Gene editing holds promise for shrinking HIV ‘reservoir’

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Gene editing holds promise for shrinking HIV ‘reservoir’

Study mimicking Timothy Ray Brown’s HIV-resistant mutation led to fewer latently infected cells — a key step toward driving the virus into remission without the need for antivirals

April 25, 2018
Fred Hutch's Dr. Chris Peterson presents his work at the AIDS2016 conference in Durban, South Africa in July 2016.

Fred Hutch's Dr. Chris Peterson presents his work at the AIDS2016 conference in Durban, South Africa in July 2016. On the screen behind him is a photo of Timothy Ray Brown, the only known case of HIV cure to date. Brown's case, first widely reported in 2009, has energized HIV cure research.

Photo by Robert Hood / Fred Hutch News Service

By transplanting blood stem cells that had been gene-edited to resist HIV infection, scientists at Fred Hutchinson Cancer Research Center were able to shrink the size of dormant viral “reservoirs” in infected animals, according to research results published last week in PLOS Pathogens. Reducing or eliminating these persistent reservoirs is a key step toward curing HIV or, to use a term borrowed from cancer, driving the virus into remission so that daily antiretroviral drugs aren’t needed.

“The number of latently infected cells, which we call the viral reservoir, was reduced,” said lead author Dr. Chris Peterson, a staff scientist in the laboratory of stem cell transplant and gene therapy specialist Dr. Hans-Peter Kiem, the paper’s senior author. “We took samples from different tissues and measured viral RNA and DNA. Both were significantly lower in transplanted animals relative to controls.”

The edited cells made up about 4 percent of total white blood cells — not yet enough to induce remission, Peterson said. The next step will be to tweak editing techniques so that more of the gene-altered cells “take,” or engraft, and multiply after transplantation, driving up the percentage and further driving down the reservoir.

Shrinking the reservoir is key because HIV integrates itself into the DNA of some of the longest-lived cells in the body, where it goes into a dormant state but can wake up at any time and produce new virus. Scientists at first thought that antiretroviral drug cocktails, which in 1996 transformed HIV from a death sentence to a chronic disease, would cure HIV if taken long enough. But it turns out that the drugs alone cannot clear the reservoirs. Stopping daily medication allows HIV to roar back in as little as two weeks.

A handful of other research teams have published results showing some reservoir reductions in animal studies: Dr. Louis Picker and colleagues at Oregon Health & Science University’s Vaccine and Gene Therapy Institute, using a vaccine; Dr. Dan Barouch and his team at the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center-Harvard Medical School, using a drug that “kicks” the sleeping cells awake combined with a powerful antibody; and Dr. Mirko Paiardini and colleagues at Emory University, who reduced harmful inflammation as a means to enable the immune system to better fight the virus.

Peterson used a gene-editing technique called zinc-finger nucleases, or ZFNs, to disrupt a receptor used as a doorway by most forms of HIV (or, in this and other animal studies, a hybrid of HIV and its simian version, called SHIV). The modified stem cells were then returned to repopulate the immune system in what is known as an autologous transplant, which means using the patient’s own stem cells rather than a donor’s.

Previously, he had shown that gene-edited cells delivered via autologous transplantation were safe and would engraft and multiply in healthy, uninfected animals, a finding for which he was awarded the Young Investigator Award Special HIV Cure Prize in 2015 from the International AIDS Society and the French National Agency for AIDS Research.

Dr. Hans-Peter Kiem

Peterson's work is part of the Hutch-based defeatHIV, a public-private research group investigating HIV cure research that is co-led by Dr. Hans-Peter Kiem (above) and Dr. Keith Jerome. Peterson is a researcher in Kiem's lab.

Fred Hutch file photo

The blueprint: Timothy Ray Brown

Peterson’s work is part of the Hutch-based defeatHIV, a consortium headed by Kiem and virologist Dr. Keith Jerome that was first funded in 2011 by the National Institutes of Health as one of three public-private research groups investigating different HIV cure strategies. (Funded again in 2016, it is now one of six such groups.) Under its first round of funding, defeatHIV focused on autologous transplantation using genetically modified stem cells as a safer, more scalable way to cure HIV based on the only known case of HIV cure to date: that of Timothy Ray Brown.

Brown’s case, first widely reported in 2009, has energized HIV-cure research. He had received an allogeneic bone marrow transplant — using matched donor cells — in 2007 to treat life-threatening leukemia. Because Brown also had HIV, his doctor in Berlin, where he was living at the time, sought out a donor with two copies of a mutation on the CCR5 gene, which results in natural HIV resistance. This is the mutation that Peterson mimicked using ZFNs.

 In 2008, Brown’s cancer returned and he required a second transplant. But he had stopped taking antiretroviral medicine for his HIV after the first transplant, and scientists have not detected the virus since. (His leukemia also remains in remission.)

A high-risk bone marrow transplant — Brown barely survived his second one — is no way to try to cure the vast majority of people with HIV who do not also face a deadly blood cancer. But until Brown’s case, no one believed HIV could be cured at all because of those reservoirs of latently infected cells.

Researchers are pretty sure that the donor’s HIV-resistant cells played a role in Brown’s cure; in at least two cases, people with both cancer and HIV who underwent transplants without HIV-resistant donors relapsed after being HIV-free for months. But they’re less sure about the role played by the rest of the transplant process. What about Brown’s intensive pre-transplant “conditioning” — a chemotherapy and radiation regimen that destroys the immune system to make room for transplanted cells to grow — or the graft-vs.-host disease he developed after the second transplant?

“Even for a cancer patient, he went through an extraordinarily intensive treatment, with two transplants and the chemotherapy,” Peterson said. “He went through a lot.”

The goal of defeatHIV is to not put anyone who is otherwise healthy through such a harsh treatment, which Brown himself thoroughly endorses. So although some conditioning is needed to make room for new stem cells to grow, Peterson is using a far less harsh version. Also, autologous transplantation avoids the potentially lethal graft-vs.-host disease that can arise when a donor immune system sees and attacks its new host as foreign.

At the same time, it also loses a potential graft-vs.-reservoir effect, similar to the graft-vs.-leukemia effect that researchers learned is part of a leukemia cure. (That is, the donor’s immune cells attack and kill leukemia cells missed by chemotherapy or radiation.) For that reason, Peterson and other defeatHIV researchers believe that a second step may be needed beyond making stem cells resistant to HIV.

Next steps

In a study published in December, also  in PLOS Pathogens, Peterson and collaborators at the University of California, Los Angeles modified stem cells by adding a chimeric antigen receptor, or CAR, programmed to kill HIV-infected cells, a process similar to a type of gene therapy being tested against cancer.  

Most of the still-experimental cancer therapies genetically reprogram a patient’s own T cells — a type of immune cell that searches out and destroys abnormal or infected cells. Fred Hutch HIV cure researchers are working instead to reprogram stem cells, which give rise to T cells.

Why stem cells?

“Long story short: They’re going to persist for the lifetime of the individual,” Peterson said. In the earlier CAR study published in December, the researchers noted that the stem cells appeared to produce anti-HIV T cells when needed.

“The interesting thing there is we could see that the CAR cells come and go as the virus comes and goes,” he said. “When we put the animals on antiretroviral therapy, the CAR cells go down. When we take them off, they go back up. They act as sentinels, going to sleep and waking back up as needed.”

Ideally, treatment would combine the CCR5 and CAR gene modifications — marrying a defense against HIV infection with an offense against already-infected cells.

“We think that by enabling a cell that’s CCR5-edited and infection-resistant to also seek out infected cells using a CAR molecule, we can enhance the ability to reduce or eliminate reservoirs even more,” Peterson said. “It would be more of an active approach rather than a passive approach.”

Peterson and his colleagues, along with collaborators at UCLA, continue to refine techniques to boost the proportion of gene-edited cells as well as to plan a study combining the protective CCR5 mutation with a CAR to play offense.

In the meantime, City of Hope Medical Center in California and ZFN creator and defeatHIV member Sangamo Therapeutics have opened a small human clinical trial testing a CCR5-edited autologous transplant, which is similar to Peterson’s animal studies but uses a different conditioning regimen.

“We’re excited to see where they go,” Peterson said.

Mary Engel is a former staff writer at Fred Hutchinson Cancer Research Center. Previously, she covered medicine and health policy for the Los Angeles Times, where she was part of a team that won a Pulitzer Prize for Public Service. She was also a fellow at the Knight Science Journalism Program at MIT. Follow her on Twitter @Engel140.

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