[Source: Science, full page: (LINK). Abstract, edited.]
A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses
Jon M. Steichen1,2,3,*, Ying-Cing Lin4,*, Colin Havenar-Daughton3,5,*, Simone Pecetta4,*, Gabriel Ozorowski2,3,6,*, Jordan R. Willis1,2,3,*, Laura Toy3,5, Devin Sok1,2,3, Alessia Liguori1,2,3, Sven Kratochvil4, Jonathan L. Torres2,3,6, Oleksandr Kalyuzhniy1,2,3, Eleonora Melzi4, Daniel W. Kulp1,2,3,7, Sebastian Raemisch1,2,3, Xiaozhen Hu1,2,3, Steffen M. Bernard2,3,6, Erik Georgeson1,2,3, Nicole Phelps1,2,3, Yumiko Adachi1,2,3, Michael Kubitz1,2,3, Elise Landais1,2,3, Jeffrey Umotoy1,2,3, Amanda Robinson1,2,3, Bryan Briney1,2,3,8, Ian A. Wilson2,3,6,9, Dennis R. Burton1,2,3, Andrew B. Ward2,3,6, Shane Crotty3,5,10,†, Facundo D. Batista4,11,†, William R. Schief1,2,3,4,†
1 Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA. 2 IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. 3 Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA. 4 The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA. 5 Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA. 6 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. 7 Vaccine and Immune Therapy Center, The Wistar Institute, Philadelphia, PA 19104, USA. 8 Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. 9 Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. 10 Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA. 11 Department of Immunology, Harvard Medical School, Boston, MA 02115, USA.
†Corresponding author. Email: email@example.com (W.R.S.); firstname.lastname@example.org (F.D.B.); email@example.com (S.C.)
* These authors contributed equally to this work.
Science 06 Dec 2019: Vol. 366, Issue 6470, eaax4380 / DOI: 10.1126/science.aax4380
Engineering better bnAbs
A highly effective HIV vaccine has been the goal of vaccinologists for nearly 35 years. A successful vaccine would need to induce broadly neutralizing antibodies (bnAbs) that are capable of neutralizing multiple HIV strains (see the Perspective by Agazio and Torres). Steichen et al. report a strategy in which the first vaccine shot can lead to immune responses that generate desired bnAbs. By combining knowledge of human antibody repertoires and structure to guide design, they validated candidate immunogens through functional preclinical testing. Saunders et al. designed immunogens with differences in binding strength for bnAb precursors, which enabled selection of rare mutations after immunization. The immunogens promoted bnAb precursor maturation in humanized mice and macaques.
Science, this issue p. eaax4380, p. eaay7199; see also p. 1197
HIV newly infects 1.8 million people each year, making development of an HIV vaccine a global health priority. Nearly all licensed vaccines protect by inducing antibodies, but highly variable pathogens such as HIV and influenza virus have eluded traditional vaccine strategies. The discoveries of broadly neutralizing antibodies (bnAbs) that bind to conserved epitopes on the surface proteins of these viruses have inspired vaccine design strategies to induce bnAbs. Antibodies are produced by B cells, and highly effective antibodies like bnAbs acquire affinity-enhancing mutations when a bnAb-precursor B cell mutates and matures from the original naïve B cell (or germline) state. Among several new vaccine strategies, germline-targeting vaccine design aims to induce bnAbs by first stimulating bnAb-precursor B cells and then shepherding B cell affinity maturation with a series of rationally designed boosting immunogens. A key rationale for this strategy is that germline-reverted forms of bnAbs—precursors with all recognizable amino acid mutations reverted to germline—typically have no detectable affinity for HIV envelope (Env). Thus, for a vaccine to initiate bnAb induction, a germline-targeting priming immunogen with appreciable affinity for bnAb precursors must be engineered.
Most HIV bnAbs (and most antibodies to any pathogen) bind to their target by using their heavy chain complementarity-determining region 3 (HCDR3) as a major binding determinant. Hence, an optimal HIV vaccine that induces multiple bnAbs, and a general solution to germline-targeting vaccine design that could be applied broadly to other pathogens, will need to work with HCDR3-dependent antibodies. However, the need to design germline-targeting immunogens to initiate HCDR3-dependent bnAb responses faces major technical challenges. Although each B cell expresses a single unique antibody, different B cells produce diverse antibodies encoded by different combinations of antibody genes, with the greatest antibody genetic diversity encoded in the HCDR3 portion of the molecule. The exceptional diversity in the human B cell repertoire makes any single HCDR3 sequence an impractical vaccine target. Rather, a pool of precursors sharing a set of bnAb-associated genetic features must be identified and targeted. Thus, owing to the enormous diversity of human antibodies, a germline-targeting immunogen should have affinity for diverse bnAb precursors in order to succeed in diverse vaccine recipients.
Herein we report a solution to the above challenges. Using the strongly HCDR3-dependent bnAb BG18 that binds a conserved site on HIV Env as a high-value target and a proof of principle, we demonstrate a method to identify pools of potential bnAb precursors in an ultradeep human antibody sequence database, guided by key genetic features that enable bnAb structural recognition of the antigen. We then use a representative set of those potential bnAb precursors as design targets to guide our engineering of HIV Env immunogens that bind to diverse potential bnAb precursors. Lastly, we provide critical preclinical validation of immunogen design by assessing these immunogens for (i) their ability to select rare potential bnAb-precursor naïve B cells from the blood of healthy human donors, (ii) their modes of binding to bnAb precursors, and (iii) their capacity to prime rare bnAb-precursor B cells with physiologically relevant affinities in a mouse model.
Overall, we demonstrate a new approach to defining diverse precursors for a target antibody and designing vaccine immunogens that take advantage of that information. The approach lays out a generalizable pathway for the development and preclinical validation of germline-targeting immunogens to stimulate precursors for HCDR3-dependent antibodies.
Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer–based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens.
Keywords: HIV/AIDS; Vaccines.