A team led by Bill Schief from the Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery has unveiled a new technique for vaccine design that could be particularly useful against HIV and other fast-changing viruses.
The report, which is feature on the cover of Science, offers a step toward solving what has been one of the central problems of modern vaccine design: how to stimulate the immune system to produce the right kind of antibody response to protect a wide range of viral strains. The team demonstrated their new technique by engineering an immunogen that has promise to reliably initiate an otherwise rare response effective against many types of HIV.
"We're hoping to test this immunogen soon in mice engineered to produce human antibodies, and eventually in humans," said Schief, Associate Professor of Immunology and member of the IAVI Neutralizing Antibody Center at The Scripps Research Institute.
Joe Jardine, a TSRI graduate student in the Schief laboratory, evaluated the genes of VRC01-producing B cells in order to deduce the identities of the less mature B cells from which they originate. He used a protein modeling software, Rosetta, to improve the binding of VRC01 germline B cell antibodies to HIV's envelope protein.
"We asked Rosetta to look for mutations on the side of the HIV envelope protein that would help it bind tightly to our germline antibodies," Jardine said.
Rosetta identified dozens of mutations that could help improve binding to germline antibodies. Jardine then generated libraries that contained all possible combinations of beneficial mutations, resulting in millions of mutants, and screened them using yeast surface display and FACS. This combination successfully produced a few mutant envelope proteins with high affinity for germline VRC01-class antibodies.
Jardine then focused on making an immunogen much smaller than HIV envelope and continued development using the "engineered outer domain (eOD)" previously developed by Po-Ssu Huang in the Schief lab. Several iterative rounds of design and selection using a panel of germline antibodies produced a final, optimized immunogen - a construct they called eOD-GT6.
To get a better look at eOD-GT6 and its interaction with germline antibodies, the team turned to the laboratory of Ian Wilson, Chair of the Department of Integrative Structural and Computational Biology and a member of the IAVI NAC at TSRI.
Jean-Philippe Julien, a postdoc in the Wilson laboratory, determined the 3D atomic structure of the designed immunogen using x-ray crystallography - and, in an unusual feat, also determined the crystal structure of a germline VRC01 antibody, plus the structure of the immunogen and antibody bound together.
"We wanted to know whether eOD-GT6 looked the way we anticipated and whether it bound to the antibody in the way that we predicted - and in both cases the answer was yes," said Julien. "We also were able to identify the key mutations that conferred its reactivity with germline VRC01 antibodies."
Such an immunogen typically does better at stimulating an antibody response when it is presented not as a single copy but in a closely spaced cluster of multiple copies, and with only its antibody-binding end exposed. "We wanted it to look like a virus," said Sergey Menis, a visiting graduate student in the Schief laboratory.
Menis therefore devised a tiny virus-mimicking particle made from 60 copies of an obscure bacterial enzyme and coated it with 60 copies of eOD-GT6. The particle worked well at activating VRC01 germline B cells and even mature B cells in the lab dish, whereas single-copy eOD-GT6 did not.
"Essentially it's a self-assembling nanoparticle that presents the immunogen in a properly oriented way," Menis said. "We're hoping that this approach can be used not just for an HIV vaccine but for many other vaccines, too."
The next step for the eOD-GT6 immunogen project is to test its ability to stimulate an antibody response in lab animals that are themselves engineered to produce human germline antibodies. The team is collaborating with other researchers who are engineering mice to produce human germline antibodies, after which Schief hopes to learn how to derive the response, from activation of the germline B cells all the way to production of mature, broadly neutralizing VRC01-class antibodies, using a series of designed immunogens.
Schief also hopes they will be able to test their germline-targeting approach in humans sooner rather than later, noting "it will be really important to find out if this works in a human being."
The first authors of the paper, "Rational HIV immunogen design to target specific germline B cell receptors," were Jardine, Julien, and Menis. Co-authors were Takayuki Ota, Devin Sok, Travis Nieusma, John Mathison, Oleksandr Kalyuzhniy, Skye MacPherson, Po-Ssu Huang, David Baker, Andrew McGuire, Leonidas Stamatatos, David Nemazee, and Scripps CHAVI-ID principal investigators Andrew Ward, Ian Wilson, and Dennis Burton.
The project was partially funded by IAVI, NIH, and the Ragon Institute.