CD4 binding site immunogens elicit heterologous anti–HIV-1 neutralizing antibodies in transgenic and wild-type animals

Creators: Gristick, Harry B.; Hartweger, Harald; Loewe, Maximilian; van Schooten, Jelle; Ramos, Victor; Oliveira, Thiago Y.; Nishimura, Yoshiaki; Koranda, Nicholas S.; Wall, Abigail; Yao, Kai-Hui; Poston, Daniel; Gazumyan, Anna; Wiatr, Marie; Horning, Marcel; Keeffe, Jennifer R.; Hoffmann, Magnus A. G.; Yang, Zhi; Abernathy, Morgan E.; Dam, Kim-Marie A.; Gao, Han; Gnanapragasam, Priyanthi N. P.; Kakutani, Leesa M.; Pavlovitch-Bedzyk, Ana Jimena; Seaman, Michael S.; Howarth, Mark; McGuire, Andrew T.; Stamatatos, Leonidas; Martin, Malcolm A.; West, Anthony P., Jr.; Nussenzweig, Michel C.; Bjorkman, Pamela J.¹

1. California Institute of Technology

Abstract

Passive transfer of broadly neutralizing anti–HIV-1 antibodies (bNAbs) protects against infection, and therefore, eliciting bNAbs by vaccination is a major goal of HIV-1 vaccine efforts. bNAbs that target the CD4 binding site (CD4bs) on HIV-1 Env are among the most broadly active, but to date, responses elicited against this epitope in vaccinated animals have lacked potency and breadth. We hypothesized that CD4bs bNAbs resembling the antibody IOMA might be easier to elicit than other CD4bs antibodies that exhibit higher somatic mutation rates, a difficult-to-achieve mechanism to accommodate Env's N276 gp120 N-glycan, and rare five-residue light chain complementarity-determining region 3. As an initial test of this idea, we developed IOMA germline–targeting Env immunogens and evaluated a sequential immunization regimen in transgenic mice expressing germline-reverted IOMA. These mice developed CD4bs epitope–specific responses with heterologous neutralization, and cloned antibodies overcame neutralization roadblocks, including accommodating the N276_(gp120) glycan, with some neutralizing selected HIV-1 strains more potently than IOMA. The immunization regimen also elicited CD4bs-specific responses in mice containing polyclonal antibody repertoires as well as rabbits and rhesus macaques. Thus, germline targeting of IOMA-class antibody precursors represents a potential vaccine strategy to induce CD4bs bNAbs.

Additional Information

© 2023 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. We thank J. Moore (Weill Cornell Medical College), R.W. Sanders, and M.J. van Gils (Amsterdam UMC) for SOSIP expression plasmids; M. Silva, M. B. Melo, and D. J. Irvine (MIT) for providing the SMNP adjuvant; L. von Boehmer (Stanford University) for discussion; J. Vielmetter, P. Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance; T. Eisenreich and S. Tittley for animal husbandry; and K. Gordon and K. Chosphel for FACS at Rockefeller University. EM was performed in the Caltech Cryo-EM Center with assistance from S. Chen and A. Malyutin. This work was supported by the NIAID grants HIVRAD P01 AI100148 (to P.J.B. and M.C.N.), HIVRAD P01 AI138212 (to L.S., A.T.M., and M.C.N.), and R21 AI127249 (to A.T.M.); the Bill and Melinda Gates Foundation CAVD grant INV-002143 (to P.J.B., M.C.N., and M.A.M.); a Bill and Melinda Gates Foundation grant # OPP1146996 (to M.S.S.); the Intramural Research Program of the NIAID (to M.A.M. and Y.N.); and NIH P50 AI150464 (to P.J.B.). M.E.A. was supported by a NSF Graduate Research Fellowship. Author contributions: H.B.G., H.H., A.P.W., M.C.N., M.A.M., and P.J.B. conceived the experiments. H.B.G. and H.H. designed and performed all experiments with assistance from other authors. M.L. assisted with Ab cloning. J.v.S. set up the yeast libraries and helped develop the original IGT variants, and M.E.A. and A.J.P.-B. assisted in developing the later IGT variants. V.R. and T.Y.O. performed computational analysis of the Ab sequencing data. Y.N. performed the rhesus macaque experiments. N.S.K. and H.G. performed cloning and purification of antigens and Abs. A.W., A.T.M., and L.S. generated the anti-idiotypic Abs. K.-H.Y. assisted with the mouse experiments, D.P. assisted with IOMAgl mouse generation, A.G. helped with the recombinant Ab production, and M.W. and M. Horning assisted with mouse experiments and cell sorting. J.R.K. provided project administration, M.A.G.H., P.N.P.G., and L.M.K. performed neutralization assays, Z.Y. performed the EM experiments, and K.-M.A.D. helped in understanding IOMA-like Ab clones isolated from transgenic mice. M.S.S. helped with recombinant Ab neutralization assays. M. Howarth assisted with nanoparticle conjugations. The paper was written by H.B.G., H.H., P.J.B., M.C.N., and M.A.M. with assistance from other authors. Data and materials availability: The structure of IOMA iGL Fab is available in the Protein Data Bank under accession code 7TQG. 10x Genomics V(D)J sequencing data are available from Gene Expression Omnibus accession number GSE197951. All other data, mice, and reagents used in this study are available from the corresponding authors upon reasonable request. Ab HC and LC genes were analyzed using our previously described IgPipeline (96, 97). The code for the IgPipeline is available at https://github.com/stratust/igpipeline/tree/igpipeline2_timepoint_v2. This article is subject to HHMI's Open Access to Publications policy. HHMI laboratory heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication. Under the grant conditions of the Bill and Melinda Gates Foundation Collaboration, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. Further information and reasonable requests for reagents and resources should be directed to P.J.B. (bjorkman@caltech.edu). Competing interests: M.C.N. is an HHMI investigator. H.B.G., P.J.B., H.H., and M.C.N. are coinventors on a patent (CIT 8845-P) covering IGT immunogens. P.J.B. is on the Scientific Advisory Board of Vir Biotechnology. M.C.N is on the Scientific Advisory Board of Celdex, Fronteir Bio, Areium Therapeutics, and Apriori Bio. M. Howarth is an inventor on patents on spontaneous amide bond formation (EP2534484) and SpyTag003:SpyCatcher003 (WO/2020/183198) and is a cofounder, shareholder, and former consultant of SpyBiotech. All other authors declare that they have no competing interests. Data and materials availability: The structure of IOMA iGL Fab is available in the Protein Data Bank under accession code 7TQG. 10x Genomics V(D)J sequencing data are available from Gene Expression Omnibus accession number GSE197951. All other data, mice, and reagents used in this study are available from the corresponding authors upon reasonable request. Ab HC and LC genes were analyzed using our previously described IgPipeline (96, 97). The code for the IgPipeline is available at https://github.com/stratust/igpipeline/tree/igpipeline2_timepoint_v2. This article is subject to HHMI's Open Access to Publications policy. HHMI laboratory heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication. Under the grant conditions of the Bill and Melinda Gates Foundation Collaboration, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. Further information and reasonable requests for reagents and resources should be directed to P.J.B. (bjorkman@caltech.edu).

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