The development of CRISPR-Cas9 gene-editing technology has introduced a new possibility in the fight against human immunodeficiency virus (HIV). This tool offers the potential to directly interact with the virus’s genetic material, a capability that current treatments lack. Researchers are now exploring CRISPR-Cas9 as a way to achieve a functional cure for HIV, moving beyond management of the virus to its potential eradication from the body.
The Mechanism of CRISPR-Cas9 Against HIV
The primary challenge in curing HIV is its ability to insert its own genetic blueprint into the DNA of a person’s immune cells, particularly CD4+ T-cells. This integrated viral DNA, known as a provirus, can remain dormant for years, creating latent reservoirs. These reservoirs are invisible to the immune system and unaffected by current antiretroviral drugs, which only work on replicating viruses. This latency means that if a person stops their medication, the provirus can reactivate and begin producing new virus particles, leading to a rebound of the infection.
The CRISPR-Cas9 system provides a direct method to address this proviral DNA. It functions as a precise, programmable tool to alter an organism’s genome. The system consists of two main components: a guide RNA (gRNA) and a DNA-cutting enzyme called Cas9. The gRNA is engineered to match a specific sequence of the integrated HIV DNA, acting like a molecular GPS to find the exact location of the HIV provirus.
Once the gRNA locates and binds to the target viral DNA, the Cas9 enzyme acts like a pair of molecular scissors. It makes a precise double-strand break in the DNA at that specific site. This action physically cuts the viral genetic code embedded within the human chromosome. The process is designed to be highly specific, targeting only the HIV sequences and leaving the surrounding human DNA unharmed.
Different Therapeutic Strategies
Excision
One direct strategy is excision, which aims to completely remove the integrated HIV provirus from the host cell’s genome. This “cut and remove” approach uses two guide RNAs to target conserved regions at both ends of the viral DNA. The Cas9 enzyme then makes two cuts, snipping out the entire 9,700-base-pair sequence of HIV DNA. The cell’s natural DNA repair mechanisms then join the severed ends of the human chromosome, leaving the cell free of the provirus.
Viral Inactivation
Another approach focuses on viral inactivation rather than complete removal. This method uses CRISPR-Cas9 to introduce small mutations into essential HIV genes, such as gag or pol. These genes are responsible for creating structural proteins and enzymes that the virus needs to assemble and replicate. By making a single cut in one of these genes, the cell’s repair pathway can introduce errors that render the gene non-functional, permanently disabling it.
Host Cell Modification
A third strategy modifies the host’s cells to make them resistant to HIV infection. This approach targets a human gene called CCR5, which produces a co-receptor on the surface of T-cells that most strains of HIV use as a doorway to enter the cell. By using CRISPR-Cas9 to disable the CCR5 gene in a patient’s immune cells, those cells become resistant to infection. This concept is demonstrated by the “Berlin patient,” who was functionally cured of HIV after receiving a stem cell transplant from a donor with a natural mutation in the CCR5 gene.
From Laboratory to Clinical Trials
CRISPR-based HIV therapies underwent extensive preclinical research before human trials. Scientists first demonstrated proof-of-concept in laboratory-grown human cells, showing that the system could successfully find and cut out HIV DNA. These results were then replicated in animal models, including humanized mice and non-human primates, where the therapy was shown to reduce viral load and, in some cases, eliminate the virus from tissues.
These studies paved the way for human clinical trials. The first of these is the Phase 1/2 trial for a therapy named EBT-101. This therapy is designed to excise the HIV provirus using an adeno-associated virus (AAV) to deliver the CRISPR-Cas9 machinery into the patient’s cells. The primary goal of this initial trial, which began dosing participants in 2022, was to evaluate the safety and tolerability of the treatment.
Data from the EBT-101 trial presented in 2024 showed the therapy was well-tolerated and met its safety endpoints, with no serious adverse events reported. However, the therapy did not achieve a functional cure at the first dose level tested. Among participants who paused their standard antiretroviral therapy, the virus eventually rebounded, though one individual showed a significant delay. These results show that while the approach appears safe, optimization is needed to make it effective.
Safety and Delivery Hurdles
Despite its promise, technical and biological challenges must be overcome before CRISPR can become a widespread treatment for HIV. The primary safety concern is the potential for “off-target effects.” This occurs when the CRISPR system mistakenly cuts the human genome at a site that is similar to the intended HIV DNA sequence. Such unintended cuts could disrupt important human genes, leading to harmful health consequences.
Delivering the CRISPR-Cas9 system is a major logistical challenge. For a cure to be effective, the therapeutic machinery must reach every latently infected cell in the body. These viral reservoirs are hidden in various tissues, including the lymph nodes, gut, and even the brain, making comprehensive delivery difficult. Current delivery methods, relying on viral vectors like AAV, may not be efficient enough to reach all these sanctuary sites.
This delivery challenge leads directly to the issue of mosaicism. This term describes a situation where only a portion of the targeted cells are successfully edited, leaving a mixture of edited and unedited cells. Because even a small number of remaining, unedited cells can reactivate and restart the infection, achieving nearly 100% editing efficiency is a major barrier. Incomplete editing would allow the virus to rebound once standard treatment is stopped, a likely reason for the outcomes seen in the EBT-101 trial.
Comparison with Current Antiretroviral Therapy
CRISPR-based treatments are explored alongside the current standard of care: antiretroviral therapy (ART). ART involves a daily regimen of drugs that suppress HIV replication. This therapy is successful at reducing the amount of virus in the blood to undetectable levels, which prevents the progression of the disease to AIDS and stops transmission to others.
However, ART is a lifelong treatment, not a cure. Because the drugs do not affect the latent HIV provirus explained earlier, stopping the medication leads to viral rebound. This necessitates continuous adherence, which can come with long-term side effects and financial costs.
CRISPR-based therapies differ in their objective. Instead of managing the infection, the goal is to provide a “functional cure” by directly targeting and eliminating the latent provirus. A successful CRISPR treatment would permanently remove or disable the viral DNA, potentially freeing a person from the need for daily medication. This one-time approach represents a shift from lifelong management to permanent resolution.