Jeffrey Perkel has been a scientific writer and editor since 2000. He holds a PhD in Cell and Molecular Biology from the University of Pennsylvania, and did postdoctoral work at the University of Pennsylvania and at Harvard Medical School.
When novel pathogens with pandemic potential emerge, researchers and epidemiologists race to develop vaccines to block them. It’s a rush against the clock, and sometimes the good guys lose: It simply takes too long to identify an effective antigen and produce enough of it to make a dent.
In early 2009, for instance, a pandemic strain of influenza called H1N1 arose. The outbreak peaked six months later, in October, but it wasn’t until November that a vaccine became widely available, at which point the outbreak was already subsiding [1].
The traditional vaccine-development process is decades old. It involves shipping a sample of the purified virus to a vaccine-development laboratory, developing a nonpathogenic variant of the virus, propagating that new variant in eggs or cultured cells and harvesting them to produce the vaccine. But an emerging alternative promises to sharply rein in that development cycle: Synthetic biology.
Vaccine development is an “emerging application” for synthetic biology, says James Collins, the Termeer Professor of Medical Engineering and Science at Massachusetts Institute of Technology (MIT), an expert in synthetic biology. “We can read and write DNA quite readily. And the notion that you can very quickly develop a [DNA] vaccine makes it attractive” in terms of development cycle, he adds—not to mention providing the flexibility to handle sequence diversity and variation.
“In 2009, it took nearly 3 months from March 18, when the first case occurred, to June 7, when vaccine manufacturing started. This could probably be reduced to a couple of weeks by early detection of the first case and the use of fully synthetic seed viruses for vaccine production,” wrote Rino Rappuoli and Philip Dormitzer of Novartis Vaccines and Diagnostics in a 2012 article in Science [1].
Accelerating the process
Take, for instance, the case of the flu strain H7N9, whose genomic sequence was reported online by Chinese researchers in March 2013. Researchers at Novartis Vaccines and Diagnostics, the J. Craig Venter Institute, Synthetic Genomics and others demonstrated that by treating the viral sequence like open-source software, they could prepare their own viral material and have a vaccine seed stock ready in days.
The team downloaded the viral gene sequences from the Internet, synthesized and validated artificial genes from the published sequence, inserted those into a pre-existing viral backbone, infected eukaryotic cells in culture and harvested virus. Total time: 100 hours [2,3].
“In one week, without shipping any virus around, using only sequence information [available] on the Internet, we’d been able to do what usually would take six months,” says Rappuoli, now chief scientist at GSK Vaccines.
In a later study, Novartis researchers prepared a vaccine from that material and applied it in a phase 1 trial of 402 individuals. When combined with an immune stimulant called an adjuvant, the vaccines produced a “potentially protective immune response” after two doses, the authors reported [3].
The case of H7N9 demonstrates the power of synthetic biology to accelerate the vaccine-development process. But the potential exists to go even faster, simply by skipping the protein middle man and injecting nucleic acids into the body directly—a so-called nucleic acid vaccine. All you need is a nucleic acid capable of expressing the desired antigens, packaged in a liposome and ready for delivery.
The entire process could in fact be automated, says Rappuoli. “You can have a robot take the sequence information, make the genes, [transcribe] the synthetic RNA, put it together with a synthetic delivery system and make a vaccine. So in the future, it could be a totally automated thing.”
Favoring RNAs
Originally, says Oliwia Andries, a junior innovation manager at Omega Pharma who as a graduate student at Ghent University coauthored a review on the topic, nucleic acid vaccines were built of DNA [4]. But DNA must enter the nucleus to be functional, and there’s always the possibility of genomic integration and mutation. Delivery of therapeutically sufficient levels of DNA into human patients poses another severe challenge. Thus, many researchers today favor RNA vaccines, which need only enter the cytoplasm.
Indeed, RNA vaccines offer numerous advantages over traditional protein-based vaccines, says Tasuku Kitada, a post-doctoral associate at MIT and coauthor of the Andries review. They are faster to develop, modify and distribute, and they can be designed to temporally express multiple antigens and immunostimulatory cytokines.
For instance, says Andries, RNA vaccines can be built to express the cytokine IL-12 (which acts as an adjuvant to create a stronger immune response) and also to express multiple antigens in stepwise fashion, producing a more comprehensive antibody repertoire. Furthermore, the RNA itself can act as a sort of “self-adjuvant.”
In their review, Andries and Kitada describe sophisticated gene-control schemes that could be assembled from RNA. For instance, using an RNA expressing a fusion of an RNA-binding protein and a drug-binding destabilizing domain, it should be possible to control when after injection the antigen is expressed with, for instance, trimethoprim; this combines the antigen priming and boost steps (typically accomplished with two shots) in a single injection. Another design uses a drug and two RNA-binding proteins to control when each of two antigens is expressed.
Rappuoli’s team at Novartis demonstrated the feasibility of this all-nucleic acid approach in mice in 2013, again using H7N9 [5]. The researchers cloned the viral hemagglutinin antigen into a “self-amplifying mRNA,” or SAM—a molecule derived from an RNA-based alphavirus—encased in a lipid nanoparticle, and they injected it intramuscularly. (The SAM offers an advantage over traditional mRNA in that it replicates in the cell, amplifying its efficacy.)
“You’re using the injectee as the factory to make the antigen,” explains Brett Robb, scientific director at New England Biolabs, a company that sells synthetic-biology tools. “The antigen is being made within the target cells at the injection site—which I think is so cool and takes a huge amount of time off the normal process of vaccine development.”
In this case, says Rappuoli, “We were able to vaccinate mice three weeks after discovery of the new virus, and by 40 days [i.e., six weeks after discovery of the virus], they were protected.”
According to Robb, nucleic acid vaccines also have application in the field of oncology, where their sequence flexibility provides significant benefits. For instance, the MERIT (Mutanome Engineered RNA Immuno-Therapy) Consortium is pursuing a strategy that uses each patient’s individualized cancer genome sequence to identify antigens that are likely to be immunogenic. The team then encodes those in “multivalent” RNA vaccines and—eventually—will inject them into human patients. According to the project website, a phase 1/2 clinical trial on patients with triple-negative breast cancer is slated to start in 2015.
Need time for change
Still, for all their promise, don’t expect to see nucleic acid-based vaccines becoming mainstream any time soon, says Tonya Jackson, head of the synthetic-biology division at Sigma-Aldrich, a company that offers a broad portfolio of synthetic-biology tools. Researchers already know how to do vaccine development the old-fashioned way, and their manufacturing facilities are set up accordingly. The regulatory approvals required to produce their vaccines are geared to this older technology, as well, and updating those processes and approvals could take considerable time, she says—“many years to a decade or two.”
Thus, Jackson concludes, “While I’m confident we’ll see this shift to a new way of engineering these vaccines, it’ll be slow.”
References
[1] Rappuoli, R, and Dormitzer, PR, “Influenza: Options to improve pandemic preparation,” Science, 336:1531-3, 2012. [PubMed ID: 22723412]
[2] Dormitzer, PR, et al., “Synthetic generation of influenza vaccine viruses for rapid response to pandemics,” Sci Transl Med, 5:185ra68, 2013. [PubMed ID: 23677594]
[3] Bart, SA, et al., “A cell culture-derived MF59-adjuvanted pandemic A/H7N9 vaccine is immunogenic in adults,” Sci Transl Med, 6:234ra55, 2014. [PubMed ID: 24786323]
[4] Andries, O, et al., “Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: A propositional review,” Expert Rev Vaccines, 14:313-31, 2015. [PubMed ID: 25566800]
[5] Hekele, A, et al., “Rapidly produced SAM® vaccine against H7N9 influenza is immunogenic in mice,” Emerging Microbes & Infection, 2:e52, 2013.