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What viruses can teach us about ourselves

Dr. Daphne Avgousti studies viruses that can give us a window into fundamental human biology that we can use to improve our health
Dr. Daphne Avgousti
Dr. Daphne Avgousti's work on viruses could help us find new ways to protect against infection and inflammation or even help us better understand cancer. Photo by Robert Hood / Fred Hutch News Service

Dr. Daphne Avgousti studies viruses and the ways that they hijack fundamental structures in our cells. She focuses on how viral proteins take advantage of our DNA packaging system that enables all six feet of our DNA to fit into a single cell.

The DNA packaging system that we and other organisms have evolved, called chromatin, ensures that our DNA fits into the nucleus, a membrane-bound “room” within the cell. Histones are a major component of chromatin and facilitate this storage by allowing the DNA to wind around them like thread around a spool. Chromatin also helps cells control which genes are turned off or on: Tighter packaging (including more histones) helps keep genes off, while looser packaging helps turn them on.

Viruses also use DNA packaging to fit their genetic material into viral particles. Adenovirus, one of the viruses that Avgousti studies, uses a histone-like protein called protein VII. This viral protein also changes the chromatin structure of cells it infects. Avgousti has shown that protein VII’s activity has wide-ranging implications for its host.

She also studies how herpes simplex virus, or HSV, takes advantage of our DNA packaging system. In a preprint posted to bioRxiv, her team recently reported that HSV co-opts an infection-induced change in host chromatin to get out of infected cells, the first step to infecting other cells.

We sat down with Avgousti to learn more about her work, how we can use basic biology lessons from viruses to improve other aspects of human health, and how HSV takes advantage of our chromatin. The conversation has been condensed and edited for clarity.

Why study viruses at this basic level?

You can look at it from the cell side and also from the virus side. If we understand how the cell defends itself, it will help us enhance that defense to fight viruses.

From the virus side of things, viruses take over the cell, that's what they do — and most of the time they win. Depending on the virus, the immune system of a person overcomes the infection on a systemic [whole-body] level. But in any one cell that's infected? Usually it's curtains for that cell.

Understanding how the virus does that means that we can do two things. We can put roadblocks in the way to prevent further infection. But we can also use what we learn from the virus to come up with other tools.

Do you have an example from your own work?

As a postdoctoral fellow, I discovered that protein VII, a DNA-packaging protein from adenovirus, changes the chromatin structure of the cell and brings proteins into the nucleus and into the chromatin. It sticks them there like glue so they can't get out of the cell.

One of those proteins is actually an immune signaling protein. By keeping it in the cell, adenovirus prevents the immune response on a systemic level. That allows the virus to spread more.

That was life changing for me. Like ‘oh, this actually means something on a bigger level’ — it's not just important within the one cell. What’s happening in the nucleus and in the chromatin has implications on a systemic level.

This protein from adenovirus is a neat way to turn off the immune response. We could take this lesson and potentially develop a drug that could help people with chronic inflammation. We’re trying to figure out how to pare down this viral protein to a really small sequence to block inflammation.  

You look at how viruses interact with our DNA packaging system. Why do we need to know more about that?

On the positive side, how chromatin works is just a basic, fundamental process of how a cell divides. It’s not an easy task. We have to understand how DNA opens and closes at very specific stages of cell division.

And on a fundamental level, all the things that we study inform that: How does DNA compaction happen and why? DNA viruses also compact their genomes inside a virus particle, and they do that in different ways. Some of them steal histones from the cell. Some of them have their own histones, some of them use completely different molecules.

The negative reason [for understanding chromatin] is that when DNA compaction goes wrong, you get cancer. It's pretty simple. There are thousands of mutations in genes for histones or chromatin modifiers that correlate with cancer. If you understand how those things function, then you can start to correct those mistakes.

There are many therapies on the market that change how chromatin is modified. A lot of those are very blunt instruments, because you have histones on hundreds of thousands of genes. So if you target one type of chromatin modification, you've just affected 100 genes that matter [to that cancer] and a thousand that don’t.

The more we understand about how histones work, the more targeted those therapies can become. And viruses are good at pinpointing exactly what has to change. By following the virus, we learn something about the key mechanisms in the chromatin.

Graduate student Hannah Lewis works at a tissue culture hood in the Avgousti lab.
Avgousti Lab graduate student Hannah Lewis studies how HSV interacts with the chromatin of host cells, and how this could benefit the virus. Photo by Robert Hood / Fred Hutch News Service

Which viruses are you studying, and how did you choose them?

Adenovirus has been studied in biology and molecular biology for a good 60-70 years because it's easy to work with. You can make it in the lab, you can grow buckets of it and you can manipulate its DNA. It’s how we discovered some really important cellular proteins and processes.

I encountered adenovirus as a postdoc, when I knew I wanted to study viruses, but not which one. I heard about protein VII. Is it a histone or not? Nobody seemed to know. We need treatments for adenovirus because it’s really bad for immunocompromised people. There’s no real treatment. There is an adenovirus vaccine, but vaccination isn’t very effective for immunocompromised people.

Herpes simplex virus is a more complicated virus than adenoviruses. Unlike adenovirus, it has a membrane, and I wanted to see how an enveloped virus interacts with chromatin. HSV also has lytic (active) and latent stages. It can go latent in peripheral neurons and then hang out through a person’s lifetime, but doesn't really cause systemic [widespread] disease in most people. It’s primarily problematic for immunocompromised people.

For example, newborns can get infected with HSV — in particular, HSV-2 — at birth from mothers who don't even know that they're infected. It's not the most common thing, but 30% of babies who get infected go on to develop central nervous system infections, and then they have lifelong problems. There's still a lot that we don't know [about HSV infection].

We’ve also just started looking at vaccinia virus, which is a pox virus. It’s a DNA virus, but it replicates outside the nucleus. The nucleus is normally a nice ellipsoid shape, but when vaccinia infects a cell, the nucleus forms a kind of Pac-Man shape and actually has a little dimple. And that hole is where the vaccinia replication center is. I got really excited about that. How do you get the nuclear membrane to do this?

What are the big questions your team is working on right now?

In adenovirus, we’re continuing to study protein VII, the histone-like protein. How is protein VII modified, how does it localize, how did it evolve? Edward Arnold, a graduate student in the lab, is working to understand how and why certain molecular modifications are made to protein VII. We know that it’s hijacking a host chromatin modifier to make these, but we don’t yet know what that is or why.

Edward is also studying how protein VII evolved. Histones all the way down to yeast are highly conserved [similar]. Adenoviruses infect all vertebrate species, down to ducks and snakes, but protein VII from the adenoviruses that infect those species is very, very different. What does it mean for the virus? What does it mean for us?

Dr. Hannah Arbach, a postdoctoral fellow in my lab, works on vaccinia virus. They just started, but it looks like there are proteins in the virus replication center that are usually in the nucleus. Instead of replicating in the nucleus, the virus decides to take some nucleus out and form its own thing. Han is trying to figure out how and why.

Electron microscopy images of viral particles near the nuclear membrane in an infected cell.
Getting out of an infected cell is a key step in furthering a viral infection. Herpesvirus particles (indicated by arrows) need open "channels" in tightly packed host DNA (dark regions indicated by arrowheads) to get to the edge of the nucleus. Avgousti and Lewis discovered that an unusual type of DNA-packaging protein called macroH2A plays a key role in channel formation and viral particle escape. Electron microscopy image courtesy of the Avgousti Lab

What have you learned about how HSV takes advantage of our chromatin?

For this project, we started by screening for proteins that change during HSV infection. And one of the things that we hit upon is a histone variant called macroH2A.

MacroH2A is thought to repress gene expression [turn genes off]. We found that macroH2A goes up a lot during HSV infection, which was really weird: That's not a normal thing, that you have more of any particular histone. And in the literature, the only instances of upregulation of macroH2A are in cancers. Having too much macroH2A is just bad for the cell.

So what does this mean? How is this affecting the virus? Hannah Lewis, the first graduate student to join my lab, bravely took on this project. We realized we needed to get a global view, and we worked with a former postdoc from Steve Henikoff's lab who now has his own group at the University of Colorado, Srinivas Ramachandran. We found that macroH2A forms really large chromatin domains that increase in certain regions [of the cell] and decrease in others. When you have more macroH2A [on DNA], you have less transcription because it is repressive.

The increase in macroH2A is probably driven by the stress response of the cell shutting down anything it doesn't need [when it’s infected]. Hannah tried to measure what’s different about the virus when we get rid of macroH2A. Viral transcription, viral replication — totally fine. It was actually the viral titer [level of virus outside cells] that was different. Those viruses were not getting out of the cell.

The way that HSV gets out of the cell is that the capsids [protein virus shells] go to the inner nuclear membrane, bud into the inner nuclear membrane, and then bud off and go through it.

It turns out that the broad chromatin regions that macroH2A makes are really important at the nuclear membrane. Condensed chromatin supports the nuclear membrane. In a totally separate study, another group had knocked out macroH2A. When they looked at cells by electron microscopy [EM], they found that these dark regions of supportive chromatin were missing.

Another set of studies looked at herpes virus egress by EM and found that the [compacted] chromatin that is so important in the nuclear periphery — which is macroH2A dependent — has these little gaps in it that are called channels. And that’s how the capsids find the inner nuclear membrane.

We took our cells that didn't have macroH2A, and infected them and we looked at them by EM. And sure enough, all capsids are stuck in the nucleus. And in our control [with macroH2A], we see these beautiful little lines of viruses going out.

Why this was exciting to us, especially for me, is because this is now saying that chromatin is not just a transcriptional regulator, it is a structural barrier to the virus getting out. And the virus takes advantage of changes in chromatin to get out.

 

On April 1, 2022, Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance became Fred Hutchinson Cancer Center, a single, independent, nonprofit organization that is also a clinically integrated part of UW Medicine and UW Medicine’s cancer program. Read more about the restructure.

Sabrina Richards, a staff writer at Fred Hutchinson Cancer Center, has written about scientific research and the environment for The Scientist and OnEarth Magazine. She has a Ph.D. in immunology from the University of Washington, an M.A. in journalism and an advanced certificate from the Science, Health and Environmental Reporting Program at New York University. Reach her at srichar2@fredhutch.org.

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Last Modified, August 31, 2022