CRISPR gene therapy EBT-101 does not prevent HIV viral rebound

A CRISPR-based gene-editing therapy called EBT-101 was safe and well tolerated but did not prevent viral rebound in three participants who stopped antiretroviral treatment in an early study, according to a presentation last week at the American Society of Gene & Cell Therapy annual meeting.

As aidsmap previously reported, researchers presented findings at a conference last October showing that EBT-101 was well distributed in the body and did not cause serious side effects in the first three treated study participants. Although the presentation did not include data about whether the treatment actually worked to control HIV, that didn’t stop the Daily Mail from proclaiming that a cure for HIV “could be months away” – one of the many exaggerated claims over the years about the state of HIV cure research.

But those data are out now, and the news is generally unfavourable. EBT-101 did not maintain HIV viral suppression when used alone at the initial dose tested, though it may have delayed viral rebound in one participant. Also, its good safety profile suggests that similar CRISPR approaches may be feasible for other latent viral infections such as herpes simplex and hepatitis B.

“We know that many people were hopeful that a first trial could provide evidence of a possible cure for HIV because the field has been waiting over 20 years for a cure,” Excision BioTherapeutics senior vice president Dr William Kennedy said in a news release. “However, it was essential that this clinical trial establish safety for EBT-101 as a gene therapy product as well as safety related to the use of CRISPR for the field.”

CRISPR for HIV

Antiretroviral therapy can keep HIV replication suppressed indefinitely, but the virus inserts its genetic blueprints into the DNA of human cells and establishes a long-lasting reservoir that the drugs can’t reach. This integrated HIV DNA lies dormant in resting T cells during treatment, but it can start producing new virus when antiretrovirals are stopped, making a cure nearly impossible. The only way to determine whether an experimental intervention leads to long-term remission is to discontinue antiretroviral therapy with careful monitoring in an analytic treatment interruption.

Professor Kamel Khalili of Temple University in Philadelphia and colleagues have been studying gene therapy with the aim of curing HIV for more than a decade. Their work employs CRISPR/Cas9 – sometimes referred to as ‘molecular scissors’ – a technology that combines guide RNAs that home in on specific segments of DNA and a nuclease enzyme that cuts the genetic material at the desired site.

In 2014 and 2016, the researchers reported that a CRISPR/Cas9 tool could cut out HIV genes from CD4 cells in laboratory studies. A study published in 2019 showed that this approach could remove integrated HIV genes and clear latent viral reservoirs in mice. And at the 2019 Conference on Retroviruses and Opportunistic Infections, the Temple University team reported that CRISPR/Cas9 therapy successfully removed segments of an HIV-like virus from viral reservoirs in monkeys.

This research led to the development of EBT-101, a CRISPR-based therapy delivered by an adeno-associated virus vector that uses two guide RNAs to target three sites on the integrated HIV genome. Making cuts at these locations prevents the production of intact new virus. Last August, researchers reported that a single dose of a simian version of the therapy safely and effectively removed integrated SIV in monkeys on antiretroviral therapy. But this study did not include a treatment interruption, so it could not show whether the animals were functionally cured.

The first human clinical trial of EBT-101 (NCT05144386) started in 2022, testing the therapy in people on antiretroviral treatment with a stable undetectable viral load. Excision announced that the first participant in the phase I/II trial received EBT-101 that July, and the study protocol called for participants who maintained viral suppression at 12 weeks after receiving the gene therapy to undergo an analytic treatment interruption.

At last week’s conference, Dr Rachel Presti of Washington University St. Louis School of Medicine provided updated study results. Of the five participants who received a single infusion of the initial dose of EBT-101, three stopped antiretroviral therapy. All three experienced viral rebound and had to restart antiretrovirals. This likely occurred because the gene therapy did not reach all cells harbouring latent HIV, and even a very small number of cells containing residual HIV DNA is enough to re-establish viral replication.

One EBT-101 recipient was able to maintain viral suppression for 16 weeks after treatment discontinuation, considerably longer than it typically takes for the virus to rebound after stopping antiretrovirals. This suggests that EBT-101 or similar CRISPR therapies might one day play a role in a combination cure strategy.

“Initial data from the EBT-101-001 trial provides important clinical evidence that a gene editing treatment modality can be safely delivered for targeting the HIV DNA reservoirs in human cells,” Presti said. “This study provides researchers with invaluable insights for how CRISPR technology can be applied for addressing infectious disease and was an important first step towards additional programs designed to optimize this treatment modality for treating the millions of individuals who are impacted by HIV and other infectious disease.”

Excision is now testing a higher dose of EBT-101 in a second cohort and is exploring new CRISPR delivery methods that might be more efficient than the adeno-associated virus vector. One possibility is lipid nanoparticles like the ones used to deliver messenger RNA in COVID-19 vaccines.

“Viral rebound likely occurred because the gene therapy did not reach all cells harbouring latent HIV”

The company is also exploring CRISPR-based approaches for other latent infections. In other presentations at last week’s meeting, researchers reported promising preclinical results for experimental therapies for herpes simplex (EBT-104) and hepatitis B (EBT-107). Herpes simplex virus (HSV) persists in nerve cells, from which it can reactivate to cause cold sores, genital herpes and keratitis (eye inflammation). Hepatitis B virus (HBV) establishes chronic infection in the liver, where it can lead to cirrhosis and liver cancer. Unlike HIV and other retroviruses, however, HSV and HBV do not integrate their genetic blueprints into the chromosomes of host cells, so they may be easier to remove.

Many lessons have been learned from the small number of people who naturally control HIV, the somewhat larger group of post-treatment controllers and the handful of people who have been cured after stem cell transplants. But for now, a broadly applicable functional cure remains a long-term prospect.