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Article ; Online: Prefusion stabilization of the Hendra and Langya virus F proteins.

Byrne, Patrick O / Blade, Elizabeth G / Fisher, Brian E / Ambrozak, David R / Ramamohan, Ajit R / Graham, Barney S / Loomis, Rebecca J / McLellan, Jason S

Journal of virology

2024 Volume 98, Issue 2, Page(s) e0137223

Abstract: Nipah virus (NiV) and Hendra virus (HeV) are pathogenic paramyxoviruses that cause mild-to-severe disease in humans. As members of ... ...

Abstract	Nipah virus (NiV) and Hendra virus (HeV) are pathogenic paramyxoviruses that cause mild-to-severe disease in humans. As members of the
MeSH term(s)	Humans ; Glycoproteins/metabolism ; Hendra Virus/physiology ; Henipavirus/physiology ; Henipavirus Infections ; Nipah Virus/genetics ; Nipah Virus/metabolism ; Peptides/metabolism ; Viral Fusion Proteins ; Viral Proteins/metabolism
Chemical Substances	Glycoproteins ; Peptides ; Viral Fusion Proteins ; Viral Proteins
Language	English
Publishing date	2024-01-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.01372-23
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Article ; Online: Multilevel human secondary lymphoid immune system compartmentalization revealed by complementary imaging approaches.

Oyler, Benjamin L / Valencia-Dávila, Jeferson A / Moysi, Eirini / Molyvdas, Adam / Ioannidou, Kalliopi / March, Kylie / Ambrozak, David / De Leval, Laurence / Fabozzi, Giulia / Woods, Amina S / Koup, Richard A / Petrovas, Constantinos

iScience

2023 Volume 26, Issue 8, Page(s) 107261

Abstract: Secondary human lymphoid tissue immune reactions take place in a highly coordinated environment with compartmentalization representing a fundamental feature of this organization. ...

Abstract	Secondary human lymphoid tissue immune reactions take place in a highly coordinated environment with compartmentalization representing a fundamental feature of this organization.
Language	English
Publishing date	2023-07-03
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107261
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Article ; Online: Structural basis for antibody recognition of vulnerable epitopes on Nipah virus F protein.

Byrne, Patrick O / Fisher, Brian E / Ambrozak, David R / Blade, Elizabeth G / Tsybovsky, Yaroslav / Graham, Barney S / McLellan, Jason S / Loomis, Rebecca J

Nature communications

2023 Volume 14, Issue 1, Page(s) 1494

Abstract: Nipah virus (NiV) is a pathogenic paramyxovirus that causes fatal encephalitis in humans. Two envelope glycoproteins, the attachment protein (G/RBP) and fusion protein (F), facilitate entry into host cells. Due to its vital role, NiV F presents an ... ...

Abstract	Nipah virus (NiV) is a pathogenic paramyxovirus that causes fatal encephalitis in humans. Two envelope glycoproteins, the attachment protein (G/RBP) and fusion protein (F), facilitate entry into host cells. Due to its vital role, NiV F presents an attractive target for developing vaccines and therapeutics. Several neutralization-sensitive epitopes on the NiV F apex have been described, however the antigenicity of most of the F protein's surface remains uncharacterized. Here, we immunize mice with prefusion-stabilized NiV F and isolate ten monoclonal antibodies that neutralize pseudotyped virus. Cryo-electron microscopy reveals eight neutralization-sensitive epitopes on NiV F, four of which have not previously been described. Novel sites span the lateral and basal faces of NiV F, expanding the known library of vulnerable epitopes. Seven of ten antibodies bind the Hendra virus (HeV) F protein. Multiple sequence alignment suggests that some of these newly identified neutralizing antibodies may also bind F proteins across the Henipavirus genus. This work identifies new epitopes as targets for therapeutics, provides a molecular basis for NiV neutralization, and lays a foundation for development of new cross-reactive antibodies targeting Henipavirus F proteins.
MeSH term(s)	Humans ; Animals ; Mice ; Nipah Virus/metabolism ; Epitopes ; Cryoelectron Microscopy ; Viral Envelope Proteins ; Antibodies, Neutralizing/metabolism ; Antibodies, Monoclonal ; Henipavirus Infections
Chemical Substances	Epitopes ; Viral Envelope Proteins ; Antibodies, Neutralizing ; Antibodies, Monoclonal
Language	English
Publishing date	2023-03-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36995-y
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Article ; Online: Rhesus macaque Bcl-6/Bcl-xL B cell immortalization: Discovery of HIV-1 neutralizing antibodies from lymph node.

Samsel, Jakob / Boswell, Kristin L / Watkins, Timothy / Ambrozak, David R / Mason, Rosemarie / Yamamoto, Takuya / Ko, Sungyoul / Yang, Yongping / Zhou, Tongqing / Doria-Rose, Nicole A / Foulds, Kathryn E / Roederer, Mario / Mascola, John R / Kwong, Peter D / Gama, Lucio / Koup, Richard A

Journal of immunological methods

2023 Volume 516, Page(s) 113445

Abstract: Many HIV-1 vaccines are designed to elicit neutralizing antibodies, and pre-clinical testing is often carried out in rhesus macaques (RMs). We have therefore adapted a method of B cell immortalization for use with RM B cells. In this system, RM B cells ... ...

Abstract	Many HIV-1 vaccines are designed to elicit neutralizing antibodies, and pre-clinical testing is often carried out in rhesus macaques (RMs). We have therefore adapted a method of B cell immortalization for use with RM B cells. In this system, RM B cells are activated with CD40 ligand and RM IL-21 before transduction with a retroviral vector encoding Bcl-6, Bcl-xL, and green fluorescent protein. Importantly, RM B cells from lymph nodes are more effectively immortalized by this method than B cells from PBMC, a difference not seen in humans. We suggest the discrepancy between these two tissues is due to increased expression of CD40 on RM lymph node B cells. Immortalized RM B cells expand long-term, undergo minimal somatic hypermutation, express surface B cell receptor, and secrete antibodies into culture. This allows for the identification of cells based on antigen specificity and/or functional assays. Here, we show the characterization of this system and its application for the isolation of HIV-1 neutralizing antibodies from a SHIV.CH505-infected animal, both with and without antigen probe. Taken together, we show that Bcl-6/xL immortalization is a valuable and flexible tool for antibody discovery in RMs, but with important distinctions from application of the system in human cells.
MeSH term(s)	Animals ; Humans ; Macaca mulatta ; HIV-1 ; Leukocytes, Mononuclear ; HIV Antibodies ; Antibodies, Neutralizing ; AIDS Vaccines ; Lymph Nodes ; Simian Immunodeficiency Virus ; Simian Acquired Immunodeficiency Syndrome
Chemical Substances	HIV Antibodies ; Antibodies, Neutralizing ; AIDS Vaccines
Language	English
Publishing date	2023-02-25
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	120142-6
ISSN	1872-7905 ; 0022-1759
ISSN (online)	1872-7905
ISSN	0022-1759
DOI	10.1016/j.jim.2023.113445
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Article ; Online: Rhesus macaque Bcl-6/Bcl-xL B cell immortalization: Discovery of HIV-1 neutralizing antibodies from lymph node

Samsel, Jakob / Boswell, Kristin L. / Baron / Ambrozak, David R. / Mason, Rosemarie / Yamamoto, Takuya / Ko, Sungyoul / Yang, Yongping / Zhou, Tongqing / Doria-Rose, Nicole A. / Foulds, Kathryn E. / Roederer, Mario / Mascola, John R. / Kwong, Peter D. / Gama, Lucio / Koup, Richard A.

Journal of Immunological Methods. 2023 May, v. 516 p.113445-

2023

Abstract	Many HIV-1 vaccines are designed to elicit neutralizing antibodies, and pre-clinical testing is often carried out in rhesus macaques (RMs). We have therefore adapted a method of B cell immortalization for use with RM B cells. In this system, RM B cells are activated with CD40 ligand and RM IL-21 before transduction with a retroviral vector encoding Bcl-6, Bcl-xL, and green fluorescent protein. Importantly, RM B cells from lymph nodes are more effectively immortalized by this method than B cells from PBMC, a difference not seen in humans. We suggest the discrepancy between these two tissues is due to increased expression of CD40 on RM lymph node B cells. Immortalized RM B cells expand long-term, undergo minimal somatic hypermutation, express surface B cell receptor, and secrete antibodies into culture. This allows for the identification of cells based on antigen specificity and/or functional assays. Here, we show the characterization of this system and its application for the isolation of HIV-1 neutralizing antibodies from a SHIV.CH505-infected animal, both with and without antigen probe. Taken together, we show that Bcl-6/xL immortalization is a valuable and flexible tool for antibody discovery in RMs, but with important distinctions from application of the system in human cells.
Keywords	B-lymphocytes ; Macaca mulatta ; antibodies ; antigens ; green fluorescent protein ; humans ; interleukin-21 ; ligands ; lymph ; lymph nodes ; retroviral vectors ; Antibody discovery ; B cell immortalization ; HIV ; Vaccination ; Rhesus macaque
Language	English
Dates of publication	2023-05
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	120142-6
ISSN	1872-7905 ; 0022-1759
ISSN (online)	1872-7905
ISSN	0022-1759
DOI	10.1016/j.jim.2023.113445
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Article ; Online: Interaction dynamics between innate and adaptive immune cells responding to SARS-CoV-2 vaccination in non-human primates.

Schramm, Chaim A / Moon, Damee / Peyton, Lowrey / Lima, Noemia S / Wake, Christian / Boswell, Kristin L / Henry, Amy R / Laboune, Farida / Ambrozak, David / Darko, Samuel W / Teng, I-Ting / Foulds, Kathryn E / Carfi, Andrea / Edwards, Darin K / Kwong, Peter D / Koup, Richard A / Seder, Robert A / Douek, Daniel C

Nature communications

2023 Volume 14, Issue 1, Page(s) 7961

Abstract: As SARS-CoV-2 variants continue evolving, testing updated vaccines in non-human primates remains important for guiding human clinical practice. To date, such studies have focused on antibody titers and antigen-specific B and T cell frequencies. Here, we ... ...

Abstract	As SARS-CoV-2 variants continue evolving, testing updated vaccines in non-human primates remains important for guiding human clinical practice. To date, such studies have focused on antibody titers and antigen-specific B and T cell frequencies. Here, we extend our understanding by integrating innate and adaptive immune responses to mRNA-1273 vaccination in rhesus macaques. We sorted innate immune cells from a pre-vaccine time point, as well as innate immune cells and antigen-specific peripheral B and T cells two weeks after each of two vaccine doses and used single-cell sequencing to assess the transcriptomes and adaptive immune receptors of each cell. We show that a subset of S-specific T cells expresses cytokines critical for activating innate responses, with a concomitant increase in CCR5-expressing intermediate monocytes and a shift of natural killer cells to a more cytotoxic phenotype. The second vaccine dose, administered 4 weeks after the first, elicits an increase in circulating germinal center-like B cells 2 weeks later, which are more clonally expanded and enriched for epitopes in the receptor binding domain. Both doses stimulate inflammatory response genes associated with elevated antibody production. Overall, we provide a comprehensive picture of bidirectional signaling between innate and adaptive components of the immune system and suggest potential mechanisms for the enhanced response to secondary exposure.
MeSH term(s)	Animals ; Humans ; COVID-19 Vaccines ; Macaca mulatta ; SARS-CoV-2 ; COVID-19/prevention & control ; Vaccination ; Blood Group Antigens ; Antibodies, Viral
Chemical Substances	COVID-19 Vaccines ; Blood Group Antigens ; Antibodies, Viral
Language	English
Publishing date	2023-12-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-43420-x
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Article ; Online: Vaccine elicitation and structural basis for antibody protection against alphaviruses

Sutton, Matthew S. / Pletnev, Sergei / Callahan, Victoria / Ko, Sungyoul / Tsybovsky, Yaroslav / Bylund, Tatsiana / Casner, Ryan G. / Cerutti, Gabriele / Gardner, Christina L. / Guirguis, Veronica / Verardi, Raffaello / Zhang, Baoshan / Ambrozak, David / Beddall, Margaret / Lei, Hong / Yang, Eun Sung / Liu, Tracy / Henry, Amy R. / Rawi, Reda /

Schön, Arne / Schramm, Chaim A. / Shen, Chen-Hsiang / Shi, Wei / Stephens, Tyler / Yang, Yongping / Florez, Maria Burgos / Ledgerwood, Julie E. / Burke, Crystal W. / Shapiro, Lawrence / Fox, Julie M. / Kwong, Peter D. / Roederer, Mario

Cell. 2023 June, v. 186, no. 12 p.2672-2689.e25

2023

Abstract: Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine encephalitis virus-like particles (VLPs), a regimen that ... ...

Abstract	Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine encephalitis virus-like particles (VLPs), a regimen that protects against aerosol challenge with all three viruses. Single- and triple-virus-specific antibodies were isolated, and we identified 21 unique binding groups. Cryo-EM structures revealed that broad VLP binding inversely correlated with sequence and conformational variability. One triple-specific antibody, SKT05, bound proximal to the fusion peptide and neutralized all three Env-pseudotyped encephalitic alphaviruses by using different symmetry elements for recognition across VLPs. Neutralization in other assays (e.g., chimeric Sindbis virus) yielded variable results. SKT05 bound backbone atoms of sequence-diverse residues, enabling broad recognition despite sequence variability; accordingly, SKT05 protected mice against Venezuelan equine encephalitis virus, chikungunya virus, and Ross River virus challenges. Thus, a single vaccine-elicited antibody can protect in vivo against a broad range of alphaviruses.
Keywords	Chikungunya virus ; RNA ; Ross River virus ; Sindbis virus ; Venezuelan equine encephalitis virus ; aerosols ; antibodies ; encephalitis ; genetic variation ; horses ; neutralization ; peptides ; public health ; vaccines ; alphavirus ; broadly neutralizing antibody ; cryo-EM ; in vivo challenge ; vaccine
Language	English
Dates of publication	2023-06
Size	p. 2672-2689.e25.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.05.019
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Article ; Online: Vaccine Generation of Protective Ebola Antibodies and Identification of Conserved B-Cell Signatures.

Cagigi, Alberto / Misasi, John / Ploquin, Aurélie / Stanley, Daphne A / Ambrozak, David / Tsybovsky, Yaroslav / Mason, Rosemarie D / Roederer, Mario / Sullivan, Nancy J

The Journal of infectious diseases

2018 Volume 218, Issue suppl_5, Page(s) S528–S536

Abstract: We recently identified a single potently neutralizing monoclonal antibody (mAb), mAb114, isolated from a human survivor of natural Zaire ebolavirus (EBOV) infection, which fully protects nonhuman primates (NHPs) against lethal EBOV challenge. To evaluate ...

Abstract	We recently identified a single potently neutralizing monoclonal antibody (mAb), mAb114, isolated from a human survivor of natural Zaire ebolavirus (EBOV) infection, which fully protects nonhuman primates (NHPs) against lethal EBOV challenge. To evaluate the ability of vaccination to generate mAbs such as mAb114, we cloned antibodies from NHPs vaccinated with vectors encoding the EBOV glycoprotein (GP). We identified 14 unique mAbs with potent binding to GP, 4 of which were neutralized and had the functional characteristics of mAb114. These vaccine-induced macaque mAbs share many sequence similarities with mAb114 and use the same mAb114 VH gene (ie, IGHV3-13) when classified using the macaque IMGT database. The antigen-specific VH-gene repertoire present after each immunization indicated that IGHV3-13 mAbs populate an EBOV-specific B-cell repertoire that appears to become more prominent with subsequent boosting. These findings will support structure-based vaccine design aimed at enhanced induction of antibodies such as mAb114.
MeSH term(s)	Animals ; Antibodies, Monoclonal/immunology ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; B-Lymphocytes/immunology ; Ebola Vaccines/immunology ; Ebolavirus/immunology ; Humans ; Hydrogen-Ion Concentration ; Macaca fascicularis ; Vaccination ; Viral Envelope Proteins/immunology
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Ebola Vaccines ; Viral Envelope Proteins ; envelope glycoprotein, Ebola virus
Language	English
Publishing date	2018-06-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiy333
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Article ; Online: Procedures for Flow Cytometry-Based Sorting of Unfixed Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infected Cells and Other Infectious Agents.

Reifel, Kristen M / Swan, Brandon K / Jellison, Evan R / Ambrozak, David / Baijer, Jan / Nguyen, Richard / Monard, Simon / Lyon, Geoffrey / Fontes, Benjamin / Perfetto, Stephen P

Cytometry. Part A : the journal of the International Society for Analytical Cytology

2020 Volume 97, Issue 7, Page(s) 674–680

Abstract: In response to the recent COVID-19 pandemic, many laboratories are involved in research supporting SARS-CoV-2 vaccine development and clinical trials. Flow cytometry laboratories will be responsible for a large part of this effort by sorting unfixed ... ...

Abstract	In response to the recent COVID-19 pandemic, many laboratories are involved in research supporting SARS-CoV-2 vaccine development and clinical trials. Flow cytometry laboratories will be responsible for a large part of this effort by sorting unfixed antigen-specific lymphocytes. Therefore, it is critical and timely that we have an understanding of risk assessment and established procedures of infectious cell sorting. Here we present procedures covering the biosafety aspects of sorting unfixed SARS-CoV-2-infected cells and other infectious agents of similar risk level. These procedures follow the ISAC Biosafety Committee guidelines and were recently approved by the National Institutes of Health Institutional Biosafety Committee for sorting SARS-CoV-2-infected cells. © 2020 International Society for Advancement of Cytometry.
MeSH term(s)	Betacoronavirus/isolation & purification ; COVID-19 ; Containment of Biohazards/methods ; Coronavirus Infections/diagnosis ; Coronavirus Infections/prevention & control ; Flow Cytometry/methods ; Humans ; Laboratories/standards ; Medical Laboratory Personnel/standards ; Pandemics/prevention & control ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/prevention & control ; Risk Assessment ; SARS-CoV-2 ; Specimen Handling/methods
Keywords	covid19
Language	English
Publishing date	2020-06-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2099868-5
ISSN	1552-4930 ; 0196-4763 ; 1552-4922
ISSN (online)	1552-4930
ISSN	0196-4763 ; 1552-4922
DOI	10.1002/cyto.a.24040
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Article ; Online: Acquisition of optimal TFH cell function is defined by specific molecular, positional, and TCR dynamic signatures.

Padhan, Kartika / Moysi, Eirini / Noto, Alessandra / Chassiakos, Alexander / Ghneim, Khader / Perra, Maria Maddalena / Shah, Sanjana / Papaioannou, Vasilis / Fabozzi, Giulia / Ambrozak, David R / Poultsidi, Antigoni / Ioannou, Maria / Fenwick, Craig / Darko, Samuel / Douek, Daniel C / Sekaly, Rafick-Pierre / Pantaleo, Giuseppe / Koup, Richard A / Petrovas, Constantinos

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 18

Abstract: The development of follicular helper CD4 T (TFH) cells is a dynamic process resulting in a heterogenous pool of TFH subsets. However, the cellular and molecular determinants of this heterogeneity and the possible mechanistic links between them is not ... ...

Abstract	The development of follicular helper CD4 T (TFH) cells is a dynamic process resulting in a heterogenous pool of TFH subsets. However, the cellular and molecular determinants of this heterogeneity and the possible mechanistic links between them is not clear. We found that human TFH differentiation is associated with significant changes in phenotypic, chemokine, functional, metabolic and transcriptional profile. Furthermore, this differentiation was associated with distinct positioning to follicular proliferating B cells. Single-cell T cell receptor (TCR) clonotype analysis indicated the transitioning toward PD-1
MeSH term(s)	CD4-Positive T-Lymphocytes/immunology ; CD57 Antigens/genetics ; Cell Communication/immunology ; Cell Differentiation/genetics ; Cell Differentiation/immunology ; Cell Lineage/genetics ; Cell Lineage/immunology ; Chemokines/genetics ; Germinal Center/immunology ; Germinal Center/metabolism ; Humans ; Immunological Synapses/genetics ; Immunological Synapses/immunology ; Lymphocyte Activation/immunology ; Phenotype ; Programmed Cell Death 1 Receptor/genetics ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell/immunology ; T Follicular Helper Cells/immunology ; T Follicular Helper Cells/metabolism ; T-Lymphocyte Subsets/immunology
Chemical Substances	CD57 Antigens ; Chemokines ; PDCD1 protein, human ; Programmed Cell Death 1 Receptor ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2021-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2016855118
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