1
|
Klenchin VA, Clark NM, Keles NK, Capuano S, Mason R, Gao G, Broman A, Kose E, Immonen TT, Fennessey CM, Keele BF, Lifson JD, Roederer M, Gardner MR, Evans DT. Adeno-associated viral delivery of Env-specific antibodies prevents SIV rebound after discontinuing antiretroviral therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.593694. [PMID: 38895320 PMCID: PMC11185534 DOI: 10.1101/2024.05.30.593694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
An alternative to lifelong antiretroviral therapy (ART) is needed to achieve durable control of HIV-1. Here we show that adeno-associated virus (AAV)-delivery of two rhesus macaque antibodies to the SIV envelope glycoprotein (Env) with potent neutralization and antibody-dependent cellular cytotoxicity can prevent viral rebound in macaques infected with barcoded SIVmac239M after discontinuing suppressive ART. Following AAV administration, sustained antibody expression with minimal anti-drug antibody responses was achieved in all but one animal. After ART withdrawal, SIV replication rebounded within two weeks in all of the control animals but remained below the threshold of detection in plasma (<15 copies/mL) for more than a year in four of the eight animals that received AAV vectors encoding Env-specific antibodies. Viral sequences from animals with delayed rebound exhibited restricted barcode diversity and antibody escape. Thus, sustained expression of antibodies with potent antiviral activity can afford durable, ART-free containment of pathogenic SIV infection.
Collapse
Affiliation(s)
- Vadim A. Klenchin
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, 53705, USA
| | - Natasha M. Clark
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, 53705, USA
| | - Nida K. Keles
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, 53705, USA
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, WI, 53715, USA
| | - Rosemarie Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD, 20892, USA
| | - Guangping Gao
- Deparment of Microbiology and Physiological Systems, University of Massachusetts Medical School; Worcester, MA, 01605, USA
| | - Aimee Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison; Madison, WI, 53705, USA
| | - Emek Kose
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research; Frederick, MD, 21702, USA
| | - Taina T. Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research; Frederick, MD, 21702, USA
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research; Frederick, MD, 21702, USA
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research; Frederick, MD, 21702, USA
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research; Frederick, MD, 21702, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD, 20892, USA
| | - Matthew R. Gardner
- Division of Infectious Diseases, Department of Medicine, Emory University; Atlanta, GA, 30329, USA
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - David T Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, 53705, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison; Madison, WI, 53715, USA
| |
Collapse
|
2
|
Zhou J, Wang L, Liu X, Gai Y, Dong M, Wang C, Ali MM, Ye M, Yu X, Hu L. Glycan-Imprinted Nanoparticle as Artificial Neutralizing Antibody for Efficient HIV-1 Recognition and Inhibition. NANO LETTERS 2024; 24:4423-4432. [PMID: 38568019 DOI: 10.1021/acs.nanolett.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The HIV-1 envelope is a heavily glycosylated class 1 trimeric fusion protein responsible for viral entry into CD4+ immune cells. Developing neutralizing antibodies against the specific envelope glycans is an alternative method for antiviral therapies. This work presents the first-ever development and characterization of artificial neutralizing antibodies using molecular imprinting technology to recognize and bind to the envelope protein of HIV-1. The prepared envelope glycan-imprinted nanoparticles (GINPs) can successfully prevent HIV-1 from infecting target cells by shielding the glycans on the envelope protein. In vitro experiments showed that GINPs have strong affinity toward HIV-1 (Kd = 36.7 ± 2.2 nM) and possess high anti-interference and specificity. GINPs demonstrate broad inhibition activity against both tier 1 and tier 2 HIV-1 strains with a pM-level IC50 and exhibit a significant inhibitory effect on long-term viral replication by more than 95%. The strategy provides a promising method for the inhibition and therapy of HIV-1 infection.
Collapse
Affiliation(s)
- Juntao Zhou
- Center for Supramolecular Chemical Biology, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Libian Wang
- Center for Supramolecular Chemical Biology, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxin Gai
- Center for Supramolecular Chemical Biology, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Mingming Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian, Liaoning 116023, China
| | - Chu Wang
- Center for Supramolecular Chemical Biology, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Muhammad Mujahid Ali
- Center for Supramolecular Chemical Biology, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian, Liaoning 116023, China
| | - Xianghui Yu
- Center for Supramolecular Chemical Biology, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| |
Collapse
|
3
|
Heindel DW, Figueroa Acosta DM, Goff M, Yengo CK, Jan M, Liu X, Wang XH, Petrova MI, Zhang M, Sagar M, Barnette P, Pandey S, Hessell AJ, Chan KW, Kong XP, Chen BK, Mahal LK, Bensing BA, Hioe CE. HIV-1 interaction with an O-glycan-specific bacterial lectin enhances virus infectivity and resistance to neutralization by antibodies. RESEARCH SQUARE 2024:rs.3.rs-2596269. [PMID: 36824869 PMCID: PMC9949255 DOI: 10.21203/rs.3.rs-2596269/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Bacteria dysbiosis has been associated with an increased risk of HIV-1 transmission and acquisition. The prevalent idea is that bacteria dysbiosis compromises mucosal integrity and promotes inflammatory conditions to cause recruitment and activation of immune cells that harbor or are targeted by HIV-1. However, it is also possible that HIV-1 directly binds bacteria or bacterial products to impact virus infectivity and transmissibility. This study evaluated HIV-1 interactions with bacteria through glycan-binding lectins. The Streptococcal Siglec-like lectin SLBR-N, which is part of the fimbriae shrouding the bacteria surface and recognizes α2,3 sialyated O-linked glycans, was noted for its ability to enhance HIV-1 infectivity in the context of cell-free infection and cell-to-cell transfer. Enhancing effects were recapitulated with O-glycan-binding plant lectins, signifying the importance of O-glycans. Conversely, N-glycan-binding bacterial lectins FimH and Msl had no effect. SLBR-N was demonstrated to capture and transfer infectious HIV-1 virions, bind to O-glycans on HIV-1 Env, and increase HIV-1 resistance to broadly neutralizing antibodies targeting different regions of Env. Hence, this study highlights the potential contribution of O-glycans in promoting HIV-1 infection through the exploitation of O-glycan-binding lectins from commensal bacteria at the mucosa.
Collapse
Affiliation(s)
- Daniel W Heindel
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dania M Figueroa Acosta
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marisa Goff
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clauvis Kunkeng Yengo
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Muzafar Jan
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Present address: Department of Biochemistry, Government Degree College Handwara, University of Kashmir, Jammu & Kashmir, India
| | - Xiaomei Liu
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiao-Hong Wang
- VA New York Harbor Healthcare System-Manhattan, New York, New York, United States of America
| | - Mariya I Petrova
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Present address: Microbiome Insights and Probiotics Consultancy, Karlovo, Bulgaria
| | - Mo Zhang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Manish Sagar
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Phillip Barnette
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Shilpi Pandey
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Ann J Hessell
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Kun-Wei Chan
- Department of Biochemistry and Molecular Pharmacology New York University Grossman School of Medicine, New York, NY, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology New York University Grossman School of Medicine, New York, NY, USA
| | - Benjamin K Chen
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Barbara A Bensing
- Department of Medicine, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Catarina E Hioe
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, USA
| |
Collapse
|
4
|
Heindel DW, Figueroa Acosta DM, Goff M, Yengo CK, Jan M, Liu X, Wang XH, Petrova MI, Zhang M, Sagar M, Barnette P, Pandey S, Hessell AJ, Chan KW, Kong XP, Chen BK, Mahal LK, Bensing BA, Hioe CE. HIV-1 interaction with an O-glycan-specific bacterial lectin enhances virus infectivity and resistance to neutralization by antibodies. RESEARCH SQUARE 2024:rs.3.rs-2596269. [PMID: 36824869 PMCID: PMC9949255 DOI: 10.21203/rs.3.rs-2596269/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/14/2024]
Abstract
Bacteria dysbiosis has been associated with an increased risk of HIV-1 transmission and acquisition. The prevalent idea is that bacteria dysbiosis compromises mucosal integrity and promotes inflammatory conditions to cause recruitment and activation of immune cells that harbor or are targeted by HIV-1. However, it is also possible that HIV-1 directly binds bacteria or bacterial products to impact virus infectivity and transmissibility. This study evaluated HIV-1 interactions with bacteria through glycan-binding lectins. The Streptococcal Siglec-like lectin SLBR-N, which is part of the fimbriae shrouding the bacteria surface and recognizes α2,3 sialyated O-linked glycans, was noted for its ability to enhance HIV-1 infectivity in the context of cell-free infection and cell-to-cell transfer. Enhancing effects were recapitulated with O-glycan-binding plant lectins, signifying the importance of O-glycans. Conversely, N-glycan-binding bacterial lectins FimH and Msl had no effect. SLBR-N was demonstrated to capture and transfer infectious HIV-1 virions, bind to O-glycans on HIV-1 Env, and increase HIV-1 resistance to broadly neutralizing antibodies targeting different regions of Env. Hence, this study highlights the potential contribution of O-glycans in promoting HIV-1 infection through the exploitation of O-glycan-binding lectins from commensal bacteria at the mucosa.
Collapse
Affiliation(s)
- Daniel W Heindel
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dania M Figueroa Acosta
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marisa Goff
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clauvis Kunkeng Yengo
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Muzafar Jan
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Present address: Department of Biochemistry, Government Degree College Handwara, University of Kashmir, Jammu & Kashmir, India
| | - Xiaomei Liu
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiao-Hong Wang
- VA New York Harbor Healthcare System-Manhattan, New York, New York, United States of America
| | - Mariya I Petrova
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Present address: Microbiome Insights and Probiotics Consultancy, Karlovo, Bulgaria
| | - Mo Zhang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Manish Sagar
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Phillip Barnette
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Shilpi Pandey
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Ann J Hessell
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Kun-Wei Chan
- Department of Biochemistry and Molecular Pharmacology New York University Grossman School of Medicine, New York, NY, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology New York University Grossman School of Medicine, New York, NY, USA
| | - Benjamin K Chen
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Barbara A Bensing
- Department of Medicine, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Catarina E Hioe
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, USA
| |
Collapse
|
5
|
Grunst MW, Gil HM, Grandea AG, Snow BJ, Andrabi R, Nedellec R, Burton I, Clark NM, Janaka SK, Keles NK, Moriarty RV, Weiler AM, Capuano S, Fennessey CM, Friedrich TC, O’Connor SL, O’Connor DH, Broman AT, Keele BF, Lifson JD, Hangartner L, Burton DR, Evans DT. Potent antibody-dependent cellular cytotoxicity of a V2-specific antibody is not sufficient for protection of macaques against SIV challenge. PLoS Pathog 2024; 20:e1011819. [PMID: 38252675 PMCID: PMC10833561 DOI: 10.1371/journal.ppat.1011819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/01/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Fc-mediated antibody effector functions, such as antibody-dependent cellular cytotoxicity (ADCC), can contribute to the containment HIV-1 replication but whether such activities are sufficient for protection is unclear. We previously identified an antibody to the variable 2 (V2) apex of the HIV-1 Env trimer (PGT145) that potently directs the lysis of SIV-infected cells by NK cells but poorly neutralizes SIV infectivity. To determine if ADCC is sufficient for protection, separate groups of six rhesus macaques were treated with PGT145 or a control antibody (DEN3) by intravenous infusion followed five days later by intrarectal challenge with SIVmac239. Despite high concentrations of PGT145 and potent ADCC activity in plasma on the day of challenge, all animals became infected and viral loads did not differ between the PGT145- and DEN3-treated animals. To determine if PGT145 can protect against a neutralization-sensitive virus, two additional groups of six macaques were treated with PGT145 and DEN3 and challenged with an SIVmac239 variant with a single amino acid change in Env (K180S) that increases PGT145 binding and renders the virus susceptible to neutralization by this antibody. Although there was no difference in virus acquisition, peak and chronic phase viral loads were significantly lower and time to peak viremia was significantly delayed in the PGT145-treated animals compared to the DEN3-treated control animals. Env changes were also selected in the PGT145-treated animals that confer resistance to both neutralization and ADCC. These results show that ADCC is not sufficient for protection by this V2-specific antibody. However, protection may be achieved by increasing the affinity of antibody binding to Env above the threshold required for neutralization.
Collapse
Affiliation(s)
- Michael W. Grunst
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Hwi Min Gil
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andres G. Grandea
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brian J. Snow
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Iszac Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Natasha M. Clark
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sanath Kumar Janaka
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nida K. Keles
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christine M. Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Aimee T. Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - David T. Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
6
|
Liu HF, Zhou Y, Huang Q, Piland J, Jin W, Mandel J, Du X, Martin J, Bartesaghi A. nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography. Nat Methods 2023; 20:1909-1919. [PMID: 37884796 PMCID: PMC10703682 DOI: 10.1038/s41592-023-02045-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023]
Abstract
Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high-throughput techniques for sample preparation and tilt-series acquisition are beginning to provide sufficient data to allow structural studies of proteins at physiological concentrations, the complex data analysis pipeline and the demanding storage and computational requirements pose major barriers for the development and broader adoption of this technology. Here, we present a scalable, end-to-end framework for single-particle cryo-electron tomography data analysis from on-the-fly pre-processing of tilt series to high-resolution refinement and classification, which allows efficient analysis and visualization of datasets with hundreds of tilt series and hundreds of thousands of particles. We validate our approach using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP ( http://nextpyp.app ).
Collapse
Affiliation(s)
- Hsuan-Fu Liu
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Qinwen Huang
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Jonathan Piland
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA
| | - Weisheng Jin
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Justin Mandel
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Xiaochen Du
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey Martin
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
| |
Collapse
|
7
|
Stamos JD, Rahman MA, Gorini G, Silva de Castro I, Becerra-Flores M, Van Wazer DJ, N’Guessan KF, Clark NM, Bissa M, Gutowska A, Mason RD, Kim J, Rao M, Roederer M, Paquin-Proulx D, Evans DT, Cicala C, Arthos J, Kwong PD, Zhou T, Cardozo T, Franchini G. Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or β-Sheet Conformations on Time of SIV mac251 Acquisition. J Virol 2023; 97:e0186422. [PMID: 36976017 PMCID: PMC10134845 DOI: 10.1128/jvi.01864-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
The monoclonal antibodies (MAbs) NCI05 and NCI09, isolated from a vaccinated macaque that was protected from multiple simian immunodeficiency virus (SIV) challenges, both target an overlapping, conformationally dynamic epitope in SIV envelope variable region 2 (V2). Here, we show that NCI05 recognizes a CH59-like coil/helical epitope, whereas NCI09 recognizes a β-hairpin linear epitope. In vitro, NCI05 and, to a lesser extent, NCI09 mediate the killing of SIV-infected cells in a CD4-dependent manner. Compared to NCI05, NCI09 mediates higher titers of antibody-dependent cellular cytotoxicity (ADCC) to gp120-coated cells, as well as higher levels of trogocytosis, a monocyte function that contributes to immune evasion. We also found that passive administration of NCI05 or NCI09 to macaques did not affect the risk of SIVmac251 acquisition compared to controls, demonstrating that these anti-V2 antibodies alone are not protective. However, NCI05 but not NCI09 mucosal levels strongly correlated with delayed SIVmac251 acquisition, and functional and structural data suggest that NCI05 targets a transient state of the viral spike apex that is partially opened, compared to its prefusion-closed conformation. IMPORTANCE Studies suggest that the protection against SIV/simian-human immunodeficiency virus (SHIV) acquisition afforded by the SIV/HIV V1 deletion-containing envelope immunogens, delivered by the DNA/ALVAC vaccine platform, requires multiple innate and adaptive host responses. Anti-inflammatory macrophages and tolerogenic dendritic cells (DC-10), together with CD14+ efferocytes, are consistently found to correlate with a vaccine-induced decrease in the risk of SIV/SHIV acquisition. Similarly, V2-specific antibody responses mediating ADCC, Th1 and Th2 cells expressing no or low levels of CCR5, and envelope-specific NKp44+ cells producing interleukin 17 (IL-17) also are reproducible correlates of decreased risk of virus acquisition. We focused on the function and the antiviral potential of two monoclonal antibodies (NCI05 and NCI09) isolated from vaccinated animals that differ in antiviral function in vitro and recognize V2 in a linear (NCI09) or coil/helical (NCI05) conformation. We demonstrate that NCI05, but not NCI09, delays SIVmac251 acquisition, highlighting the complexity of antibody responses to V2.
Collapse
Affiliation(s)
- James D. Stamos
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Mohammad Arif Rahman
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Giacomo Gorini
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Isabela Silva de Castro
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Manuel Becerra-Flores
- New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - David J. Van Wazer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kombo F. N’Guessan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Innate Immunology Laboratory, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Natasha M. Clark
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Massimiliano Bissa
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Anna Gutowska
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Rosemarie D. Mason
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiae Kim
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mangala Rao
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dominic Paquin-Proulx
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Innate Immunology Laboratory, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - David T. Evans
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Timothy Cardozo
- New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| |
Collapse
|
8
|
Wrapp D, Mu Z, Thakur B, Janowska K, Ajayi O, Barr M, Parks R, Mansouri K, Edwards RJ, Hahn BH, Acharya P, Saunders KO, Haynes BF. Structure-Based Stabilization of SOSIP Env Enhances Recombinant Ectodomain Durability and Yield. J Virol 2023; 97:e0167322. [PMID: 36633409 PMCID: PMC9888283 DOI: 10.1128/jvi.01673-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/09/2022] [Indexed: 01/13/2023] Open
Abstract
The envelope glycoprotein (Env) is the main focus of human immunodeficiency virus type 1 (HIV-1) vaccine development due to its critical role in viral entry. Despite advances in protein engineering, many Env proteins remain recalcitrant to recombinant expression due to their inherent metastability, making biochemical and immunological experiments impractical or impossible. Here, we report a novel proline stabilization strategy to facilitate the production of prefusion Env trimers. This approach, termed "2P," works synergistically with previously described SOSIP mutations and dramatically increases the yield of recombinantly expressed Env ectodomains without altering the antigenic or conformational properties of near-native Env. We determined that the 2P mutations function by enhancing the durability of the prefusion conformation and that this stabilization strategy is broadly applicable to evolutionarily and antigenically diverse Env constructs. These findings provide a new Env stabilization platform to facilitate biochemical research and expand the number of Env variants that can be developed as future HIV-1 vaccine candidates. IMPORTANCE Recent estimates have placed the number of new human immunodeficiency virus type 1 (HIV-1) infections at approximately 1.5 million per year, emphasizing the ongoing and urgent need for an effective vaccine. The envelope (Env) glycoprotein is the main focus of HIV-1 vaccine development, but, due to its inherent metastability, many Env variants are difficult to recombinantly express in the relatively large quantities that are required for biochemical studies and animal trials. Here, we describe a novel structure-based stabilization strategy that works synergistically with previously described SOSIP mutations to increase the yield of prefusion HIV-1 Env.
Collapse
Affiliation(s)
- Daniel Wrapp
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Zekun Mu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Bhishem Thakur
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Katarzyna Janowska
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Oluwatobi Ajayi
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Beatrice H. Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Department of Microbiology and Molecular Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| |
Collapse
|