IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37742-z.html
   My bibliography  Save this article

Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimers as HIV-1 vaccine candidates

Author

Listed:
  • Yi-Nan Zhang

    (The Scripps Research Institute)

  • Jennifer Paynter

    (The Scripps Research Institute)

  • Aleksandar Antanasijevic

    (The Scripps Research Institute
    The Scripps Research Institute)

  • Joel D. Allen

    (University of Southampton)

  • Mor Eldad

    (The Scripps Research Institute)

  • Yi-Zong Lee

    (The Scripps Research Institute)

  • Jeffrey Copps

    (The Scripps Research Institute
    The Scripps Research Institute)

  • Maddy L. Newby

    (University of Southampton)

  • Linling He

    (The Scripps Research Institute)

  • Deborah Chavez

    (Texas Biomedical Research Institute)

  • Pat Frost

    (Texas Biomedical Research Institute)

  • Anna Goodroe

    (Texas Biomedical Research Institute)

  • John Dutton

    (Texas Biomedical Research Institute)

  • Robert Lanford

    (Texas Biomedical Research Institute)

  • Christopher Chen

    (Texas Biomedical Research Institute)

  • Ian A. Wilson

    (The Scripps Research Institute
    The Scripps Research Institute
    The Scripps Research Institute)

  • Max Crispin

    (University of Southampton)

  • Andrew B. Ward

    (The Scripps Research Institute
    The Scripps Research Institute)

  • Jiang Zhu

    (The Scripps Research Institute
    The Scripps Research Institute)

Abstract

Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.

Suggested Citation

  • Yi-Nan Zhang & Jennifer Paynter & Aleksandar Antanasijevic & Joel D. Allen & Mor Eldad & Yi-Zong Lee & Jeffrey Copps & Maddy L. Newby & Linling He & Deborah Chavez & Pat Frost & Anna Goodroe & John Du, 2023. "Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimers as HIV-1 vaccine candidates," Nature Communications, Nature, vol. 14(1), pages 1-29, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37742-z
    DOI: 10.1038/s41467-023-37742-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37742-z
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-37742-z?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Ziyang Xu & Susanne Walker & Megan C. Wise & Neethu Chokkalingam & Mansi Purwar & Alan Moore & Edgar Tello-Ruiz & Yuanhan Wu & Sonali Majumdar & Kylie M. Konrath & Abhijeet Kulkarni & Nicholas J. Turs, 2022. "Induction of tier-2 neutralizing antibodies in mice with a DNA-encoded HIV envelope native like trimer," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Yang Hsia & Jacob B. Bale & Shane Gonen & Dan Shi & William Sheffler & Kimberly K. Fong & Una Nattermann & Chunfu Xu & Po-Ssu Huang & Rashmi Ravichandran & Sue Yi & Trisha N. Davis & Tamir Gonen & Nei, 2016. "Design of a hyperstable 60-subunit protein icosahedron," Nature, Nature, vol. 535(7610), pages 136-139, July.
    3. Leopold Kong & Linling He & Natalia de Val & Nemil Vora & Charles D. Morris & Parisa Azadnia & Devin Sok & Bin Zhou & Dennis R. Burton & Andrew B. Ward & Ian A. Wilson & Jiang Zhu, 2016. "Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability," Nature Communications, Nature, vol. 7(1), pages 1-15, November.
    4. Christopher N. Scanlan & John Offer & Nicole Zitzmann & Raymond A. Dwek, 2007. "Exploiting the defensive sugars of HIV-1 for drug and vaccine design," Nature, Nature, vol. 446(7139), pages 1038-1045, April.
    5. Aleksandar Antanasijevic & Leigh M. Sewall & Christopher A. Cottrell & Diane G. Carnathan & Luis E. Jimenez & Julia T. Ngo & Jennifer B. Silverman & Bettina Groschel & Erik Georgeson & Jinal Bhiman & , 2021. "Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    6. Liwei Cao & Matthias Pauthner & Raiees Andrabi & Kimmo Rantalainen & Zachary Berndsen & Jolene K. Diedrich & Sergey Menis & Devin Sok & Raiza Bastidas & Sung-Kyu Robin Park & Claire M. Delahunty & Lin, 2018. "Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    7. Linling He & Anshul Chaudhary & Xiaohe Lin & Cindy Sou & Tanwee Alkutkar & Sonu Kumar & Timothy Ngo & Ezra Kosviner & Gabriel Ozorowski & Robyn L. Stanfield & Andrew B. Ward & Ian A. Wilson & Jiang Zh, 2021. "Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    8. Daniel W. Kulp & Jon M. Steichen & Matthias Pauthner & Xiaozhen Hu & Torben Schiffner & Alessia Liguori & Christopher A. Cottrell & Colin Havenar-Daughton & Gabriel Ozorowski & Erik Georgeson & Oleksa, 2017. "Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding," Nature Communications, Nature, vol. 8(1), pages 1-14, December.
    9. Serban L. Ilca & Abhay Kotecha & Xiaoyu Sun & Minna M. Poranen & David I. Stuart & Juha T. Huiskonen, 2015. "Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes," Nature Communications, Nature, vol. 6(1), pages 1-8, December.
    10. Rory Henderson & Maolin Lu & Ye Zhou & Zekun Mu & Robert Parks & Qifeng Han & Allen L. Hsu & Elizabeth Carter & Scott C. Blanchard & R J Edwards & Kevin Wiehe & Kevin O. Saunders & Mario J. Borgnia & , 2020. "Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    11. Kwinten Sliepen & Byung Woo Han & Ilja Bontjer & Petra Mooij & Fernando Garces & Anna-Janina Behrens & Kimmo Rantalainen & Sonu Kumar & Anita Sarkar & Philip J. M. Brouwer & Yuanzi Hua & Monica Tolazz, 2019. "Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
    12. Jinghe Huang & Byong H. Kang & Marie Pancera & Jeong Hyun Lee & Tommy Tong & Yu Feng & Hiromi Imamichi & Ivelin S. Georgiev & Gwo-Yu Chuang & Aliaksandr Druz & Nicole A. Doria-Rose & Leo Laub & Kwinte, 2014. "Broad and potent HIV-1 neutralization by a human antibody that binds the gp41–gp120 interface," Nature, Nature, vol. 515(7525), pages 138-142, November.
    13. Xiping Wei & Julie M. Decker & Shuyi Wang & Huxiong Hui & John C. Kappes & Xiaoyun Wu & Jesus F. Salazar-Gonzalez & Maria G. Salazar & J. Michael Kilby & Michael S. Saag & Natalia L. Komarova & Martin, 2003. "Antibody neutralization and escape by HIV-1," Nature, Nature, vol. 422(6929), pages 307-312, March.
    14. Linling He & Natalia de Val & Charles D. Morris & Nemil Vora & Therese C. Thinnes & Leopold Kong & Parisa Azadnia & Devin Sok & Bin Zhou & Dennis R. Burton & Ian A Wilson & David Nemazee & Andrew B. W, 2016. "Presenting native-like trimeric HIV-1 antigens with self-assembling nanoparticles," Nature Communications, Nature, vol. 7(1), pages 1-15, November.
    15. Marie Pancera & Tongqing Zhou & Aliaksandr Druz & Ivelin S. Georgiev & Cinque Soto & Jason Gorman & Jinghe Huang & Priyamvada Acharya & Gwo-Yu Chuang & Gilad Ofek & Guillaume B. E. Stewart-Jones & Jon, 2014. "Structure and immune recognition of trimeric pre-fusion HIV-1 Env," Nature, Nature, vol. 514(7523), pages 455-461, October.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Jun Niu & Qi Wang & Wenwen Zhao & Bing Meng & Youwei Xu & Xianfang Zhang & Yi Feng & Qilian Qi & Yanling Hao & Xuan Zhang & Ying Liu & Jiangchao Xiang & Yiming Shao & Bei Yang, 2023. "Structures and immune recognition of Env trimers from two Asia prevalent HIV-1 CRFs," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    2. Kun-Wei Chan & Christina C. Luo & Hong Lu & Xueling Wu & Xiang-Peng Kong, 2021. "A site of vulnerability at V3 crown defined by HIV-1 bNAb M4008_N1," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. Annemart Koornneef & Kanika Vanshylla & Gijs Hardenberg & Lucy Rutten & Nika M. Strokappe & Jeroen Tolboom & Jessica Vreugdenhil & Karin Feddes-de Boer & Aditya Perkasa & Sven Blokland & Judith A. Bur, 2024. "CoPoP liposomes displaying stabilized clade C HIV-1 Env elicit tier 2 multiclade neutralization in rabbits," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    4. Wayne Delport & Konrad Scheffler & Cathal Seoighe, 2008. "Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1," PLOS Pathogens, Public Library of Science, vol. 4(12), pages 1-13, December.
    5. Dan Fu & Wenming Wang & Yan Zhang & Fan Zhang & Pinyi Yang & Chun Yang & Yufei Tian & Renqi Yao & Jingwu Jian & Zixian Sun & Nan Zhang & Zhiyu Ni & Zihe Rao & Lei Zhao & Yu Guo, 2024. "Self-assembling nanoparticle engineered from the ferritinophagy complex as a rabies virus vaccine candidate," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    6. Daniel Ellis & Julia Lederhofer & Oliver J. Acton & Yaroslav Tsybovsky & Sally Kephart & Christina Yap & Rebecca A. Gillespie & Adrian Creanga & Audrey Olshefsky & Tyler Stephens & Deleah Pettie & Mic, 2022. "Structure-based design of stabilized recombinant influenza neuraminidase tetramers," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    7. Ziyang Xu & Susanne Walker & Megan C. Wise & Neethu Chokkalingam & Mansi Purwar & Alan Moore & Edgar Tello-Ruiz & Yuanhan Wu & Sonali Majumdar & Kylie M. Konrath & Abhijeet Kulkarni & Nicholas J. Turs, 2022. "Induction of tier-2 neutralizing antibodies in mice with a DNA-encoded HIV envelope native like trimer," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    8. Ching-Lin Hsieh & Sarah R. Leist & Emily Happy Miller & Ling Zhou & John M. Powers & Alexandra L. Tse & Albert Wang & Ande West & Mark R. Zweigart & Jonathan C. Schisler & Rohit K. Jangra & Kartik Cha, 2024. "Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Zhi Yang & Kim-Marie A. Dam & Michael D. Bridges & Magnus A. G. Hoffmann & Andrew T. DeLaitsch & Harry B. Gristick & Amelia Escolano & Rajeev Gautam & Malcolm A. Martin & Michel C. Nussenzweig & Wayne, 2022. "Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    10. Ignacio Fernández & Lasse Toftdal Dynesen & Youna Coquin & Riccardo Pederzoli & Delphine Brun & Ahmed Haouz & Antoine Gessain & Félix A. Rey & Florence Buseyne & Marija Backovic, 2023. "The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    11. Mathilde Foglierini & Pauline Nortier & Rachel Schelling & Rahel R. Winiger & Philippe Jacquet & Sijy O’Dell & Davide Demurtas & Maxmillian Mpina & Omar Lweno & Yannick D. Muller & Constantinos Petrov, 2024. "RAIN: machine learning-based identification for HIV-1 bNAbs," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    12. Mallory L. Myers & John R. Gallagher & Alexander J. Kim & Walker H. Payne & Samantha Maldonado-Puga & Haralabos Assimakopoulos & Kevin W. Bock & Udana Torian & Ian N. Moore & Audray K. Harris, 2023. "Commercial influenza vaccines vary in HA-complex structure and in induction of cross-reactive HA antibodies," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    13. Svenja Weiss & Vincenza Itri & Ruimin Pan & Xunqing Jiang & Christina C. Luo & Lynn Morris & Delphine C. Malherbe & Philip Barnette & Jeff Alexander & Xiang-Peng Kong & Nancy L. Haigwood & Ann J. Hess, 2022. "Differential V2-directed antibody responses in non-human primates infected with SHIVs or immunized with diverse HIV vaccines," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    14. Fenglin Li & Chun-Feng David Hou & Ravi K. Lokareddy & Ruoyu Yang & Francesca Forti & Federica Briani & Gino Cingolani, 2023. "High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    15. Guosong Wang & Zhenghui Zha & Pengfei Huang & Hui Sun & Yang Huang & Maozhou He & Tian Chen & Lina Lin & Zhenqin Chen & Zhibo Kong & Yuqiong Que & Tingting Li & Ying Gu & Hai Yu & Jun Zhang & Qingbing, 2022. "Structures of pseudorabies virus capsids," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    16. Charles Bayly-Jones & Christopher J. Lupton & Claudia Fritz & Hariprasad Venugopal & Daniel Ramsbeck & Michael Wermann & Christian Jäger & Alex Marco & Stephan Schilling & Dagmar Schlenzig & James C. , 2022. "Helical ultrastructure of the metalloprotease meprin α in complex with a small molecule inhibitor," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    17. Hongjun Bai & Eric Lewitus & Yifan Li & Paul V. Thomas & Michelle Zemil & Mélanie Merbah & Caroline E. Peterson & Thujitha Thuraisamy & Phyllis A. Rees & Agnes Hajduczki & Vincent Dussupt & Bonnie Sli, 2024. "Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    18. Mao Hori & Angela Steinauer & Stephan Tetter & Jamiro Hälg & Eva-Maria Manz & Donald Hilvert, 2024. "Stimulus-responsive assembly of nonviral nucleocapsids," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    19. Shuang Yang & Giorgos Hiotis & Yi Wang & Junjian Chen & Jia-huai Wang & Mikyung Kim & Ellis L. Reinherz & Thomas Walz, 2022. "Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    20. Jeffrey E. Harris, 2021. "The Repeated Setbacks of HIV Vaccine Development Laid the Groundwork for SARS-CoV-2 Vaccines," NBER Working Papers 28587, National Bureau of Economic Research, Inc.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37742-z. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.