Virus World

An experiment tests whether the gene-editing technology can stop the virus from replicating, which would ultimately wipe out the infection. 

IN JULY, AN HIV-positive man became the first volunteer in a clinical trial aimed at using Crispr gene editing to snip the AIDS-causing virus out of his cells. For an hour, he was hooked up to an IV bag that pumped the experimental treatment directly into his bloodstream. The one-time infusion is designed to carry the gene-editing tools to the man’s infected cells to clear the virus. Later this month, the volunteer will stop taking the antiretroviral drugs he’s been on to keep the virus at undetectable levels. Then, investigators will wait 12 weeks to see if the virus rebounds. If not, they’ll consider the experiment a success. “What we’re trying to do is return the cell to a near-normal state,” says Daniel Dornbusch, CEO of Excision BioTherapeutics, the San Francisco-based biotech company that’s running the trial. HIV attacks immune cells in the body called CD4 cells and hijacks their machinery to make copies of itself. But some HIV-infected cells can go dormant—sometimes for years—and not actively produce new virus copies. These so-called reservoirs are a major barrier to curing HIV. “HIV is a tough foe to fight because it’s able to insert itself into our own DNA, and it’s also able to become silent and reactivate at different points in a person’s life,” says Jonathan Li, a physician at Brigham and Women’s Hospital and HIV researcher at Harvard University who’s not involved with the Crispr trial. Figuring out how to target these reservoirs—and doing it without harming vital CD4 cells—has proven challenging, Li says. While antiretroviral drugs can halt viral replication and clear the virus from the blood, they can’t reach these reservoirs, so people have to take medication every day for the rest of their lives. But Excision BioTherapeutics is hoping that Crispr will remove HIV for good.

Crispr is being used in several other studies to treat a handful of conditions that arise from genetic mutations. In those cases, scientists are using Crispr to edit peoples’ own cells. But for the HIV trial, Excision researchers are turning the gene-editing tool against the virus. The Crispr infusion contains gene-editing molecules that target two regions in the HIV genome important for viral replication. The virus can only reproduce if it’s fully intact, so Crispr disrupts that process by cutting out chunks of the genome. In 2019, researchers at Temple University and the University of Nebraska found that using Crispr to delete those regions eliminated HIV from the genomes of rats and mice. A year later, the Temple group also showed that the approach safely removed viral DNA from macaques with SIV, the monkey version of HIV. That was an important step toward testing the treatment in people, says Kamel Khalili, a professor of microbiology at Temple University who led the work and is a cofounder of Excision Biotherapeutics. “You don’t want to eliminate the viral genome but at the same time cause any disruption in another part of the human genome and then create another set of problems for the patients,” he says. “We had to make sure that we identified a region within HIV that did not overlap with the human genome.”  Dornbusch thinks this strategy will spare patients from serious side effects and “off-target” edits—unintentional cuts elsewhere in the genome that could cause problems such as cancer. The regions targeted by the company’s Crispr therapy are also in a part of the genome that tends to stay the same even when HIV evolves. That’s important because the virus mutates rapidly, and the researchers don’t want a moving target. This isn’t the first time scientists have tried to use gene editing in the hope of curing people with HIV, but other efforts have focused on a protective mutation in a gene called CCR5. In the 1990s, scientists found that people with this naturally occurring mutation didn’t get HIV when exposed to it. The mutation—known as delta 32—thwarts the virus’s ability to get inside immune cells. In 2009, California-based Sangamo Therapeutics used an older editing technology called zinc finger nucleases to add that protective mutation into patients’ T cells—an important part of the immune system. Those trials have had limited success.

In 2017, Chinese scientists combined Crispr with a bone marrow transplant in an attempt to cure a patient with HIV and leukemia. In a typical transplant, donor stem cells are transferred to a recipient to replace their cancerous blood cells. These cells go on to form new, healthy blood cells. To also address the patient’s HIV, researchers edited the donor stem cells with Crispr to disable CCR5. But after the transplant, only a small percentage of the patient’s bone marrow cells ended up with the desired edit. Then in 2018, Chinese scientist He Jiankui used Crispr to edit the CCR5 mutation into the genomes of twin baby girls to make them resistant to HIV. Fraught with ethical violations, the experiment was widely condemned by scientists. He’s research was suspended by the Chinese government, and he served a three-year prison sentence. While the twins were born healthy, only some of their cells were successfully edited, meaning the girls might in fact not be immune to HIV. As of 2022, two people have now been cured of HIV after receiving bone marrow transplants from donors with the CCR5. Known as the Berlin patient and the London patient, both had cancer and received transplants to treat their disease. But these transplants aren’t a viable option for most people—they’re highly risky, and donors with the delta 32 mutation are scarce. But a third person was declared cured of HIV earlier this year after she received a new type of transplant involving umbilical cord blood.

The Excision trial will eventually enroll nine participants and test three dosage amounts to determine which is most effective. Investigators will measure each person’s viral load and CD4 count before receiving the therapy and after they stop taking antiretroviral drugs. The ultimate goal is to get viral loads down to an undetectable level—that is, less than 200 copies of HIV per milliliter of blood. At this level, HIV can’t be passed on through sex. The challenge for Excision will be getting Crispr to enough cells to bring HIV down to undetectable levels. The company is using an engineered virus to shuttle the gene-editing components to patients’ HIV-infected CD4 cells. But so far, there’s little human data on how well Crispr works when it’s delivered directly to the body. “It’s possible that you get the virus to such low levels that if a person’s immune system were intact, they might be able to keep the virus at bay such that they don’t have to take antiretroviral therapy anymore,” says Rowena Johnston, vice president and director of research for amfAR, the Foundation for AIDS Research.

And even though these drugs are very effective, Johnston says, many people would rather be completely free of the virus. A single Crispr infusion—if it works—would eliminate the need for daily pills. “People with HIV still live with a lot of stigma and internalized shame,” she says. “I think a cure is something that addresses that much better than lifelong therapy, regardless of how easy that therapy becomes.”

Researchers found that 48 of 50 children retained their replenished immune system function two to three years later and did not require additional treatments for ADA-SCID.  An investigational gene therapy can safely restore the immune systems of infants and children who have a rare, life-threatening inherited immunodeficiency disorder, according to research supported in part by the National Institutes of Health. The researchers found that 48 of 50 children who received the gene therapy retained their replenished immune system function two to three years later and did not require additional treatments for their condition, known as severe combined immunodeficiency due to adenosine deaminase deficiency, or ADA-SCID. The findings were published today in the New England Journal of Medicine. ADA-SCID, which is estimated to occur in approximately 1 in 200,000 to 1,000,000 newborns worldwide, is caused by mutations in the ADA gene that impair the activity of the adenosine deaminase enzyme needed for healthy immune system function. This impairment leaves children with the condition highly susceptible to severe infections. If untreated, the disease is fatal, usually within the first two years of life.  “These findings suggest that this experimental gene therapy could serve as a potential treatment option for infants and older children with ADA-SCID,” said Anthony S. Fauci, M.D., director of NIH’s National Institute of Allergy and Infectious Diseases (NIAID).

“Importantly, gene therapy is a one-time procedure that offers patients the hope of developing a completely functional immune system and the chance to live a full, healthy life.” People with ADA-SCID can be treated with enzyme replacement therapy, but this treatment does not fully reconstitute immune function and must be taken for life, usually once or twice weekly. Transplants of blood-forming stem cells, ideally from a genetically matched sibling donor, can provide a more lasting solution. However, most people lack such a donor. Additionally, stem cell transplants carry risks such as graft-versus-host disease and side effects from chemotherapy medications given to help the donor stem cells establish themselves in the patient’s bone marrow.   The new research evaluated an experimental lentiviral gene therapy designed to be safer and more effective than previously tested gene-therapy strategies for ADA-SCID. This gene therapy involves inserting a normal copy of the ADA gene into the patient’s own blood-forming stem cells. First, stem cells are collected from the patient’s bone marrow or peripheral blood. Next, a harmless virus is used as a “vector,” or carrier, to deliver the normal ADA gene to these cells in the laboratory. The genetically corrected stem cells then are infused back into the patient, who has received a low dose of the chemotherapy medication busulfan to help the cells establish themselves in the bone marrow and begin producing new immune cells. 

The experimental gene therapy, developed by researchers from the University of California, Los Angeles (UCLA) and Great Ormond Street Hospital (GOSH) in London, uses a modified lentivirus to deliver the ADA gene to cells. Previous gene-therapy approaches for ADA-SCID have relied on a different type of virus called a gamma retrovirus. Some people who have received gamma retroviral gene therapies have later developed leukemia, which scientists suspect is due to the vector causing activation of genes that control cell growth. The lentiviral vector is designed to avoid this outcome and to enhance the effectiveness of gene delivery into cells. The results come from three separate Phase 1/2 clinical trials, two conducted in the United States and one in the United Kingdom. The U.S. trials, led by principal investigator Donald Kohn, M.D., of UCLA, enrolled 30 participants with ADA-SCID ranging in age from 4 months to 4 years at UCLA Mattel Children’s Hospital and the NIH Clinical Center in Bethesda, Maryland. The U.K. study, conducted at GOSH and led by principal investigator Claire Booth, M.B.B.S., Ph.D., enrolled 20 participants ranging in age from 4 months to 16 years. Most participants acquired and retained robust immune function following gene therapy — 96.7% after two years in the U.S. studies and 95% after three years in the U.K. study — and were able to stop enzyme replacement therapy and other medications. Of the two participants for whom gene therapy did not restore lasting immune function, one restarted enzyme replacement therapy and later received a successful stem cell transplant from a donor, and the other restarted enzyme replacement therapy.  The lentiviral gene therapy appeared safe overall, although all participants experienced some side effects. Most of these were mild or moderate and attributable to the chemotherapy that the participants received. Researchers observed similar outcomes in all three trials, although there were some differences between the studies. Stem cells were collected from bone marrow in the U.S. trials and from peripheral blood in the U.K. trial. In one of the U.S. trials, 10 children were treated with genetically corrected stem cells that had been frozen and later thawed. The two other trials used fresh stem cell preparations. In the future, the freezing procedure — known as cryopreservation — may allow stem cells to be more easily transported and processed at a manufacturing facility far from the patient’s home and shipped back to a local hospital, reducing the need for patients to travel long distances to specialized medical centers to receive gene therapy. A trial of the cryopreserved treatment is now underway at the Zayed Centre for Research into Rare Diseases in Children in London, in partnership with GOSH...

Research published in N.E.J.M. (May 11, 2021):

https://doi.org/10.1056/NEJMoa2027675 

/PRNewswire/ -- American Gene Technologies (AGT), a clinical-stage biotechnology company, announced treatment of the first participant in itsPhase I clinical trial to evaluate safety of the cell and gene therapy product AGT103-T. Designated as the RePAIR trial (Restore Potent Antiviral Immune Responses, NCT04561258), participants are infused once with their own CD4 T cells that were enriched, for cells capable of reacting to HIV, and genetically modified to resist infection. The first infusion took place at Washington Health Institute, Washington, D.C. on May 19.  This is a first-in-human study for AGT103-T. The primary endpoint is safety; testing related to secondary endpoints evaluates responses to treatment including changes in the immune response to HIV. Participants treated with AGT103-T will be followed for 6 months in this safety study before enrolling in an FDA-mandated 15-year long-term follow up required for all gene therapy trials. Enrollment, product manufacturing, and treatments are ongoing at AGT's clinical trial sites. "Treating the first person with our product is an important step forward and the culmination of design, development, manufacturing, and approval of the product for human testing. We believe this therapy is capable of changing the body's ability to fight HIV and the first-in-man study signals the first step to understanding what we can achieve with this innovative approach," said Dr. C. David Pauza, Chief Science Officer.

"This project represents a major step forward in the potency of an approach that has significant theoretical and empirical momentum within the HIV cure scientific community," stated CEO Jeff Galvin. He continued, "now that we have seen some evidence that the treatment can be tolerated by patients, I believe we will soon see efficacy signal that will be convincing to the scientific community that the cure for HIV has been achieved or is tremendously close. I couldn't be happier or prouder of the team. I am exceedingly optimistic about the future of this cell therapy and AGT's eventual contribution to the treatment of HIV."...

For the first time, a patient got treated for HIV and cancer at the same time, with an infusion of gene-edited stem cells. The results? Mixed. Imagine you’re 27 years old and you start feeling ill. Ill enough that you go to the hospital, and after much poking and prodding and waiting for lab results you learn you’re HIV-positive. Two weeks later you find out that’s not even the worst of it. You’ve got leukemia too.

Under any circumstances it would be a lot to take in. Especially in China, where HIV/AIDSis highly stigmatized. But for one young man living there, who this happened to in the late spring of 2016, there was one small but significant silver lining to this double whammy of a diagnosis. He would be eligible to participate in the first-ever clinical trial to assess the safety of trying to cure both the cancer and the infection in a single procedure using the gene editing tool call Crispr. In July of 2017, doctors in Beijing blasted the patient with chemicals and radiation to wipe out his bone marrow, making space for millions of stem cells they then pumped into his body through an IV. These new stem cells, donated by a healthy fellow countryman, would replace the patient’s unhealthy ones, hopefully resolving his cancer. But unlike any other routine bone marrow transplant, this time researchers edited those stem cells with Crispr to cripple a gene called CCR5, without which HIV can’t infiltrate immune cells.

Now, more than two years later, the patient is in good health, his cancer in full remission, as researchers report today in the New England Journal of Medicine. The edited stem cells survived and are still keeping his body supplied with all the necessary blood and immune cells, and a small percentage of them continue to carry the protective CCR5 mutation. Not enough to have cured him of HIV, though—he remains infected and on antiretroviral drugs to keep the virus in check. Still, experts say the new case study shows this use of Crispr appears to be safe in humans and moves the field one step closer toward creating drug-free HIV treatments.

“The safety profile appears to be acceptable,” pioneering cancer researcher Carl June wrote in an accompanying editorial, noting that the editing appeared to be precise, and that the engineered stem cells didn’t provoke an immune response in the patient. June did offer a caveat that the study’s single patient offered only limited data to draw on. What he found more striking was how quickly the science has moved from the first reports of using Crispr to treat HIV infection in mice to trying it in humans: only two years. At the University of Pennsylvania, June has led work in  a ground-breaking cancer treatment called CAR-T, which involves genetically reprogramming immune cells into a clone army of tumor-targeting assassins. But it took him five years to go from studies in animals to trials involving humans. In this case, China’s more permissive biomedical research regulations might have expedited the work, or it could be that genetic engineering is lending new momentum to the race for an HIV/AIDS cure, he wrote. “In any case, the genie is out of the bottle with genome editing.”

This is the first time an HIV-positive patient has been treated with Crispr-edited cells. But scientists have been trying to find ways to genetically disable CCR5 for more than a decade now. It all started in 2007, when a German doctor took a 41-year-old man with HIV/AIDS and leukemia off of his antiretroviral drugs and hooked a thin tube up to a vein in his chest. Through it, the so-called Berlin Patient received blood cells from a bone marrow donor who had a naturally occurring mutation called CCR5 Δ32. He was missing a chunk of DNA that ultimately allows an HIV virus to enter immune cells. The patient survived his cancer and became the first (though no longer the only) person considered to be fully cured of HIV/AIDS....

The study was published on September 11, 2019 in the New England Journal of Medicine:

https://doi.org/10.1056/NEJMoa1817426