. We use primary and differentiated neurons along with in vivo models to determine how HSV establishes a latent infection in neurons and how the virus reactivates under conditions of cell stress. Using HSV as a model system, we also aim to understand how different cell types recognize foreign DNA, the role of heterochromatin-associated proteins in gene silencing and the intersection between innate-immune responses and chromatin response to viral infection.
Some of the current projects in the lab include:

Restriction of HSV gene expression in neurons


HSV lytic gene expression becomes silenced in neurons to allow long-term persistence of the infected cell and therefore also the   virus. How this silencing occurs and is maintained specifically in neurons is not unknown. Using a variety of techniques including  restrictive infection of HSV on the axon in microfludic chambers, high resolution imaging of viral genomes, depletion of cellular  proteins using CRISPR/Cas9 technology and shRNA knock-down, chromatin immunoprecipitation and animal models of latency,  we are investigating the following:

  1. ​How is heterochromatin targeted to the viral genome in neurons
  2. What is the role of restrictive cellular proteins in the establishment of latency?
  3. How do viral gene products regulate the viral chromatin structure?
  4. How does the innate immune response intersect with the latent viral genome?
  5. How dynamic is the HSV chromatin structure during latency?

Our long-term aims are to ultimately understand how neurons sense to the foreign, HSV genome and respond by  silencing viral gene expression. In the future we also aim to manipulate the viral chromatin structure to make it more repressive and therefore refractory to reactivation.

The mechanisms of HSV reactivation

The mechanisms of HSV reactivationIn response to certain stimuli, latent HSV re-enters the lytic cycle to result in the production of infectious virus that can go on to infect neighboring cells. How the silencing viral chromatin forms a barrier for lytic gene expression and therefore the virus needs to overcome this barrier for reactivation to occur. We have developed both in vitro and animal models of HSV reactivation that allow us to investigate how the virus overcomes heterochromatin based silencing during reactivation. Using these systems, we are investigating:

  1. What are the neuronal stimuli and signaling pathways that can trigger reactivation of the virus?
  2. How are cellular proteins recruited to the viral genome during reactivation?
  3. How do cellular pathways intersect with changes to the viral chromatin structure?
  4. What determines whether a viral genome undergoes reactivation?

Our long-term goals are to understand what events trigger reactivation in humans and how these triggers modulate the viral genome to allow gene expression to occur. In addition, changes in the viral chromatin structure upon different neuronal stimuli serves as an excellent model to understand how activation of neuronal signaling pathways result in changes in gene expression.