Ancient Viruses as Gene Therapy Vectors

Researchers deploy ancestors of today’s adeno-associated viruses to deliver gene therapies without immune system interference.

By | July 31, 2015

Retinal targeting by Anc80LIVIA CARVALHOThe immune system is designed to protect the body, but it sometimes gets in the way—by rejecting potentially life-saving blood transfusions or organ transplants, for example. Because one of the most commonly used methods for delivering gene therapies involves viruses as vectors, scientists developing such treatments are working to circumnavigate the host immune response.

Adeno-associated viruses (AAVs) have shown promise as gene-therapy delivery vehicles in clinical trials evaluating treatments for hemophilia and a genetic form of blindness. Problem is, anywhere from 30 percent to 90 percent of people have already been exposed to AAVs—which are not pathogenic—and have developed immunity to them, said Luk Vandenberghe of the Schepens Eye Research Institute and Massachusetts Eye and Ear Infirmary in Boston. As a result, they are ineligible for AAV-based therapies. “And it could, for some of these diseases, actually be a life-or-death differentiation—enrolling in a gene therapy trial or not,” he said.

In an effort to generate gene therapy vectors that could evade the immune system, Vandenberghe and his colleagues deduced the evolutionary history of today’s AAVs. They then synthesized the predicted ancestral viruses and tested them as gene therapy vectors in mammalian tissues. Their results were published today (July 30) in Cell Reports.

“This is a very thorough, creative, and carefully done study,” Jean Bennett of the University of Pennsylvania, who has collaborated with Vandenberghe but was not involved in the work, told The Scientist in an e-mail. “The ancestral AAVs have promise with respect to use, although, ultimately, human testing would reveal their utility.”

“This is on par with . . . other approaches” to designing immune detection-evading viral vectors, said R. Jude Samulski, director of the University of North Carolina Gene Therapy Center in Chapel Hill, North Carolina, who also was not involved in the work.

Researchers have used a variety of approaches to modify AAVs; most involve rearranging coat proteins called capsids, rendering the viruses unrecognizable to hosts. No matter the method, “everybody’s looking for capsids that change the surface enough so that the pre-existing neutralizing antibodies don’t recognize it,” said Samulski.

Vandenberghe and his colleagues gathered the amino-acid sequences of capsid proteins from 75 viruses circulating today in primates. They then created a putative evolutionary tree for the viral family, which included nine ancestral viruses leading back to the oldest common ancestor, “Anc80.” In several places, the amino-acid sequence of Anc80 was ambiguous, with two amino acids possible at a given position, so the researchers created a library of all 2,048 possible sequences. They selected one, “Anc80L65,” based on its ability to assemble into viral particles, package the therapeutic transgene DNA, and infect mammalian cells in culture.

Anc80L65 successfully expressed a transgene in the mouse retina, skeletal muscle, and liver, and the expression was as good or better than that of AAV8—a commonly used gene therapy vector tested as a control.

“In some animals, not in all, we were able to achieve gene transfer even though these animals have pre-existing immunity against AAV8,” said Vandenberghe. “So this is one way of testing this initial hypothesis that we generated an immunologically distinct virus that can circumvent this pre-existing immunity problem.”

Beyond Anc80L65, the researchers recreated eight additional ancient viruses that represented different branching points on AAV evolutionary tree. The hope is that these viruses will further help researchers understand viral architecture and evolutionary history. “The structure-function relationships themselves will be useful for further improving gene therapy vectors,” said Bennett.

When it comes to designing AAV-vectors for gene therapy, “no one has any idea which one or if any of them are going to work,” said Samulski. “It may be a combination of ancestral mixed with library mixed with rational design [approaches]. . . . At this point in time, anything else you can add to the arsenal to attack the question in hand is valuable to the research community.”

E. Zinn et al., “In silico reconstruction of the viral evolutionary lineage yields a potent gene therapy vector,” Cell Reports, doi:10.1016/j.celrep.2015.07.019, 2015.

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Avatar of: James V. Kohl

James V. Kohl

Posts: 475

July 31, 2015

Re: "In several places, the amino-acid sequence of Anc80 was ambiguous, with two amino acids possible at a given position, so the researchers created a library of all 2,048 possible sequences. They selected one, “Anc80L65,” based on its ability to assemble into viral particles, package the therapeutic transgene DNA, and infect mammalian cells in culture."

Is anyone else willing to comment on the likelihood that this moves Dobzhansky's (1973) creationist / evolutionist perspective into the realm of only the creationist perspective on how ecological variation leads to ecological adaptations in all genera, which appears to be via RNA-mediated gene duplication and RNA-mediated amino acid substitutions that are fixed in the organized genomes of all genera via their physiology of reproduction?

This link opens the pdf:

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla. ( p. 127)

Alternatively, are you willing to wait until everyone else integrates what is currently known to serious scientists about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding? Will you wait and continue to report your results in the context of theories about mutations and evolution that have never included what is known about virus-perturbed nutrient-dependent RNA-mediated protein folding? Will you continue to ignore the fact that biodiversity cannot arise outside the context of DNA repair and the thermodynamic stability of protein biosynthesis and degradation in organized genomes?

Avatar of: James V. Kohl

James V. Kohl

Posts: 475

Replied to a comment from James V. Kohl made on July 31, 2015

July 31, 2015

While you are waiting:

Every amino acid matters: essential contributions of histone variants to mammalian development and disease

See also:

Expanding the brain: Research identifies more than 40 new imprinted genes

Does anyone know how imprinting occurs outside the context of nutrient-dependent RNA-mediated gene duplication and fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all living genera?

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