Restricted access post 3 of 3

I left the last blog touching on the fact that human schalfen 11 may potentially be able to act on influenza virus in addition to HIV. One protein that is already established as an influenza restriction factor is IFITM3, the topic of this blog post. The reason research in the field of IFITM3 is of much interest is that our current stock of drugs to tackle the virus are struggling. We currently have four licensed drugs to tackle influenza, however only two of these remain truly effective due to the emergence of resistant strains. Both Tamiflu and Relenza remain effective, but there are a growing number of cases of Tamiflu resistant influenza. If Tamiflu resistance continues to spread we will be left with only Relenza as an effective drug. Having a single drug is never a great situation as it makes it very likely that resistance will emerge, which would leave us with nothing! We therefore need novel approaches to tackle influenza; enter IFITM3…

IFITM3 was first defined in 2009. The protein was identified in a large-scale screen of proteins that are ‘turned on’ when flu infects cells. This switching on is controlled by a set of immune proteins known as interferons (IFN) that are produced by cells when they are infected (IFITM stands for InterFeron Induced TransMembrane protein). The IFN response turns on around 2000 protective proteins that produce an ‘antiviral state’ to help protect cells from the invading virus. The team wanted to find which of these 2000 or so proteins are most important for tackling influenza infection. In order to do this they systematically switched off individual proteins to see which ones provided the most protection (defined by exacerbated infection in the absence of the protein). By this approach they found 120 proteins that play an inhibitory role on influenza infection. Through further probing they found the best “hit” was the IFITM3 protein. IFITM3 is closely related to two other proteins, IFITM1 and IFITM2 (as the names would suggest), and both of these proteins were also found to inhibit influenza infection, albeit to a lesser extent.

The IFITM proteins play a major role in protecting cells from influenza based on the fact that their removal from cells allows a higher level of infection, as seen in the study published in 2009, and many other since. Interestingly it isn’t only influenza that these proteins protect us against. The team that originally identified the IFITM proteins found that they could also protect cells from West Nile and Dengue viruses (WNV and DENV). These two additional viruses are closely related to each other, but not very closely related to influenza, making the finding somewhat mysterious.  Since the original discovery, IFITM proteins have been found to act on yet more viruses including Marburg, SARS, the highly feared Ebola and HIV (though there is some debate about the link to HIV).

As with most things in biology, viruses are grouped together based on certain characteristics and their evolutionary origins, just like animals. As I have mentioned WNV and DENV are very closely related (let’s say similarly to chimps and humans) and are in the same viral evolutionary family, the Flaviviridae. The SARS virus is similar to the flaviviruses but is within a different family, known as the Coronaviridae (more distantly related, such as humans/chimps compared to orang-utans).  Influenza falls into a different viral family (Orthomyxoviridae) and is more distantly related to the flaviruses and coronaviruses (let’s say like a domestic cat compared to the apes). However influenza is reasonably closely related to the Filoviridae family that contains Ebola and Marburg viruses (like a house cat to a lion). HIV is not particularly related to any of the others mentioned here and falls into the family of Retroviridae (like a kangaroo to all the other mentioned animals). I direct your attention to the image to see how these families all interconnect. The viruses that the IFITM proteins target are all very diverse, which begs the question of how these proteins are able to target such a wide array of invaders. (I’d just like to point out that the animal examples I have used are just for demonstration).

Relationship of different viral families

 Even though the IFITM sensitive viruses are very diverse, they all, with the exception on HIV (hence the dispute), enter cells in a very similar manner. Initially the virus binds to receptors on the surface of a cell, somewhat akin to grabbing a door handle. Once bound the virus is able to enter into the cell (open the door) through a process known as endocytosis.  At this point the virus is essentially encased within a small bubble inside the cell that is known as a vesicle (think of a bubble within a glass of drink, sorry to mix metaphors). This vesicle joins up to a larger structure known as an endosome, which over time becomes acidic. This acidification eventually causes a change to the virus that allows it to fuse with the bubble and escape to the rest of the cell where it will then move on to complete its life cycle. Don’t be distracted by the names (or the metaphors), just have a look at the picture if my description has been a bit hard to follow. The main point to take from this paragraph is that all of the viruses that the IFITM proteins inhibit, except HIV, enter cells through this endocytosis and acidification process.

Entry of influenza through the endocytic pathway

Since all the viruses that IFITM has been found to have an inhibitory affect on enter cells in the same way it seems fair to assume that the IFITMs must be targeting this pathway. Evidence is stacking up that this is indeed the case as numerous studies have found that IFITM3 (less work has been done on the other two) is localised to vesicles and the endosome. However, it is still not clear exactly how the IFITM proteins actually interfere with the processes involved with the viral life cycle. The current hypothesis is that the protein may interfere with acidification, which would block exit of the virus from the endosome. This eventually leads to destruction of the virus since the acidification continues to a point that kills the virus. This idea is supported by the fact that less virus is seen inside the cell cytoplasm when IFITM3 is present (the cytoplasm is simply the contents of the cell, using the analogy of the vesicle being like a bubble in a drink from before; the cytoplasm is the liquid).

A comparison of the different entry mechanisms used by Influenza and HIV

We need to fully resolve how the IFITM proteins are functioning. Once that has been achieved it will be possible to look towards finding drugs that act in a similar fashion. If we are able achieve this, we may well be able to develop drugs that are highly active against a very broad set of viruses. In addition, these potential drugs would be targeting a human process meaning that resistance is less likely to evolve since humans mutate so very much slower than viruses. That’s a long way off yet but shows why we need basic research into these proteins.

As an extra little add-on, IFITM3 has been linked to severe flu in patients as well as simple studies in a lab. A study was conducted to look at patients hospitalised by pandemic H1N1 (Swine Flu) and season flu and found that these patients were enriched for a certain mutation to the IFITM3 gene (the mutation was more common in people who were hospitalised than the general public). This hints towards the fact that IFITM3 truly does impact on influenza and helps most people to control it (flu is rarely fatal). It also hints towards the fact that this mutation could potentially be used to find those people who are at the highest risk of influenza infection, which would help with deciding who receives the limited stocks of influenza vaccine produced each year.

IFITM3 is a very interesting protein that has the potential to make a large impact in our efforts to tackle influenza (and potentially other viruses). I will be keeping a close eye as the story develops and will, in all likelihood, write future blogs on the topic as the story evolves.

Restricted access (post 2 of 3)

Those who read my previous blog will have been introduced to viral restriction factors and will, hopefully, remember that my inspiration for writing on such a topic was the discovery of a new member of these proteins; human schlafen 11. Those who didn’t read the previous post may find it useful to go back so as to aid in the understanding of this post.  Besides the discovery of a new restriction factor, this paper caught my eye as a wonderful demonstration of how logical and step-by-step science can be. Hopefully I will be able to convey this logical progression through this blog post, as it really is a very nicely written paper.

As I mentioned in the previous post, the paper in question is from Michael David’s lab at University of California, San Diego and has now been published in theprint issue of the journal Nature, as of the 1st November.  The paper centres on the schlafen genes (SLFN), of which there are six in humans. These proteins are of particular interest since they have been consistently shown to be highly expressed in cells and organisms that are infected with viruses or bacteria, yet they had no known function. Along with the data from in vivo studies (in living organisms such as mice), the team also looked at cell lines (collections of cells grown in a lab) and found that there was differential expression between two very closely related cell lines, HEK293 and HEK293T cells. They found that HEK293 cells (hereafter referred to simply as 293 cells) express high levels of SLFN5 and SLFN11, while the HEK293T cells (293T cells) did not. Finding this different level of expression gives the team two cell lines that are easy to conduct experiments in (unlike animals) and allows for easy comparison of the situation with and without the SLFN proteins.

An example of their data. Virus titre is the level of released virus.
293 cells show low levels of release. The removal of SLFN genes from
these cells (by shRNA) causes increased release of virus. The 293T cells
show a high level of virus release.

The first experiment the team conducted was to look at the effect of removal of the SLFN genes from 293 cells (the cells that express) and compare this with the 293T cells and normal 293 cells. Any new similarities seen between the 293T cells and the 293 cells that have had the SLFN genes removed may be due to the lack of SLFN genes. If these similarities are different to normal 293 cells then it is even more likely to be due to the lack of SLFN genes (sorry if that is hard to follow with the similar nomenclature). The team infected the cells with multiple viruses including a HIV virus that causes cells to glow when it integrates into the genome (I refer you back to the previous post for details of the HIV life cycle if you are unfamiliar). They found that this HIV virus was able to integrate into all three of the different cell types. However, the cells that were lacking for SLFN11 released a much higher level of new virus that those that had the protein. This indicates that SLFN11 is applying some sort of restrictive affect on the HIV life cycle between integration and release of new virus from the cell. (The removal of SLFN5 had no affect so will not be mentioned again).

To only show that removal of SLFN11 allows more virus to be released does not give a full picture, so the team set out to further confirm the results that SLFN11 is applying a block to the HIV life cycle. To do this they went the other way, instead of removing the SLFN11 protein from cells that usually have it, they added it to cells that do not usually have it (the 293T cells). Addition of SLFN11 to 293T cells caused a substantial reduction in the level of virus released from the cells and this reduction was of a similar magnitude to that seen in the 293 cells that were naturally expressing the protein. This gives two lines of evidence that SLFN11 is indeed causing a block to the HIV life cycle after integration.

There are multiple steps between HIV DNA becoming integrated to the host and the release of viral particles. In the interest of developing a full understanding of the role SLFN11 is playing the team began to zoom in on exactly where the protein was having its restrictive affect. They took the logical approach of looking at the next step after integration. Once HIV DNA is integrated to the host genome it is used to make proteins via an intermediate of RNA. This is how all proteins are made; DNA acts as a template to make RNA that is then used as a code to make protein. The team looked to see if there was any difference in the level of HIV RNA produced in the cells that expressed SLFN11 compared to those that don’t. Unlike the results seen for release of new virus, the presence of SLFN11 had no affect on the levels of HIV RNA seen inside the cell. The window in which SLFN11 causes a block is narrowing, we now know the block occurs between production of RNA and release from the cell.

Having ruled out the first step post-integration the team moved on to look at the final step of the HIV life cycle; release from the cell. As I mentioned in the previous post, the protein tetherin acts at this final stage and causes accumulation of virus particles on the cell. The team looked for similar affects in the SLFN11 expressing cells and saw none. We now have evidence that the block is occurring between production of RNA and before the virus starts to leave the cell. This pretty much leaves two stages, production of proteins and assembly of these proteins into new virus particles.

Knowing that SLFN11 was either affecting protein expression or assembly of the virus the team looked for the presence of viral proteins inside the cells. They found that there was substantially less viral protein inside the cells that expressed SLFN11 even though there was the same amount of RNA from which the protein is made. The really interesting thing about this is that human proteins being expressed in the cells were completely unaffected. This means SLFN11 is causing a block to viral protein expression but not host protein expression; the protein is therefore highly specific to the invading pathogen. The team further confirmed this finding by adding artificial DNA to a cell that coded for a viral protein or a non-viral protein and saw that only the viral protein was blocked for expression. The evidence with both actual virus and with artificial DNA strongly supports the idea that SLFN11 is blocking viral proteins from being produced, and is doing so in a specific manner.

The question then becomes why. Why is it that SLFN11 only affects viral protein production? What is different between the RNA of the virus that makes protein compared to the human RNA that makes protein? For me to answer this question I need to tell you a small bit about DNA.  A molecule of DNA is made up of chemicals known as nucleotides of which there are four, known as A, T, C and G. In the DNA double helix, A always binds to T while C always binds to G. It has been observed that viruses and humans have different biases in the nucleotide composition of their genomes. Humans have a bias towards GC nucleotides (around 60%) in our DNA, while certain viruses have a bias towards AT nucleotides (I will however refer to the viruses as low GC, though this is obviously the same as high AT). 

An illustration of DNA. I have mentioned A, T, C and G which is the short hand
for the chemicals listed in this image.

Knowing of the difference in nucleotide bias between humans and viruses, the team asked whether SLFN11 was taking advantage of this. To address this question they produced two artificial DNA constructs for a HIV protein known as gag. One of these constructs used the normal sequence for gag (low GC content) while the other construct changed all the nucleotides that could be changed, without affecting the protein, to C or G, so to shift the bias towards that of a human gene (a gag gene that is high GC). They found that expression of the normal gag construct was inhibited, as expected, while expression of the high GC gag gene was not inhibited by SLFN11 at all. This gives good evidence that SLFN11 is indeed taking advantage of the differences between the nucleotides used by HIV compared to those used in humans.

A further validation of the findings was once again pursued. To achieve this the team took a protein known as enhanced green fluorescence protein (EGFP) that can be expressed in human cells and, as the name implies, fluoresces green. When the team changed the EGFP DNA to have low GC (so to make it like a HIV gene) it was seen that SLFN11 inhibited the levels of fluorescence in the cells, so is therefore inhibiting EGFP protein production. This evidence further supports the idea that the SLFN11 protein is specific to viral proteins as a function of their nucleotide bias, not some other function of their genome.

That concludes the story… sort of. It still isn’t clear exactly how SLFN11 blocks expression of proteins, but we know that it does, and we know why it is highly specific to viral proteins. Hopefully this post hasn’t been too hard to follow for any non-scientists reading, I’ve tried my best to explain without making the post overly long. I appreciate that I may have skipped over some parts particularly surrounding expression of proteins, so if anything is unclear please feel free to leave a comment and ask a question. I also hope I have managed to convey what I perceive as the beautifully logical progression of this paper. The team found that their protein did not stop HIV integration but did stop release of new viruses. They then looked to zoom in on exactly where this block was occurring by showing that RNA production and release of virus were not altered. This led them to look at the production of proteins where they found a substantial block in the presence of SLFN11. The question then became why was SLFN11 specifically blocking viral proteins but not human proteins. A question answered by looking at the different bias of human and viral DNA for G and C nucleotides. Hopefully it also shows how science relies on negative and positive confirmations of findings, for instance, when no SLFN11 then observe more virus release (negative), while the addition of SLFN11 to these cells causes a block (positive), giving very nice proof to the role of SLFN11.

Not only is the discovery of SLFN11 very interesting in regards to HIV but since it targets all genetic material that has a bias towards low GC content (as shown with the EGFP experiment) this implies it would be able to target other viruses. One such virus with a similar bias as HIV is influenza. If we can make drugs that act in a similar way we may well be able to make broadly acting anti-viral drugs that are highly specific to virally infected cells, helping to reduce their side affects and improve their efficacy.

The fact that SLFN11 may have the potential to act on influenza leads me nicely into the topic of my next post, the protein IFITM3. Make sure you come back for that if you’re interested.

Restricted access (post 1 of 2)

 A lot of my blog posts recently have been on viruses since this is where my main scientific interests lie (and much of my knowledge). However, there’s so much more out there in science and not everyone is as interested in virology as I am, so I like to mix it up where possible. I had originally intended this post to have nothing to do with viruses, but then an article caught my eye. I’ve now postponed leaving the virological topics, for a little while, to talk about a new discovery because I think it’s very cool.

Illustration of the HIV life cycle. This is a nice simple image to use
with my explanation in the text, but I do want to point out that the
virus does not infect the same cell it has come from as this would imply

The above-mentioned article was published on the 23^rd September on Nature online and is still awaiting publication in the printed copy of the journal. The work in the paper is by Michael David’s lab at University of California, San Diego and centres around the discovery of a novel HIV restriction factor. I’m sure everyone reading will know a bit about HIV (I’ll get to restriction factors shortly) however, I’d just like to make sure everyone is one the same page. HIV is a retrovirus; this means it has a genome made of RNA, a molecule that is very similar to the DNA that makes up our genome, but has a slightly different sugar. The virus enters into cells and converts its RNA genome into DNA through a process termed ‘reverse transcription’. This viral DNA is then inserted into the DNA of the host cell, like sliding an extra card into a deck of cards. The infected cell with inserted HIV genetic material is unaware of the deception and treats the viral DNA as any human DNA and produces the proteins it codes for. These proteins then form new viruses and allow the infection to spread within and between individuals. In the most basic possible sense the HIV life cycle therefore has five main steps: entry, production of DNA, insertion of this to the host genome, production of proteins, and exit from the cell to spread the infection.

While I’m sure most people know of HIV, I imagine less will have heard of restriction factors. Restriction factors are a collection of aptly named proteins that function to restrict the life cycle of viruses. The majority of known restriction factors target HIV, though proteins have been found that target other viruses. For the time being I will focus on HIV, but will also touch on some other viruses later on. The first HIV restriction factor discovered has the highly catchy name of APOBEC3G. Shortly afterwards the protein tetherin was discovered, followed by TRIM5a and SAMHD1. Each of these proteins has the ability to block the HIV infection at different stages in its life cycle.

The APOBEC3G protein acts early in HIV infection, though there is still debate as to exactly how. The protein has the ability to directly mutate the HIV genome when it is initially converted from RNA into DNA. The level of mutation introduced is so extensive that it is termed ‘hypermutation’. This hypermutation means that the HIV DNA would either be destroyed or, once integrated to the host cell, would be defective in producing the proteins needed for spread of infection. This is how APOBEC3G was initially thought to function. However, it now appears that the protein may simply inhibit reverse transcriptase (the HIV protein that switches RNA into DNA), and thus block infection of the cell without directly causing mutation. Either way, APOBEC3G has the ability to stop infection by blocking at the step of reverse transcription.

While APOBEC3G targets a process early on in the HIV life cycle, tetherin targets right at the end. Tetherin does as the name implies and functions to tether viruses to the cell. When new viruses are produced they need to leave the cell in order to spread infection. For some viruses they simply cause the cell to burst, thus allowing exit, however HIV uses a much less drastic approach through its use of the cell’s natural mechanisms of export. Tetherin sits in the cell membrane and grabs on to any HIV viruses that try to leave, thus preventing spread of infection. Think of this as someone grabbing your arm as you walk out the door.

An image of tetherin in action. Taken directly from Neal et al. Nature 451 (2008) - the paper that had the original discovery of the protein. The main image to look at is the box labelled G, the small black dots are HIV particles, and the big grey bulge is the cell. You can see that tetherin is holding HIV particles to the cell and blocking their escape.

Next we have TRIM5a, which perhaps I shouldn’t technically include when talking about HIV restriction factors. TRIM5a functions by binding to a virus when it first enters the cell and begins uncoating (see the above image of the life cycle). It is unclear how, but this process disrupts the initial stages of the life cycle meaning the cell is never properly infected. The reason that TRIM5a shouldn’t be included is that it does not bind to HIV, in humans at any rate. The interesting thing about TRIM5a is that in Old World monkeys it is able to block HIV infection and the addition of a single mutation to human TRIM5a leads to the same effect. If that mutation were to naturally occur to TRIM5a then it may well be able to block HIV infection, but for the time being, in terms of HIV, it is completely useless (it does protect us from other retroviruses however). 

The final restriction factor to discuss, as background, is the most recently discovered, SAMHD1. This protein inhibits HIV infection of certain cells by depleting the pool of available molecules to make DNA; it essentially starves HIV meaning it is unable to cause infection. SAMHD1 is a pretty good restriction factor unlike the others (which I’ll get to in a minute) as HIV rarely infects the cells that express it, unfortunately not many do.

Now with all of these defences you may be wondering why HIV infection happens at all. That brings us a fact that I just alluded to in that these factors don’t really work. HIV is able to cause infection since it is has the ability to subvert our defences. There is a constant battle between our cells and HIV, we evolve a defence then HIV evolves to block the effect of that defence. Since HIV evolves much faster than our cells the virus constantly has the upper hand. The HIV proteins Vif and Vpu have evolved to cause degradation of APOBEC3G and tetherin, respectively, meaning they simply have no effect on the virus. TRIM5a as I have mentioned has no effect on HIV and this is simply through mutation of the virus at the point the protein would bind to, thus blocking its ability to have any effect. We are yet to find a countermeasure to SAMHD1 but there may not be any need since it is expressed in so few cells. While we have evolved these defences to infection that work nicely when studied in a lab, in the real world HIV has one up on us through its countermeasures.

The lack of effect of these factors is obvious based on how many people have HIV infections, however that does not make them pointless to study and discover. The hope is that if we further our understanding of natural restriction to HIV we may be able to produce drugs that work in a similar way. For instance, if we could produce a molecule that functions in the same way as tetherin, but is insensitive to Vpu then this may have therapeutic use in tackling HIV. Therefore extending our knowledge of these factors, and finding more, is essential in our fight against HIV, and other viral infections.

So that sets the stage… I don’t like these blog posts to be overly long so I’m going to leave this post here and come back with a second part talking about the newly discovered restriction factor human schalfen 11. In keeping with the restriction factor theme I then plan to write a blog on another very interesting protein IFITM3. So make sure you come back for those…