Gene therapy’s comeback: how scientists are trying to make it safer


After years of disappointment, gene-therapy research has undergone a renaissance, with several high-profile drug approvals and a string of promising clinical-trial results against devastating genetic diseases, including sickle-cell disease and some blood cancers.

But as researchers attempt to develop treatments for new conditions, they are also trying to work out how to cope with worrying signs that immune responses to the therapies could hinder their efforts — and generate dangerous side effects.

The concern was a popular topic at the American Society of Gene and Cell Therapy (ASGCT) annual meeting in Washington DC, held from 16 to 19 May, as presenters discussed the effects of inflammation on gene therapy and how to mitigate them. “Inflammation is par for the course, but often we don’t talk about it,” said Christine Kay, a surgeon at Vitreoretinal Associates in Gainesville, Florida, during a talk about gene therapies for eye disorders. “I’m glad that we’re beginning to.”

Safety has long been a primary concern in gene-therapy research, particularly after the death of a gene-therapy trial participant and the discovery of gene-therapy-linked cancers around the turn of the century closed clinical trials and caused investors to pull away from the burgeoning field.

But the field has resurged over the past decade, and several gene therapies have been approved by regulators around the world to treat conditions including cancer, blindness and a metabolic disorder. “We are on a roll with gene therapy,” Francis Collins, acting science adviser to US President Joe Biden, told the ASGCT meeting. “But we still have thousands of diseases that have not been approached.”

Immune interference

Researchers have long been wary of how immune responses could make gene therapies less effective. The treatments often rely on a virus to ferry a gene into cells, but if the recipient already has antibodies against that virus, an immune response could hinder the treatment. As a result, participation in gene-therapy clinical trials is often limited to people who do not already have such antibodies.

In most gene-therapy studies, the gene is carried by one of several adeno-associated viruses (AAVs), a group of small viruses that have been studied for use in the field for nearly four decades. Thousands of people have received an AAV-based gene therapy, said Denise Sabatino, a haematology researcher at Children’s Hospital of Philadelphia in Pennsylvania, at the meeting. Some gene therapies approved by the US Food and Drug Administration — including Zolgensma (onasemnogene abeparvovec), a treatment for spinal muscular atrophy, and Luxturna (voretigene neparvovec), which treats a form of retinal dystrophy that can cause blindness — rely on these viruses.

AAV vectors are also being used in clinical trials of gene-editing therapies, including those based on the popular CRISPR–Cas9 system. And the US National Institutes of Health (NIH) has launched a programme to study AAV vectors, in the hope of fostering a gene-therapy pipeline in which developers can simply swap a new therapeutic gene into the viral genome to treat a particular disease, without having to conduct large clinical trials to establish safety. Large clinical trials are particularly difficult when it comes to treatments for rare genetic disorders.

But as researchers push to treat more conditions and improve the effectiveness of their therapies, “this has become a real and present concern in AAV gene therapy”, said Fraser Wright, a gene-therapy researcher and co-founder of Spark Therapeutics in Philadelphia, which developed Luxturna, at the meeting. “As we’ve gone up in AAV dosing in human subjects, we have seen more and more severe adverse events.” Some of those events have included deaths, Fraser added.

Inflammatory response

The main concern used to be that antibodies against an AAV or its cargo would prevent the gene therapy from working or preclude the possibility of giving multiple doses, said Wright. But more recently, researchers have realized that antibodies could stimulate the production of inflammatory molecules, activate cell-death pathways and trigger the development of killer T cells that could target AAV-containing cells for destruction.

Researchers at the ASGCT meeting reported efforts to tackle this inflammation from a variety of angles. Some are looking for alternatives to AAVs, and Collins noted that the NIH’s Somatic Cell Genome Editing programme is studying both viral and non-viral vectors. “I think a lot of us are worried about depending on AAV forever, and would like to have things with maybe less in the way of plausible risk,” he said.

At the Wyss Institute for Biologically Inspired Engineering at Harvard University in Boston, Massachusetts, viral immunologist Ying Kai Chan is trying to engineer safer AAV vectors. Risks increase when investigators use higher amounts of AAV, he said at the meeting: “I’m a huge fan of reducing the dose.” But to do so, he added, might require the development of more potent treatments that use less virus.

Some are trying to ‘humanize’ the AAV genome, to make it less likely to activate immune pathways. For example, in humans, when the DNA base C is followed directly in the genome sequence by the base G, it often carries a chemical group called a methyl. AAV has a higher percentage of CG groups without a methyl — a potential red flag to the immune system. Wright presented data showing that increasing the methylation of CG-rich regions decreased the activation of inflammation-promoting molecules called cytokines. But, he added, there is a potential trade-off: the same methylation, if used too heavily, might also suppress gene expression, including that of the therapeutic gene carried by the AAV.

Suppressed immunity

Others are working on ways to suppress harmful immune responses. Gene therapies are often given with immunosuppressants such as steroids, but there are concerns that such treatments are sometimes ineffective, and can render recipients vulnerable to infection. Anastasia Conti, who studies stem cells at the San Raffaele Telethon Institute for Gene Therapy in Milan, Italy, reported at the ASGCT meeting that a drug called anakinra reduced inflammation triggered by gene editing. The drug might also enhance the potency of gene-editing treatment by reducing the number of edited blood stem cells that become senescent — meaning that they are still alive but have stopped dividing.

At Selecta Biosciences in Watertown, Massachusetts, researchers are developing nanoparticles designed to be taken up by immune cells and coupled to a drug called rapamycin that is sometimes used to suppress the immune system after organ transplantation. In non-human primates, the team found that three monthly doses of the nanoparticles prevented antibody responses to the AAV’s protein shell, chief scientific officer Kei Kishimoto said at the meeting. And researchers at Spark have tested a drug that inhibits an immune regulator called IL-6. They found that the treatment lowered the level of antibodies against AAV shells in non-human primates. In mice, it reduced immune responses enough to allow the animals to receive multiple rounds of gene therapy.

In the end, it will probably take a “toolbox of strategies” to tackle the inflammation problem, said Chan. And as the reach of gene therapies continues to expand, researchers need to develop tools to monitor potentially dangerous inflammation in difficult-to-access parts of the body, such as the brain, he added. Many studies on inflammation have been conducted in the eye, where researchers can relatively easily visualize changes that occur even months after therapy. “How will we really know what is happening in the central nervous system or the ear?” Chan asked. “We could fool ourselves for a long time.”

Nature, 31 May 2022