Quashing human immunodeficiency virus (HIV) at its roots is a big job. The virus has many strains, and each one must be neutralized to prevent infection. People already infected with HIV may naturally generate antibodies against most strains of HIV, called broadly neutralizing antibodies (bNAbs), but they are extremely rare.  While scientists have searched for ways to induce bNAbs by vaccination, they have had little success.

Now, using the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory, a team has stimulated the production of bNAb-like antibodies by targeting naïve B cells with a modified HIV-like “spike” protein, an approach known as germline targeting. Taking an iterative approach to designing boosters, their research lays the groundwork for a vaccine regimen that may prevent HIV infection. The work was published in Cell Reports Medicine.

Our bodies fight infection by producing antibodies that block or destroy foreign substances, such as viruses. Antibodies are produced in certain types of B cells. A B cell that hasn’t encountered a virus (or other pathogen), either through infection or vaccination, is called naïve. Once it meets a virus, the B cell undergoes genetic changes to produce an antibody with the correct shape and atomic composition to neutralize the virus. These are called mature B cells.

HIV replicates very rapidly, with each replication yielding new mutations and, hence, new strains. A few rare B cells in people infected with HIV acquire huge numbers of insertions and deletions in their DNA as they mutate in response to the constantly changing virus. These are bNAbs, whose genetic changes give them the breadth and potency to neutralize most, if not all, HIV strains. 

Scientists have sought to induce bNAbs by targeting naïve B cells with bits of HIV-like virus, a process called germline targeting. Most attempts to date have failed, largely for two reasons—they don’t target the right B cells, and they use an unmodified HIV-like protein. The current research overcomes both of these problems. 

The researchers employed a two-pronged strategy. First, to increase the detection sensitivity of their testing platform, they engineered ‘knock-in’ mice to have an increased number of specialized “precursor” bNAb B cells (normally exceedingly rare in human repertoires and even more infrequent or nonexistent in other, nongenetically modified test animal models). These highly infrequent precursor bNAb B cells have broad HIV virus-recognizing potential that only materializes upon acquiring rare point mutations or insertions in their coding regions, something a successful germline-based vaccine would need to induce. 

Second, to better recognize and activate such rare B cell precursors, the researchers also modified the virus’s binding site, inserting it into a novel trimer structure that imitated the virus’s natural spike more faithfully than prior germline-targeting immunogens. By improving both the sensitivity of the animal model readouts and the vaccine immunogen’s ability to recognize naïve precursor bNAb B cells, they increased their chances of developing a successful bNAb-inducing, trimer-based vaccine regimen. 

Here begins the iterative—and time-consuming—aspect of their research. Scientists at one lab immunized the knock-in mice with the modified trimer, then sent the blood serum halfway across the world to scientists at another lab, who designed a booster vaccine based on analysis of the serum. Each repeat of the process further matured the B cells along the path toward becoming bNAb-producing cells. 

To confirm that their approach had worked, the team determined the crystal structure of the B cell receptor on a naïve B cell tightly bound to the modified HIV trimer at 3.80A resolution. Data were collected on beamline 23-ID-D at the APS and revealed that the rare insertions and deletions engendered in the B cells by the scientists’ vaccine regimen played a major role in the antibodies’ ability to bind and neutralize the virus. 

The scientists consider their work proof of concept that a sequential immunization regimen based on iterative serum analysis can elicit mature antibodies with sufficient potency and breadth to neutralize the HIV virus. A viable vaccine regimen is still a long way off; the biology of a constantly mutating virus and a responsive antibody is incredibly complex, and the iterative process of designing boosters based on previous responses is time-consuming and unlikely to receive quick approval from the FDA.

Now that they’ve developed a promising regimen, the scientists are deconstructing it to ascertain where it can be simplified. Can the genetic insertions be generated after the first boost—maybe even the first shot? Could they further streamline the regimen with mRNA or other cutting-edge/emerging vaccine delivery platforms, or improve its overall potency and breadth using more potent adjuvants and/or other novel B-cell immuno-modulatory concepts?

In addition to searching for the answers to these questions, the scientists are now designing a germline vaccine regimen for another problematic, diverse pathogen: hepatitis C. And their HIV research has already been put to use: modifications they made to the virus binding site are now being used for AI-assisted immunogen design.  – Judy Myers

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See: T. G. Caniels¹, M. Medina-Ramirez¹, J. Zhang², A. Sarkar³, S. Kumar³, A. LaBranche², R. Derking¹, J. D. Allen⁴, J. L. Snitselaar¹, J. Capella-Pujol¹, I. Del Moral Sanchez¹, A. Yasmeen⁵, M. Diaz², Y. Aldon¹, T. P. L. Bijl¹, S. Venkatayogi⁶, J. S. M. Beem⁶, A. Newman⁶, C. Jiang⁵, W-H Lee³, M. Pater¹, J. A. Burger¹, M. J. Van Breemen¹, S. W. de Taeye¹, K. Rantalainen³, C. LaBranche⁶, K. O. Saunders⁶, D. Montefiori⁶, G. Ozorowski³, A. B. Ward³, M. Crispin⁴, J. P. Moore⁵, P. J. Klasse⁵, B. F. Haynes⁶, I. A. Wilson³, K. Wiehe⁶, L. Verkoczy², R. W. Sanders¹, “Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions” Cell Rep Med 4(4) 101113 (2023)

Author affiliations: ¹University of Amsterdam; ²Applied Biomedical Science Institute; ³Scripps Research Institute; ⁴University of Southampton; ⁵Cornell University; ⁶Duke University

We are grateful to the staff of Advanced Photon Source BL 23-ID-D for assistance. GM/CA@APS has been funded by the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006, P30GM138396). This research used resources of the Advanced Photon Sciences under contract no. DE-AC02-06CH11357. This work is supported by the Netherlands Organisation for Scientific Research (N.W.O.) Vici grant (R.W.S.); Bill & Melinda Gates Foundation, Collaboration for AIDS Vaccine Discovery (C.A.V.D.) grants INV-002022 (R.W.S.) and OPP1115782/INV-002916 (A.B.W.); Fondation Dormeur, Vaduz (R.W.S.); and grants from the NIAID, Division of AIDS, NIH UM1 grants for the Duke Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery (CHAVI-ID; UM1530AI100645 and Consortia for HIV/AIDS Vaccine Development [CHAVD]) UM1AI144371 to B.F.H. and R01 grant AI087202 (L.K.V.). P.J.K. and J.P.M. are supported by R01 AI036082 and A.B.W., I.A.W., R.W.S., P.J.K., and J.P.M. are supported by a HIVRAD P01 AI110657 grant. M.C. is funded by the International AIDS Vaccine Initiative (IAVI) through grant INV-008352 and the Bill & Melinda Gates Foundation OPP1153692. Funding for the neutralization assays was provided by NIH/NIAID contract #HHSN272201800004C.

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