How synthetic versions of a common virus are helping propel gene therapies

The idea behind gene therapy sounds deceptively simple: Take an errant gene responsible for causing disease and tinker with its genetic machinery so it doesn’t do that anymore.

In truth, gene therapy is arguably one of the most difficult drug strategies in play today. The industry has been marked by failures and one tragic incident that had a chilling effect on future gene therapy research. After decades of trying only a handful of gene therapies have made it to market, in part because it is so difficult to deliver the modified DNA.

“Formulating a gene as a drug is not trivial because there are very few pathways that shuttle DNA or RNA into a cell,” says Luk Vandenberghe, PhD, Associate Professor of Ophthalmology at Harvard Medical School and Director of the Grousbeck Gene Therapy Center at Massachusetts Eye and Ear. “There are all kinds of barriers, whether it is the extracellular milieu that degrades DNA or whether it is passing the lipid bilayer to get into cell. And often if you want to activate the nucleotides that you bring into a cell, you have to be able to not just get into the cell but into the nucleus. That is asking a lot.”

Delivering the DNA or RNA has been one of the biggest battles in gene therapy. Scientists initially seized upon the unique ability of viruses—which survive by shuttling their own information into a cell and then instructing the cell to propagate the virus—as a driver for gene therapies, but the viruses they chose as chauffeurs triggered dangerous side effects or didn’t work at all.

The rise of AAVs

Despite all of this, gene therapy has once again emerged as a hot area of research, and you can credit much of the turnaround to the discovery of viral vectors that can shuttle gene therapies into cells without posing a threat to the patient. These adeno-associated viral vectors (AAV) are harmless viruses abundant in nature, and which are now the beating heart of gene therapy research. Last year the US Food and Drug Administration (FDA) approved an AAV-based drug designed to cure a rare form of blindness, and there are many more AAV-based gene therapies in development for diseases ranging from Parkinson’s disease to HIV.

Using AAV vectors to transfer genes is not without its own set of challenges. Gene therapy research for hemophilia found some AAV vectors elicit CD8+ T-cell responses that target the virus for elimination. Moreover, not all strains of AAV have enough affinity for certain tissues, which can prevent therapeutic genes from reaching their cellular manufacturing centers. And while more than 120 new AAVs have been discovered over the past decade, not all of these vectors are good transporters of genes.

One final challenge is the fact that the lineage of AAVs complicates their usefulness as vectors. Unlike HIV, a relatively young virus that likely dates back about 100 years, AAVs are ancient viruses. It is estimated that at least 50% of the global population have been exposed to AAV at some point in their life, making them ineligible for AAV-based therapies. Vandenberghe calls this the Achilles heel of the AAV field.

“So the question is, can we build something that looks as potent [as AAVs] but is also immunologically distinct to the immune system so it won’t cross-react?” Vandenberghe asked.

Engineering from nature

The answer is yes. Some laboratories have taken natural viruses and engineered around them so that over time they become sufficiently divergent from the natural viruses. Other labs are taking the chemical route, trying to rebuild all of the vector’s functions that nature, over eons of evolution, have built in.

Vandenberghe’s laboratory is using a hybrid of these two approaches. First, they took a computational modeling approach to trace the evolutionary history of AAV back to the oldest common ancestor, Anc80. Next, they integrated an algorithm into the mix, and then asked the algorithm to predict sequences that were far removed from natural AAVs but still functional. From this they recreated a library of more than 700 distinct variants of Anc80, then tested their ability to infect liver, muscle, and retinal cells in mice.

One sequence in particular, Anc80L65, hit three important goals: it was able to assemble into viral particles, package the therapeutic transgene DNA, and infect mammalian cells in culture, according to findings reported in Cell Reports.

There are now multiple studies showing that Anc80 can effectively and safely shuttle genes to the inner ear of mice that AAVs in nature could not, including into cells that cause diseases of the ear. One such disease is Usher syndrome, an inherited condition that leaves its victims both blind and deaf. Other studies have found that Anc80 can also target cells in the eye.

Different companies are now trying to leverage the power of the AAV vector in gene therapy, including Odylia Therapeutics, a non-profit Vandenberghe founded. Odylia is exploring the use of Anc80 in Usher.

Challenges remain. One of the key impediments in using synthetic vectors is scaling up production, both for clinical use and, if approved, for the market. Because the ability of the viral vector to replicate has been edited out for safety reasons, scientists must now mass produce each viral particle, one by one.

Still, Vandenberghe says the synthetic vectors look promising. “We are getting incredible results with these types of vector systems for niche indications,” he says. “It demonstrates how transformative gene therapy can be.”