Coronavirus structure, illustration

By using a technique known as DNA origami to fold DNA into a virus-like structure, MIT researchers have designed HIV-like particles coated with HIV antigens in precise patterns, which may eventually be used as an HIV vaccine. In vitro studies showed that the DNA origami particles, which mimic the size and shape of viruses, provoked a strong immune response from human immune cells. The researchers anticipate that the same approach could be used to design DNA origami vaccines for a wide variety of viral diseases, and they are now working on adapting the technology to develop a potential vaccine for SARS-CoV-2.

“The rough design rules that are starting to come out of this work should be generically applicable across disease antigens and diseases,” said Darrell Irvine, PhD, who is the Underwood-Prescott professor with appointments in the departments of biological engineering and materials science and engineering; an associate director of MIT’s Koch Institute for Integrative Cancer Research; and a member of the Ragon Institute of MGH, MIT, and Harvard. “Our platform technology allows you to easily swap out different subunit antigens and peptides from different types of viruses to test whether they may potentially be functional as vaccines,” added Mark Bathe, PhD, an MIT professor of biological engineering and an associate member of the Broad Institute of MIT and Harvard.

Irvine and Bathe are senior authors of the team’s published study in Nature Nanotechnology, which is titled, “Role of nanoscale antigen organization on B-cell activation probed using DNA origami.” The paper’s lead authors are former MIT postdocs Rémi Veneziano, PhD, and Tyson Moyer, PhD.

Viruses are effectively nanoparticles with antigens arrayed on their surface, and it is thought that the immune system—especially B cells—has evolved to efficiently recognize such particulate antigens. Vaccines are now being developed to mimic natural viral structures, and nanoparticle vaccines are expected to be very effective at generating a B-cell immune response because they are the right size to be carried to the lymphatic system, which send them directly to B cells waiting in the lymph nodes. The particles are also the right size to interact with B cells and can present a dense array of viral particles.

Efficient activation of antigen-specific B cells is a central goal for vaccine development. One way of helping to boost B-cell activation is to increase the numbers of antigens that the B cells encounter on the vaccine particle. “Vaccine efficacy can be increased by arraying immunogens in a multivalent form on virus-like nanoparticles to enhance B-cell activation,” the authors explained. “Antigen multimers, antigen-conjugated polymers, and virus-like nanoparticles (NPs) displaying immunogens at high density have all been shown to strongly initiate early B-cell signaling.” However, determining the right particle size, spacing between antigens, and number of antigens per particle to optimally stimulate B cells (which bind to target antigens through their B-cell receptors) has been a challenge.

Over recent decades scientists have been working on methods to design DNA molecules that could be used for drug delivery and many other applications. In 2016, Bathe’s lab developed an algorithm that can automatically design and build arbitrary three-dimensional virus-like shapes using DNA origami. This method offers precise control over the structure of synthetic DNA, allowing researchers to attach a variety of molecules, such as viral antigens, at specific locations. Scientists have tried to create subunit vaccines using other kinds of synthetic particles, such as polymers, liposomes, or self-assembling proteins, but with these approaches it is not possible to control the placement of viral proteins as precisely as with DNA origami.

“The DNA structure is like a pegboard where the antigens can be attached at any position,” commented Bathe, who, with Irvine, set out to use these DNA scaffolds to mimic viral and vaccine particle structures, with the goal of discovering the best particle designs for B-cell activation. “There is a lot of interest in the use of virus-like particle structures, where you take a vaccine antigen and array it on the surface of a particle, to drive optimal B-cell responses,” Irvine commented. “However, the rules for how to design that display are really not well-understood.”

For their reported study, the researchers designed icosahedral particles with a similar size and shape as a typical virus. They attached an engineered HIV antigen related to the gp120 protein to the scaffold at a variety of distances and densities. “ … to independently probe the relative roles of immunogen valency and spacing on immunoglobulin-M (IgM)-BCR activation, we used scaffolded DNA origami NPs to display discrete antigen copy numbers with controlled inter-antigen spacings on the scale of an individual virus-like NP,” they explained. To the investigators’ surprise, the results showed that the vaccines that produced the strongest response B-cell responses were not necessarily those that packed the antigens as closely as possible on the scaffold surface. “We find that B-cell signaling is maximized by as few as five antigens maximally spaced on the surface of a 40-nm viral-like nanoparticle,” they wrote. “Increasing antigen spacing up to ~25–30 nm monotonically increases B-cell receptor activation.”

“It is often assumed that the higher the antigen density, the better, with the idea that bringing B-cell receptors as close together as possible is what drives signaling,” Irvine said. “However, the experimental result, which was very clear, was that actually the closest possible spacing we could make was not the best. And, and as you widen the distance between two antigens, signaling increased.” Bathe added: “These virus-like particles have now enabled us to reveal fundamental molecular principles of immune cell recognition for the first time.”

Based on their data, the MIT researchers worked with Jayajit Das, PhD, a professor of immunology and microbiology at Ohio State University, to develop a model to explain why greater distances between antigens produce better results. When antigens bind to receptors on the surface of B cells, the activated receptors crosslink with each other inside the cell, enhancing their response. However, the model suggests that if the antigens are too close together, this response is diminished.

The findings from the study have the potential to guide HIV vaccine development, as the HIV antigen used in these studies is currently being tested in a clinical trial, using a protein nanoparticle scaffold. In recent months, Bathe’s lab been working with the Aaron Schmidt, PhD, and Daniel Lingwood, PhD, labs at the Ragon Institute, to develop an alternative to the HIV vaccine, for which they swapped out the HIV antigens for a protein found on the surface of the SARS-CoV-2 virus. They are now testing whether this vaccine will produce an effective response against the coronavirus SARS-CoV-2 in isolated B cells, and in mice.

And because this approach allows for antigens from different viruses to be carried on the same DNA scaffold, it could be possible to design variants that target multiple types of coronaviruses, including past and potentially future variants that may emerge, the researchers suggested. “… for the purpose of the rational design of molecular vaccines for robust triggering of B-cell responses, here DNA origami has offered crucial insight into the spatial relationships between immunogens, which may be generalized to other viral pathogens such as SARS-CoV-2 and Zika, and offered important foundations for the rational design of protein-based and other vaccine platforms,” they concluded.

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