LASER ART: Eliminating HIV from the genome

by James Fawcett

A team of researchers recently claimed to have developed a new treatment to remove all traces of the human immunodeficiency virus (HIV) from the mammalian genome through a combination of using an antiviral drug regime and genetic engineering. 

Published this summer in Nature Communications, the landmark paper describes how a combination of pre-treating HIV-1 infected mice with the specially formulated drug regime and then employing CRISPR-Cas9 gene editing, resulted in undetectable levels of viral DNA: effectively curing the HIV infection in some rodents.

How is HIV infection usually treated?

Since the introduction of the first antiviral drugs in the 1980s, steady advancements in treatments of HIV have helped millions living with the disease to enjoy longer and healthier lives. However, due to the way HIV evades the immune system by integrating its own genome into the DNA of the host it inhabits, no drug combination has allowed for the complete eradication of all traces of the virus from the body. 

The best available treatments for HIV are customizable drug cocktails, collectively known as antiretroviral therapies (ART) [2]. A daily treatment regime of ART can be personalized to fit the patient’s medical history, lifestyle and sensitivity to side-effects. ART has played an enormous role in transforming an HIV diagnosis from a death sentence into a chronic but manageable condition; the life expectancies of patients using ART is considered to be “near normal”, according to a 2017 study by the Antiretroviral Therapy Cohort Collaboration [3]. 

Long-acting, slow-effective release antiretroviral therapy, or LASER ART, involves a cocktail of highly lipophilic ART prodrugs packaged tightly into a nano-crystal, which is easily taken up by immune cells such as the common HIV human target, the CD4+ T-cell. The drugs are then slowly but consistently released over a long time period, so that detected levels of the drug in the subject’s blood plasma remain constant for weeks after initial treatment.

ART, however, is not enough to eliminate the infection of HIV completely: interrupting therapy leads to the re-establishment of the viral infection cycle in the host, as latently infected cells containing integrated HIV genes begin to quickly produce and release viral particles. With rapid advancements in genetic manipulation technologies, such as the CRISPR-Cas9 system, many labs now concentrate on developing an HIV “cure”, by attempting to inhibit or reverse HIV’s integration in the host’s genome to remove its ability to produce more infectious particles. However, the speeds at which targeted mutagens, such as CRISPR-Cas9, can remove integrated viral DNA sequences are much lower than the speed at which HIV propagates and integrates into the genomes of neighboring cells, meaning that this treatment alone is likely not enough to eliminate all HIV sequences hiding throughout the body.

A combination approach

In the study led by Dr. Khalili, the researchers made the decision to first pre-treat HIV-positive mice, which had been engineered to express human CD4+ T-cells, with LASER ART to suppress production of the virus before attempting to excise any integrated HIV sequences. 

The study found that in two of the seven HIV infected mice that had been given both treatments, all traces of HIV proteins, DNA and RNA were removed from the animal’s plasma, spleen, central nervous system and other areas of the body defined as “revisors” of infection, or where HIV is typically found laying dormant and protected from the immune system. Additionally, these two “cured” mice had higher counts of CD4+ T-cells by the end of the treatment than those that underwent LASER ART or CRISPR-Cas9 treatments alone, their lower T-cell count being characteristic of HIV infection. Plasma taken from the “cured” mice was, when transplanted into other mice, unable to induce detectable HIV infection, suggesting that the mice who underwent the treatment were unable to transmit the disease.

Although these results indicate some success in eradicating the virus on a genomic scale, the utility of this technique in treating human HIV infection remains unclear. For reasons the researchers say they have yet to understand, only two of the seven mice that experienced both LASER-ART and CRISPR treatments demonstrated a complete absence of the virus, while the other five had varying levels of detectable HIV genetic material in their genomes.  When coupled with the low excision efficiency of HIV DNA, estimated to be between 60-80% by the authors, this suggests that the treatment may have a success rate too low to be a reliable therapy, at least in its current formulation. 

The study’s authors, however, believe that the results are promising enough to invest into further, with the technology already licensed for further development and plans for trials in non-human primates already set in motion.

Does the promise of a cure warrant the risk?

Although no off-target effects from the treatment with CRISPR-Cas9 were detected in any of the mice in the study, the potential for hidden dangers when using gene modification technologies in humans is an important consideration. While these technologies should always be approached with caution, their use in this case may, arguably, be unnecessary; many in the scientific community, including officials from NIH’s National Institute of Allergy and Infectious Diseases [4], agree that undetectable viral loads in the blood of HIV patients undergoing ART treatments means that the disease cannot be transmitted, potentially making genetic interventions to remove HIV from the genome a needless risk.

These risks became especially apparent in the aftermath of a recent controversial study involving the use of CRISPR in human embryos by researchers in China [5], who chose to remove a gene implicated in HIV entry into the cell. Shortly after, another research group provided evidence linking the absence of this gene to a significant decrease in life expectancy [6], leading many onlookers to adopt a more conservative outlook when considering genetic editing in humans, especially as a permanent solution to health issues where the collateral effects of the intended modifications are not yet fully understood.

The study on the use of CRISPR in conjunction with LASER-ART, however, has had a positive reception in both the media and scientific community as a novel take on HIV therapy, which signifies that more innovative and permanent treatment options that build on this study’s findings could soon follow.

ORIGINAL ARTICLE: Dash, P. K. et al. Sequential LASER ART and CRISPR Treatments Eliminate HIV-1 in a Subset of Infected Humanized Mice. Nat Commun 10, 1–20 (2019). https://www.nature.com/articles/s41467-019-10366-y

Further reading:

1. HIV Eliminated from the Genomes of Living Animals. Temple Health Available at: https://www.templehealth.org/about/news/hiv-eliminated-from-the-genomes-of-living-animals. (Accessed: 7th August 2019)
2. Pickrell, J. Timeline: HIV and AIDS. New Scientist Available at: https://www.newscientist.com/article/dn9949-timeline-hiv-and-aids/. (Accessed: 7th August 2019)
3. Trickey, A. et al. Survival of HIV-positive patients starting antiretroviral therapy between 1996 and 2013: a collaborative analysis of cohort studies. The Lancet HIV 4, e349–e356 (2017).
4. The science is clear: with HIV, undetectable equals untransmittable. National Institutes of Health (NIH) (2019). Available at: https://www.nih.gov/news-events/news-releases/science-clear-hiv-undetectable-equals-untransmittable. (Accessed: 7th August 2019)
5. Cyranoski, D. & Ledford, H. Genome-edited baby claim provokes international outcry. Nature 563, 607–608 (2018).
6. Wei, X. & Nielsen, R. CCR5-∆32 is deleterious in the homozygous state in humans. Nat. Med. 25, 909–910 (2019).