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Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors

Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors
Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors

Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy-chain complementarity-determining region 3 (HCDR3), suggesting that the rarity of bnAb precursors poses a challenge for vaccine priming. We created precursor sequence definitions for V2-apex HCDR3-dependent bnAbs and searched for related precursors in human antibody heavy-chain ultradeep sequencing data from 14 HIV-unexposed donors. We found potential precursors in a majority of donors for only two long-HCDR3 V2-apex bnAbs, PCT64 and PG9, identifying these bnAbs as priority vaccine targets. We then engineered ApexGT Env trimers that bound inferred germlines for PCT64 and PG9 and had higher affinities for bnAbs, determined cryo-EM structures of ApexGT trimers complexed with inferred-germline and bnAb forms of PCT64 and PG9, and developed an mRNA-encoded cell-surface ApexGT trimer. These methods and immunogens have promise to assist HIV vaccine development.

1097-4180
2149-2167.e9
Willis, Jordan R.
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Berndsen, Zachary T.
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Ma, Krystal M
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Steichen, Jon M.
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Schiffner, Torben
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Landais, Elise
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Liguori, Alessia
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Kalyuzhniy, Oleksandr
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Allen, Joel D
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Baboo, Sabyasachi
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Omorodion, Oluwarotimi
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Diedrich, Jolene K
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Hu, Xiaozhen
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Georgeson, Erik
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Phelps, Nicole
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Eskandarzadeh, Saman
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Groschel, Bettina
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Kubitz, Michael
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Adachi, Yumiko
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Mullin, Tina-Marie
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Alavi, Nushin B
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Falcone, Samantha
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Himansu, Sunny
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Carfi, Andrea
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Wilson, Ian A.
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Yates, John R.
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Paulson, James C.
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Crispin, Max
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Ward, Andrew B.
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Schief, William R.
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Willis, Jordan R.
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Berndsen, Zachary T.
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Ma, Krystal M
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Steichen, Jon M.
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Schiffner, Torben
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Landais, Elise
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Liguori, Alessia
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Kalyuzhniy, Oleksandr
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Allen, Joel D
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Baboo, Sabyasachi
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Omorodion, Oluwarotimi
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Diedrich, Jolene K
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Hu, Xiaozhen
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Georgeson, Erik
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Phelps, Nicole
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Eskandarzadeh, Saman
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Groschel, Bettina
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Kubitz, Michael
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Adachi, Yumiko
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Mullin, Tina-Marie
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Alavi, Nushin B
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Falcone, Samantha
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Himansu, Sunny
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Carfi, Andrea
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Wilson, Ian A.
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Yates, John R.
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Paulson, James C.
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Crispin, Max
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Ward, Andrew B.
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Schief, William R.
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Willis, Jordan R., Berndsen, Zachary T., Ma, Krystal M, Steichen, Jon M., Schiffner, Torben, Landais, Elise, Liguori, Alessia, Kalyuzhniy, Oleksandr, Allen, Joel D, Baboo, Sabyasachi, Omorodion, Oluwarotimi, Diedrich, Jolene K, Hu, Xiaozhen, Georgeson, Erik, Phelps, Nicole, Eskandarzadeh, Saman, Groschel, Bettina, Kubitz, Michael, Adachi, Yumiko, Mullin, Tina-Marie, Alavi, Nushin B, Falcone, Samantha, Himansu, Sunny, Carfi, Andrea, Wilson, Ian A., Yates, John R., Paulson, James C., Crispin, Max, Ward, Andrew B. and Schief, William R. (2022) Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors. Immunity, 55 (11), 2149-2167.e9. (doi:10.1016/j.immuni.2022.09.001).

Record type: Article

Abstract

Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy-chain complementarity-determining region 3 (HCDR3), suggesting that the rarity of bnAb precursors poses a challenge for vaccine priming. We created precursor sequence definitions for V2-apex HCDR3-dependent bnAbs and searched for related precursors in human antibody heavy-chain ultradeep sequencing data from 14 HIV-unexposed donors. We found potential precursors in a majority of donors for only two long-HCDR3 V2-apex bnAbs, PCT64 and PG9, identifying these bnAbs as priority vaccine targets. We then engineered ApexGT Env trimers that bound inferred germlines for PCT64 and PG9 and had higher affinities for bnAbs, determined cryo-EM structures of ApexGT trimers complexed with inferred-germline and bnAb forms of PCT64 and PG9, and developed an mRNA-encoded cell-surface ApexGT trimer. These methods and immunogens have promise to assist HIV vaccine development.

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Accepted/In Press date: 31 August 2022
e-pub ahead of print date: 29 September 2022
Published date: 8 November 2022
Additional Information: This work was supported by the IAVI Neutralizing Antibody Center through the Collaboration for AIDS Vaccine Discovery grants OPP1084519 , OPP1196345 / INV-008813 , OPP1147787 , and INV-034657 funded by the Bill and Melinda Gates Foundation (to M.C., I.A.W., A.B.W., and W.R.S.), National Institute of Allergy and Infectious Diseases ( NIAID ) UM1 Al100663 ( Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery), and UM1 AI144462 ( Scripps Consortium for HIV/AIDS Vaccine Development) (to I.A.W., A.B.W., and W.R.S.) and by the Ragon Institute of MGH, MIT, and Harvard (to W.R.S.). Funding Information: This work was supported by the IAVI Neutralizing Antibody Center through the Collaboration for AIDS Vaccine Discovery grants OPP1084519, OPP1196345/INV-008813, OPP1147787, and INV-034657 funded by the Bill and Melinda Gates Foundation (to M.C. I.A.W. A.B.W. and W.R.S.), National Institute of Allergy and Infectious Diseases (NIAID) UM1 Al100663 (Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery), and UM1 AI144462 (Scripps Consortium for HIV/AIDS Vaccine Development) (to I.A.W. A.B.W. and W.R.S.) and by the Ragon Institute of MGH, MIT, and Harvard (to W.R.S.). J.R.W. and K.M.M. designed ApexGT immunogens. Z.T.B. conducted EM studies. J.M.S. assisted ApexGT immunogen design and, with T.S. developed the MD39 gp151 immunogen platform. J.R.W. wrote bioinformatic applications and conducted precursor frequency analysis. E.L. provided information about the PCT64 lineage prior to its original publication. A.L. conducted ELISA studies. O.K. conducted surface plasmon resonance (SPR) studies. J.D.A. S.B. and J.K.D. conducted mass-spec glycan profiling studies. O.O. solved the crystal structure of apo PCT64 LMCA. X.H. conducted differential scanning calorimetry (DSC) and size-exclusion chromatography with multi-angle light scattering (SECMALS) studies. S.E. and K.M.M. conducted the cell surface antigenic profiling studies. E.G. N.P. S.E. M.K. Y.A. T.-M.M. and N.B.A. produced all proteins, antibodies, and Fabs for all reported studies. B.G. supervised reagent production. S.F. S.H. and A.C. provided mRNA. I.A.W. supervised crystal structure determination. J.R.Y. J.C.P. and M.C. supervised glycan profiling. A.B.W. supervised ns- and cryo-EM studies. W.R.S. conceived the studies with J.R.W. K.M.M. and J.M.S. and W.R.S. supervised the studies. J.R.W. Z.T.B. and W.R.S. wrote the paper. K.M.M. J.M.S. S.H. A.C. and A.B.W. helped write the paper. J.R.W. K.M.M. J.M.S. and W.R.S. are named inventors on patent applications filed by Scripps and IAVI regarding ApexGT immunogens in this manuscript. Publisher Copyright: © 2022 The Author(s)

Identifiers

Local EPrints ID: 472336
URI: http://eprints.soton.ac.uk/id/eprint/472336
ISSN: 1097-4180
PURE UUID: 4530aab9-fe13-4cb4-bf56-e75bde8e7c4e
ORCID for Joel D Allen: ORCID iD orcid.org/0000-0003-2547-968X
ORCID for Max Crispin: ORCID iD orcid.org/0000-0002-1072-2694

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Date deposited: 01 Dec 2022 17:49
Last modified: 02 May 2024 02:00

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Contributors

Author: Jordan R. Willis
Author: Zachary T. Berndsen
Author: Krystal M Ma
Author: Jon M. Steichen
Author: Torben Schiffner
Author: Elise Landais
Author: Alessia Liguori
Author: Oleksandr Kalyuzhniy
Author: Joel D Allen ORCID iD
Author: Sabyasachi Baboo
Author: Oluwarotimi Omorodion
Author: Jolene K Diedrich
Author: Xiaozhen Hu
Author: Erik Georgeson
Author: Nicole Phelps
Author: Saman Eskandarzadeh
Author: Bettina Groschel
Author: Michael Kubitz
Author: Yumiko Adachi
Author: Tina-Marie Mullin
Author: Nushin B Alavi
Author: Samantha Falcone
Author: Sunny Himansu
Author: Andrea Carfi
Author: Ian A. Wilson
Author: John R. Yates
Author: James C. Paulson
Author: Max Crispin ORCID iD
Author: Andrew B. Ward
Author: William R. Schief

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