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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
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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: Immune memory shapes human polyclonal antibody responses to H2N2 vaccination.

Yang, Yuhe R / Han, Julianna / Perrett, Hailee R / Richey, Sara T / Rodriguez, Alesandra J / Jackson, Abigail M / Gillespie, Rebecca A / O'Connell, Sarah / Raab, Julie E / Cominsky, Lauren Y / Chopde, Ankita / Kanekiyo, Masaru / Houser, Katherine V / Chen, Grace L / McDermott, Adrian B / Andrews, Sarah F / Ward, Andrew B

Cell reports

2024 Volume 43, Issue 5, Page(s) 114171

Abstract: Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase 1 clinical trial investigating a ferritin nanoparticle vaccine displaying H2 hemagglutinin (HA) in H2-naive and H2-exposed adults enabled us ...

Abstract	Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase 1 clinical trial investigating a ferritin nanoparticle vaccine displaying H2 hemagglutinin (HA) in H2-naive and H2-exposed adults enabled us to perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited. We temporally map the epitopes targeted by serum antibodies after vaccine prime and boost, revealing that previous H2 exposure results in higher responses to the variable HA head domain. In contrast, initial responses in H2-naive participants are dominated by antibodies targeting conserved epitopes. We use cryoelectron microscopy and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the HA head, including the receptor-binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses post-vaccination.
Language	English
Publishing date	2024-05-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.114171
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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: Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.

Hurlburt, Nicholas K / Homad, Leah J / Sinha, Irika / Jennewein, Madeleine F / MacCamy, Anna J / Wan, Yu-Hsin / Boonyaratanakornkit, Jim / Sholukh, Anton M / Jackson, Abigail M / Zhou, Panpan / Burton, Dennis R / Andrabi, Raiees / Ozorowski, Gabriel / Ward, Andrew B / Stamatatos, Leonidas / Pancera, Marie / McGuire, Andrew T

Communications biology

2022 Volume 5, Issue 1, Page(s) 342

Abstract: Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with ...

Abstract	Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with zoonotic potential in animal reservoirs suggests that additional outbreaks could occur. Monoclonal antibodies targeting conserved neutralizing epitopes on diverse CoVs can form the basis for prophylaxis and therapeutic treatments and enable the design of vaccines aimed at providing pan-CoV protection. We previously identified a neutralizing monoclonal antibody, CV3-25 that binds to the SARS-CoV-2 spike, neutralizes the SARS-CoV-2 Beta variant comparably to the ancestral Wuhan Hu-1 strain, cross neutralizes SARS-CoV-1 and binds to recombinant proteins derived from the spike-ectodomains of HCoV-OC43 and HCoV-HKU1. Here, we show that the neutralizing activity of CV3-25 is maintained against the Alpha, Delta, Gamma and Omicron variants of concern as well as a SARS-CoV-like bat coronavirus with zoonotic potential by binding to a conserved linear peptide in the stem-helix region. Negative stain electron microscopy and a 1.74 Å crystal structure of a CV3-25/peptide complex demonstrates that CV3-25 binds to the base of the stem helix at the HR2 boundary to an epitope that is distinct from other stem-helix directed neutralizing mAbs.
MeSH term(s)	Animals ; Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 ; Epitopes ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-04-11
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-03262-7
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Article ; Online: One dose of COVID-19 nanoparticle vaccine REVC-128 protects against SARS-CoV-2 challenge at two weeks post-immunization.

Gu, Maggie / Torres, Jonathan L / Li, Yijia / Van Ry, Alex / Greenhouse, Jack / Wallace, Shannon / Chiang, Chi-I / Pessaint, Laurent / Jackson, Abigail M / Porto, Maciel / Kar, Swagata / Li, Yuxing / Ward, Andrew B / Wang, Yimeng

Emerging microbes & infections

2021 Volume 10, Issue 1, Page(s) 2016–2029

Abstract: ... ...

Abstract	ABSTRACT
MeSH term(s)	Animals ; Antibodies, Neutralizing ; Antibodies, Viral/blood ; Antibody Formation ; COVID-19/prevention & control ; COVID-19 Vaccines/administration & dosage ; COVID-19 Vaccines/immunology ; Cricetinae ; Humans ; Immunization ; Immunization Schedule ; Immunogenicity, Vaccine ; Mesocricetus ; Mice ; Nanoparticles/chemistry ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Vaccination ; Viral Load
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2021-10-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2681359-2
ISSN	2222-1751 ; 2222-1751
ISSN (online)	2222-1751
ISSN	2222-1751
DOI	10.1080/22221751.2021.1994354
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Article: Immune memory shapes human polyclonal antibody responses to H2N2 vaccination.

Yang, Yuhe R / Han, Julianna / Perrett, Hailee R / Richey, Sara T / Jackson, Abigail M / Rodriguez, Alesandra J / Gillespie, Rebecca A / O'Connell, Sarah / Raab, Julie E / Cominsky, Lauren Y / Chopde, Ankita / Kanekiyo, Masaru / Houser, Katherine V / Chen, Grace L / McDermott, Adrian B / Andrews, Sarah F / Ward, Andrew B

bioRxiv : the preprint server for biology

2023

Abstract: Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could ... ...

Abstract	Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited after H2 vaccination. We temporally map the epitopes targeted by serum antibodies after first and second vaccinations and show previous H2 exposure results in higher responses to the variable head domain of hemagglutinin while initial responses in H2-naïve participants are dominated by antibodies targeting conserved epitopes. We use cryo-EM and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the hemagglutinin head including the receptor binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses.
Language	English
Publishing date	2023-08-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.23.554525
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Article: Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants.

Yuan, Meng / Huang, Deli / Lee, Chang-Chun D / Wu, Nicholas C / Jackson, Abigail M / Zhu, Xueyong / Liu, Hejun / Peng, Linghang / van Gils, Marit J / Sanders, Rogier W / Burton, Dennis R / Reincke, S Momsen / Prüss, Harald / Kreye, Jakob / Nemazee, David / Ward, Andrew B / Wilson, Ian A

bioRxiv : the preprint server for biology

2021

Abstract: The protective efficacy of neutralizing antibodies (nAbs) elicited during natural infection with SARS-CoV-2 and by vaccination based on its spike protein has been compromised with emergence of the recent SARS-CoV-2 variants. Residues E484 and K417 in the ...

Abstract	The protective efficacy of neutralizing antibodies (nAbs) elicited during natural infection with SARS-CoV-2 and by vaccination based on its spike protein has been compromised with emergence of the recent SARS-CoV-2 variants. Residues E484 and K417 in the receptor-binding site (RBS) are both mutated in lineages first described in South Africa (B.1.351) and Brazil (B.1.1.28.1). The nAbs isolated from SARS-CoV-2 patients are preferentially encoded by certain heavy-chain germline genes and the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2) can each bind the RBS in two different binding modes. However, their binding and neutralization are abrogated by either the E484K or K417N mutation, whereas nAbs to the cross-reactive CR3022 and S309 sites are largely unaffected. This structural and functional analysis illustrates why mutations at E484 and K417 adversely affect major classes of nAbs to SARS-CoV-2 with consequences for next-generation COVID-19 vaccines.
Language	English
Publishing date	2021-02-17
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.02.16.430500
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Article ; Online: Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants.

Science (New York, N.Y.)

2021 Volume 373, Issue 6556, Page(s) 818–823

Abstract: Neutralizing antibodies (nAbs) elicited against the receptor binding site (RBS) of the spike protein of wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are generally less effective against recent variants of concern. RBS residues ... ...

Abstract	Neutralizing antibodies (nAbs) elicited against the receptor binding site (RBS) of the spike protein of wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are generally less effective against recent variants of concern. RBS residues Glu
MeSH term(s)	Angiotensin-Converting Enzyme 2/metabolism ; Antibodies, Neutralizing/immunology ; Antibodies, Neutralizing/metabolism ; Antibodies, Viral/immunology ; Antibodies, Viral/metabolism ; Antigenic Variation ; Antigens, Viral/chemistry ; Antigens, Viral/genetics ; Antigens, Viral/immunology ; Antigens, Viral/metabolism ; Binding Sites ; Binding Sites, Antibody ; COVID-19/immunology ; COVID-19/virology ; Epitopes ; Humans ; Immune Evasion ; Mutation ; Protein Binding ; Protein Domains ; Receptors, Coronavirus/metabolism ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Antigens, Viral ; Epitopes ; Receptors, Coronavirus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-05-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abh1139
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Article ; Online: One dose of COVID-19 nanoparticle vaccine REVC-128 provides protection against SARS-CoV-2 challenge at two weeks post immunization

Gu, Maggie / Torres, Jonathan L / Greenhouse, Jack / Wallace, Shannon / Chiang, Chi-I / Jackson, Abigail M / Porto, Maciel / Kar, Swagata / Li, Yuxing / Ward, Andrew B / Wang, Yimeng

bioRxiv

Abstract: A COVID-19 vaccine with capability to induce early protection is needed to efficiently eliminate viral spread. Here, we demonstrate the development of a nanoparticle vaccine candidate, REVC-128, in which multiple trimeric spike ectodomain subunits with ... ...

Abstract	A COVID-19 vaccine with capability to induce early protection is needed to efficiently eliminate viral spread. Here, we demonstrate the development of a nanoparticle vaccine candidate, REVC-128, in which multiple trimeric spike ectodomain subunits with glycine (G) at position 614 were multimerized onto a nanoparticle. In-vitro characterization of this vaccine confirms its structural and antigenic integrity. In-vivo immunogenicity evaluation in mice indicates that a single dose of this vaccine induces potent serum neutralizing antibody titer at two weeks post immunization, which is significantly higher than titer induced by trimeric spike protein without nanoparticle presentation. The comparison of serum binding to spike subunits between animals immunized by spike with and without nanoparticle presentation indicates that nanoparticle prefers the display of spike RBD (Receptor-Binding Domain) over S2 subunit, likely resulting in a more neutralizing but less cross-reactive antibody response. Moreover, a Syrian golden hamster in-vivo model for SARS-CoV-2 virus challenge was implemented at two weeks post a single dose of REVC-128 immunization. The results show that vaccination protects hamsters against SARS-CoV-2 virus challenge with evidence of steady body weight, suppressed viral loads and alleviation of tissue damage (lung and nares) for protected animals, compared with ~10% weight loss, higher viral loads and tissue damage in unprotected animals. Furthermore, the data show that vaccine REVC-128 is thermostable at up to 37 degree for at least 4 weeks. These findings, along with a long history of safety for protein vaccines, suggest that the REVC-128 is a safe, stable and efficacious single-shot vaccine candidate to induce the earliest protection against SARS-CoV-2 infection.
Keywords	covid19
Language	English
Publishing date	2021-04-02
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.04.02.438218
Database	COVID19

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