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Article: Anti-Immune Complex Antibodies are Elicited During Repeated Immunization with HIV Env Immunogens.

Brown, Sharidan / Antanasijevic, Aleksandar / Sewall, Leigh M / Garcia, Daniel Montiel / Brouwer, Philip J M / Sanders, Rogier W / Ward, Andrew B

bioRxiv : the preprint server for biology

2024

Abstract: Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Early antibody responses to easily accessible epitopes on these antigens are directed to non- ... ...

Abstract	Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Early antibody responses to easily accessible epitopes on these antigens are directed to non-neutralizing epitopes instead of bnAb epitopes. Autologous neutralizing antibody responses appear upon boosting once immunodominant epitopes are saturated. Here we report another type of antibody response that arises after repeated immunizations with HIV Env immunogens and present the structures of six anti-immune complexes discovered using polyclonal epitope mapping. The anti-immune complex antibodies target idiotopes composed of framework regions of antibodies bound to Env. This work sheds light on current vaccine development efforts for HIV, as well as for other pathogens, in which repeated exposure to antigen is required.
Language	English
Publishing date	2024-03-17
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.15.585257
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Article ; Online: Protocol for analyzing antibody responses to glycoprotein antigens using electron-microscopy-based polyclonal epitope mapping.

Turner, Hannah L / Jackson, Abigail M / Richey, Sara T / Sewall, Leigh M / Antanasijevic, Aleksandar / Hangartner, Lars / Ward, Andrew B

STAR protocols

2023 Volume 4, Issue 3, Page(s) 102476

Abstract: Electron microscopy-based polyclonal epitope mapping (EMPEM) can delineate epitope specificities of serum antibodies to a given antigen following vaccination or infection. Here, we present a protocol for the EMPEM method for rapid high-throughput ... ...

Abstract	Electron microscopy-based polyclonal epitope mapping (EMPEM) can delineate epitope specificities of serum antibodies to a given antigen following vaccination or infection. Here, we present a protocol for the EMPEM method for rapid high-throughput assessment of antibody responses to glycoprotein antigens in vaccination and infection studies. We describe steps for antibody isolation and digestion, antigen complex and purification, and electron microscope imaging. We then detail procedures for processing and analysis of EMPEM data. For complete details on the use and execution of this protocol, please refer to Bianchi et al. (2018).
MeSH term(s)	Epitope Mapping ; Antibody Formation ; Electrons ; Microscopy, Electron ; Antibodies ; Glycoproteins
Chemical Substances	Antibodies ; Glycoproteins
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Journal Article
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2023.102476
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Increasing sensitivity of antibody-antigen interactions using photo-cross-linking.

Torrents de la Peña, Alba / Sewall, Leigh M / de Paiva Froes Rocha, Rebeca / Jackson, Abigail M / Pratap, Payal P / Bangaru, Sandhya / Cottrell, Christopher A / Mohanty, Subhasis / Shaw, Albert C / Ward, Andrew B

Cell reports methods

2023 Volume 3, Issue 6, Page(s) 100509

Abstract: Understanding antibody-antigen interactions in a polyclonal immune response in humans and animal models is critical for rational vaccine design. Current approaches typically characterize antibodies that are functionally relevant or highly abundant. Here, ...

Abstract	Understanding antibody-antigen interactions in a polyclonal immune response in humans and animal models is critical for rational vaccine design. Current approaches typically characterize antibodies that are functionally relevant or highly abundant. Here, we use photo-cross-linking and single-particle electron microscopy to increase antibody detection and unveil epitopes of low-affinity and low-abundance antibodies, leading to a broader structural characterization of polyclonal immune responses. We employed this approach across three different viral glycoproteins and showed increased sensitivity of detection relative to currently used methods. Results were most noticeable in early and late time points of a polyclonal immune response. Additionally, the use of photo-cross-linking revealed intermediate antibody binding states and demonstrated a distinctive way to study antibody binding mechanisms. This technique can be used to structurally characterize the landscape of a polyclonal immune response of patients in vaccination or post-infection studies at early time points, allowing for rapid iterative design of vaccine immunogens.
MeSH term(s)	Animals ; Humans ; Antibodies, Neutralizing ; Epitopes/chemistry ; Vaccination ; Vaccines
Chemical Substances	Antibodies, Neutralizing ; Epitopes ; Vaccines
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2667-2375
ISSN (online)	2667-2375
DOI	10.1016/j.crmeth.2023.100509
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Article ; Online: Structural mapping of antibody landscapes to human betacoronavirus spike proteins.

Bangaru, Sandhya / Antanasijevic, Aleksandar / Kose, Nurgun / Sewall, Leigh M / Jackson, Abigail M / Suryadevara, Naveenchandra / Zhan, Xiaoyan / Torres, Jonathan L / Copps, Jeffrey / de la Peña, Alba Torrents / Crowe, James E / Ward, Andrew B

Science advances

2022 Volume 8, Issue 18, Page(s) eabn2911

Abstract: Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based ... ...

Abstract	Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based polyclonal epitope mapping (EMPEM) to characterize the antibody specificities against β-CoV spike proteins in prepandemic (PP) sera or SARS-CoV-2 convalescent (SC) sera. We observed that most PP sera had antibodies specific to seasonal human CoVs (HCoVs) OC43 and HKU1 spike proteins while the SC sera showed reactivity across all human β-CoVs. Detailed molecular mapping of spike-antibody complexes revealed epitopes that were differentially targeted by preexisting antibodies and SC serum antibodies. Our studies provide an antigenic landscape to β-HCoV spikes in the general population serving as a basis for cross-reactive epitope analyses in SARS-CoV-2-infected individuals.
MeSH term(s)	Antibodies, Viral ; COVID-19 ; Coronavirus OC43, Human ; Epitopes ; Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Chemical Substances	Antibodies, Viral ; Epitopes ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.abn2911
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Article ; Online: Structure and immune recognition of the porcine epidemic diarrhea virus spike protein.

Kirchdoerfer, Robert N / Bhandari, Mahesh / Martini, Olnita / Sewall, Leigh M / Bangaru, Sandhya / Yoon, Kyoung-Jin / Ward, Andrew B

Structure (London, England : 1993)

2020 Volume 29, Issue 4, Page(s) 385–392.e5

Abstract: Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good ... ...

Abstract	Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components, including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.
MeSH term(s)	Animals ; Antibodies, Viral/metabolism ; Cell Line ; Coronavirus Infections/immunology ; Cryoelectron Microscopy ; Epitopes/immunology ; Fatty Acids, Monounsaturated/chemistry ; Models, Molecular ; Molecular Conformation ; Polysaccharides/chemistry ; Porcine epidemic diarrhea virus/chemistry ; Porcine epidemic diarrhea virus/immunology ; Porcine epidemic diarrhea virus/metabolism ; Protein Binding ; Sf9 Cells ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/immunology ; Swine
Chemical Substances	Antibodies, Viral ; Epitopes ; Fatty Acids, Monounsaturated ; Polysaccharides ; Spike Glycoprotein, Coronavirus ; palmitoleic acid (209B6YPZ4I)
Language	English
Publishing date	2020-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2020.12.003
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Article: Focusing antibody responses to the fusion peptide in rhesus macaques.

Cottrell, Christopher A / Pratap, Payal P / Cirelli, Kimberly M / Carnathan, Diane G / Enemuo, Chiamaka A / Antanasijevic, Aleksandar / Ozorowski, Gabriel / Sewall, Leigh M / Gao, Hongmei / Greene, Kelli M / Allen, Joel D / Ngo, Julia T / Choe, Yury / Nogal, Bartek / Silva, Murillo / Bhiman, Jinal / Pauthner, Matthias / Irvine, Darrell J / Montefiori, David /

Crispin, Max / Burton, Dennis R / Silvestri, Guido / Crotty, Shane / Ward, Andrew B

bioRxiv : the preprint server for biology

2023

Abstract: Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an ... ...

Abstract	Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to elicit immune responses against the conserved fusion peptide. Antibody specificities and GC responses were tracked longitudinally using electron microscopy polyclonal epitope mapping (EMPEM) and lymph node fine-needle aspirates, respectively. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design.
Language	English
Publishing date	2023-06-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.26.545779
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Article ; Online: Mapping Polyclonal Antibody Responses in Non-human Primates Vaccinated with HIV Env Trimer Subunit Vaccines.

Nogal, Bartek / Bianchi, Matteo / Cottrell, Christopher A / Kirchdoerfer, Robert N / Sewall, Leigh M / Turner, Hannah L / Zhao, Fangzhu / Sok, Devin / Burton, Dennis R / Hangartner, Lars / Ward, Andrew B

Cell reports

2020 Volume 30, Issue 11, Page(s) 3755–3765.e7

Abstract: Rational immunogen design aims to focus antibody responses to vulnerable sites on primary antigens. Given the size of these antigens, there is, however, potential for eliciting unwanted, off-target responses. Here, we use our electron microscopy ... ...

Abstract	Rational immunogen design aims to focus antibody responses to vulnerable sites on primary antigens. Given the size of these antigens, there is, however, potential for eliciting unwanted, off-target responses. Here, we use our electron microscopy polyclonal epitope mapping approach to describe the antibody specificities elicited by immunization of non-human primates with soluble HIV envelope trimers and subsequent repeated viral challenge. An increased diversity of epitopes recognized and the approach angle by which these antibodies bind constitute a hallmark of the humoral response in most protected animals. We also show that fusion peptide-specific antibodies are likely responsible for some neutralization breadth. Moreover, cryoelectron microscopy (cryo-EM) analysis of a fully protected animal reveals a high degree of clonality within a subset of putatively neutralizing antibodies, enabling a detailed molecular description of the antibody paratope. Our results provide important insights into the immune response against a vaccine candidate that entered into clinical trials in 2019.
MeSH term(s)	Animals ; Antibodies, Neutralizing/immunology ; Antibody Formation/immunology ; Cross Reactions/immunology ; Cryoelectron Microscopy ; Epitopes/chemistry ; Epitopes/immunology ; HEK293 Cells ; HIV Antibodies/chemistry ; HIV Antibodies/immunology ; Humans ; Immunity, Humoral ; Macaca mulatta ; Models, Molecular ; Protein Multimerization ; Vaccination ; Vaccines, Subunit/immunology ; env Gene Products, Human Immunodeficiency Virus/immunology
Chemical Substances	Antibodies, Neutralizing ; Epitopes ; HIV Antibodies ; Vaccines, Subunit ; env Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2020-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2020.02.061
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The C3/465 glycan hole cluster in BG505 HIV-1 envelope is the major neutralizing target involved in preventing mucosal SHIV infection.

Charles, Tysheena P / Burton, Samantha L / Arunachalam, Prabhu S / Cottrell, Christopher A / Sewall, Leigh M / Bollimpelli, Venkata S / Gangadhara, Sailaja / Dey, Antu K / Ward, Andrew B / Shaw, George M / Hunter, Eric / Amara, Rama R / Pulendran, Bali / van Gils, Marit J / Derdeyn, Cynthia A

PLoS pathogens

2021 Volume 17, Issue 2, Page(s) e1009257

Abstract: Stabilized HIV-1 envelope (Env) trimers elicit tier 2 autologous neutralizing antibody (nAb) responses in immunized animals. We previously demonstrated that BG505 SOSIP.664.T332N gp140 (BG505 SOSIP) immunization of rhesus macaques (RM) provided robust ... ...

Abstract	Stabilized HIV-1 envelope (Env) trimers elicit tier 2 autologous neutralizing antibody (nAb) responses in immunized animals. We previously demonstrated that BG505 SOSIP.664.T332N gp140 (BG505 SOSIP) immunization of rhesus macaques (RM) provided robust protection against autologous intra-vaginal simian-human immunodeficiency virus (SHIV) challenge that was predicted by high serum nAb titers. Here, we show that nAb in these protected RM targeted a glycan hole proximal to residue 465 in gp120 in all cases. nAb also targeted another glycan hole at residues 241/289 and an epitope in V1 at varying frequencies. Non-neutralizing antibodies directed at N611-shielded epitopes in gp41 were also present but were more prevalent in RM with low nAb titers. Longitudinal analysis demonstrated that nAb broadened in some RM during sequential immunization but remained focused in others, the latter being associated with increases in nAb titer. Thirty-eight monoclonal antibodies (mAbs) isolated from a protected RM with an exceptionally high serum neutralization titer bound to the trimer in ELISA, and four of the mAbs potently neutralized the BG505 Env pseudovirus (PV) and SHIV. The four neutralizing mAbs were clonally related and targeted the 465 glycan hole to varying degrees, mimicking the serum. The data demonstrate that the C3/465 glycan hole cluster was the dominant neutralization target in high titer protected RM, despite other co-circulating neutralizing and non-neutralizing specificities. The isolation of a neutralizing mAb family argues that clonotype expansion occurred during BG505 SOSIP immunization, leading to high titer, protective nAb and setting a desirable benchmark for HIV vaccines.
MeSH term(s)	Animals ; Antibodies, Neutralizing/immunology ; Epitopes/immunology ; Female ; HIV Antibodies/immunology ; HIV Infections/immunology ; HIV Infections/virology ; HIV-1/immunology ; Humans ; Immunization ; Macaca mulatta ; Polysaccharides/immunology ; Simian Acquired Immunodeficiency Syndrome/immunology ; Simian Acquired Immunodeficiency Syndrome/prevention & control ; Simian Acquired Immunodeficiency Syndrome/virology ; Simian Immunodeficiency Virus/immunology ; Vaccination ; env Gene Products, Human Immunodeficiency Virus/immunology
Chemical Substances	Antibodies, Neutralizing ; Epitopes ; HIV Antibodies ; Polysaccharides ; env Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2021-02-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1009257
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Article ; Online: Structure and immune recognition of the porcine epidemic diarrhea virus spike protein

Kirchdoerfer, Robert N. / Bhandari, Mahesh / Martini, Olnita / Sewall, Leigh M. / Bangaru, Sandhya / Yoon, Kyoung-Jin / Ward, Andrew B.

bioRxiv

Abstract: Porcine epidemic diarrhea virus is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate ... ...

Abstract	Porcine epidemic diarrhea virus is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides new insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.
Keywords	covid19
Publisher	BioRxiv; MedRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.02.18.955195
Database	COVID19

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Article ; Online: Structure and immune recognition of the porcine epidemic diarrhea virus spike protein

Kirchdoerfer, Robert N. / Bhandari, Mahesh / Martini, Olnita / Sewall, Leigh M. / Bangaru, Sandhya / Yoon, Kyoung-Jin / Ward, Andrew B.

bioRxiv

Keywords	covid19
Language	English
Publishing date	2020-02-19
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.02.18.955195
Database	COVID19

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