The Hidden Threat: HIV Latency and How to Find it

Human Immunodeficiency Virus also known as HIV has been at the center of public view and of virus based research since it was discovered. This focus has most been driven by the fact that as HIV infection continues in a majority of cases it leads to acquired immune deficiency syndrome (AIDS). AIDS is a terrifying occurrence where your immune system is basically gone and you are extremely susceptible to opportunistic infections.  These infections then lead to a drastic reduction of your life span and in many cases an unpleasant death. One of the major issues with HIV is that the virus is able to become latent in cells.  Latency is when a virus inserts its genome into the genome of the host cell in areas that are not being actively expressed. By doing this the virus is effectively able to hide from the hosts immune system and at a later time become active and produce viral particles. A very recent paper in Nature, specifically the structural and molecular biology section, titled Position Effects Influence HIV Latency Reversal by Heng-Chang Chen et al (1), attempts to address the idea of HIV latency through the creation of a new method to study this effect.

HIV in modern day is treated by antiretroviral therapy (ART), which suppresses HIV’s ability to replicated. The issue is, however, that this viruses that have already gain latency in cells are not target by this type of therapy or even the hosts own immune system. Thus, in recent years’ new research has develop around the idea of treating a patient with drugs that reactivate latent viruses to make them susceptible to clearance by the immune system. (2) By combining these two methods researchers believe that the treatment of HIV can become much more effective.  Research in  past has not provided very much information on how latency is establish or how viruses actually come out of latency other than the hand waving idea of stress.  Previous data has had shown that the virus preferentially integrates into active genes and gene rich chromosomes. (3,4) This leads to the idea that something about the insertion site matters and thus the reactivation agent used would also need to be specific and not only based on the idea that a histone deacetylase inhibitor will do the trick.
The new method that the authors create is called Barcoded HIV ensembles (B-HIVE) and allows for the mapping of individual HIV proviruses in the chromosome while also tracking each of the virus’s transcriptional activity. In a very broad in general way (see paper for more information), B-HIVE works by assigning a unique 20 nucleotide barcode to individual HIV genomes, then these barcodes can provide the location in the host genome. These barcodes are also then paired with a green fluorescent protein gene so that cells that have the inserted barcode can be separated through fluorescent sorting. The viral expression levels are determined by looking at the ratio of barcode abundance of the RT-PCR of the RNA pool and the PCR of the DNA pool. All of this can be seen below in figure 1:

From this method, the authors were able to find two really interesting results. First,  they found that the expression of HIV is strongest close to endogenous enhancers. (1) This is a really important finding because this demonstrates a possible mechanism for how the infection works. HIV might have, if it is going to be active and not latent, a signal that helps it search and ingrate near the host’s enhancers. By having this specificity, the virus is able to increase its productivity. This finding leads to an idea of future directs as one could possibly investigate the molecular interaction that HIV is experiencing around the enchanter regions. The second major finding is that the authors found that the latency-reversing agents only effect or reactivate at distinct locations. (1) This means that the one general drug approach that is currently being utilized is not as effective as it could be. Thus, the authors propose that patients should be treated with a drug cocktail to revert as many latent viruses as possible. This also provides an area of future direction for identify what these drugs are that will cause reactivation. One note to make on this when the treat the cell lines with the two reactivating drugs then removed them the expression of the viruses decreased. This hints that there might be a mechanism that is actively silencing the virus to maintain its latency.  If latency was more of a switch, then once reactivated it would continue to have expression even after the drugs had been removed. This is yet another area where research can begin. This effect can be seen below in Figure 5C:

 

Overall, this method helped immensely to understand HIV latency.

So why do we care about this? Like any good research, you need to start broad then begin to work your way down into the details and that is exactly what the authors did here. Little to nothing was known about the positional effects on HIV latency and really not too much was understood about the latency itself so the authors set out to fix this. They started broad and by doing this they create a lot of areas where new research can be completed. It is also important to note that from these new areas of research new targets for treatment can be found. These will then prove to help the lives of many individuals. Although the authors of this paper might not get the millions of dollars or fame from find a drug that cures HIV, it is important that the scientific community pays due respect to the process and not only the results. They potentially made the process possible and thus deserve to be appreciated for it.

Source Paper:
1.Chen, Heng-Chang et al. "Position Effects Influence HIV Latency Reversal". Nature Structural & Molecular Biology (2016): n. pag. Web.

Additional Sources:
2. Deeks, S.G. HIV: shock and kill. Nature 487, 439–440 (2012).
3. Schröder, A.R.W. et al. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110, 521–529 (2002).
4.Lewinski, M.K. et al. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. J. Virol. 79, 6610–6619 (2005).

Images:
All images taken from source paper.