1
|
Moyano A, Ndlovu B, Mbele M, Naidoo K, Khan N, Mann JK, Ndung'u T. Differing natural killer cell, T cell and antibody profiles in antiretroviral-naive HIV-1 viraemic controllers with and without protective HLA alleles. PLoS One 2023; 18:e0286507. [PMID: 37267224 DOI: 10.1371/journal.pone.0286507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
Previous work suggests that HIV controllers with protective human leukocyte antigen class I alleles (VC+) possess a high breadth of Gag-specific CD8+ T cell responses, while controllers without protective alleles (VC-) have a different unknown mechanism of control. We aimed to gain further insight into potential mechanisms of control in VC+ and VC-. We studied 15 VC+, 12 VC- and 4 healthy uninfected individuals (UI). CD8+ T cell responses were measured by ELISpot. Flow cytometry was performed to analyse surface markers for activation, maturation, and exhaustion on natural killer (NK) cell and T cells, as well as cytokine secretion from stimulated NK cells. We measured plasma neutralization activity against a panel of 18 Env-pseudotyped viruses using the TZM-bl neutralization assay. We found no significant differences in the magnitude and breadth of CD8+ T cell responses between VC+ and VC-. However, NK cells from VC- had higher levels of activation markers (HLA-DR and CD38) (p = 0.03), and lower cytokine expression (MIP-1β and TNF-α) (p = 0.05 and p = 0.04, respectively) than NK cells from VC+. T cells from VC- had higher levels of activation (CD38 and HLA-DR co-expression) (p = 0.05), as well as a trend towards higher expression of the terminal differentiation marker CD57 (p = 0.09) when compared to VC+. There was no difference in overall neutralization breadth between VC+ and VC- groups, although there was a trend for higher neutralization potency in the VC- group (p = 0.09). Altogether, these results suggest that VC- have a more activated NK cell profile with lower cytokine expression, and a more terminally differentiated and activated T cell profile than VC+. VC- also showed a trend of more potent neutralizing antibody responses that may enhance viral clearance. Further studies are required to understand how these NK, T cell and antibody profiles may contribute to differing mechanisms of control in VC+ and VC-.
Collapse
Affiliation(s)
- Ana Moyano
- Africa Health Research Institute, KwaZulu-Natal, South Africa, Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Bongiwe Ndlovu
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Msizi Mbele
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kewreshini Naidoo
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nasreen Khan
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute, KwaZulu-Natal, South Africa, Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
| |
Collapse
|
2
|
Yang L, Caradonna TM, Schmidt AG, Chakraborty AK. Mechanisms that promote the evolution of cross-reactive antibodies upon vaccination with designed influenza immunogens. Cell Rep 2023; 42:112160. [PMID: 36867533 PMCID: PMC10184763 DOI: 10.1016/j.celrep.2023.112160] [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: 02/15/2022] [Revised: 07/18/2022] [Accepted: 02/09/2023] [Indexed: 03/04/2023] Open
Abstract
Immunogens that elicit broadly neutralizing antibodies targeting the conserved receptor-binding site (RBS) on influenza hemagglutinin may serve as candidates for a universal influenza vaccine. Here, we develop a computational model to interrogate antibody evolution by affinity maturation after immunization with two types of immunogens: a heterotrimeric "chimera" hemagglutinin that is enriched for the RBS epitope relative to other B cell epitopes and a cocktail composed of three non-epitope-enriched homotrimers of the monomers that comprise the chimera. Experiments in mice find that the chimera outperforms the cocktail for eliciting RBS-directed antibodies. We show that this result follows from an interplay between how B cells engage these antigens and interact with diverse helper T cells and requires T cell-mediated selection of germinal center B cells to be a stringent constraint. Our results shed light on antibody evolution and highlight how immunogen design and T cells modulate vaccination outcomes.
Collapse
Affiliation(s)
- Leerang Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
3
|
Desikan R, Linderman SL, Davis C, Zarnitsyna VI, Ahmed H, Antia R. Vaccine models predict rules for updating vaccines against evolving pathogens such as SARS-CoV-2 and influenza in the context of pre-existing immunity. Front Immunol 2022; 13:985478. [PMID: 36263031 PMCID: PMC9574365 DOI: 10.3389/fimmu.2022.985478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, vaccines for SARS-CoV-2 and influenza viruses are updated if the new vaccine induces higher antibody-titers to circulating variants than current vaccines. This approach does not account for complex dynamics of how prior immunity skews recall responses to the updated vaccine. We: (i) use computational models to mechanistically dissect how prior immunity influences recall responses; (ii) explore how this affects the rules for evaluating and deploying updated vaccines; and (iii) apply this to SARS-CoV-2. Our analysis of existing data suggests that there is a strong benefit to updating the current SARS-CoV-2 vaccines to match the currently circulating variants. We propose a general two-dose strategy for determining if vaccines need updating as well as for vaccinating high-risk individuals. Finally, we directly validate our model by reanalysis of earlier human H5N1 influenza vaccine studies.
Collapse
Affiliation(s)
- Rajat Desikan
- Clinical Pharmacology Modeling & Simulation, GlaxoSmithKline (GSK), Stevenage, Hertfordshire, United Kingdom
- *Correspondence: Rajat Desikan, ; Rustom Antia,
| | - Susanne L. Linderman
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Carl Davis
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | | | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, United States
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, United States
- *Correspondence: Rajat Desikan, ; Rustom Antia,
| |
Collapse
|
4
|
Arulraj T, Binder SC, Meyer-Hermann M. Investigating the Mechanism of Germinal Center Shutdown. Front Immunol 2022; 13:922318. [PMID: 35911680 PMCID: PMC9329532 DOI: 10.3389/fimmu.2022.922318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Germinal centers (GCs) are transient structures where affinity maturation of B cells gives rise to high affinity plasma and memory cells. The mechanism of GC shutdown is unclear, despite being an important phenomenon maintaining immune homeostasis. In this study, we used a mathematical model to identify mechanisms that can independently promote contraction of GCs leading to shutdown. We show that GC shutdown can be promoted by antigen consumption by B cells, antigen masking by soluble antibodies, alterations in follicular dendritic cell (FDC) network area, modulation of immune complex cycling rate constants, alterations in T follicular helper signaling, increased terminal differentiation and reduced B cell division capacity. Proposed mechanisms promoted GC contraction by ultimately decreasing the number of B cell divisions and recycling cells. Based on the in-silico predictions, we suggest a combination of experiments that can be potentially employed by future studies to unravel the mechanistic basis of GC shutdown such as measurements of the density of pMHC presentation of B cells, FDC network size per B cell, fraction of cells expressing differentiation markers. We also show that the identified mechanisms differentially affect the efficiency of GC reaction estimated based on the quantity and quality of resulting antibodies.
Collapse
Affiliation(s)
- Theinmozhi Arulraj
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sebastian C. Binder
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
- *Correspondence: Michael Meyer-Hermann,
| |
Collapse
|
5
|
Desikan R, Linderman SL, Davis C, Zarnitsyna V, Ahmed H, Antia R. Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.21.492928. [PMID: 35665010 PMCID: PMC9164442 DOI: 10.1101/2022.05.21.492928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
When should vaccines to evolving pathogens such as SARS-CoV-2 be updated? Our computational models address this focusing on updating SARS-CoV-2 vaccines to the currently circulating Omicron variant. Current studies typically compare the antibody titers to the new variant following a single dose of the original-vaccine versus the updated-vaccine in previously immunized individuals. These studies find that the updated-vaccine does not induce higher titers to the vaccine-variant compared with the original-vaccine, suggesting that updating may not be needed. Our models recapitulate this observation but suggest that vaccination with the updated-vaccine generates qualitatively different humoral immunity, a small fraction of which is specific for unique epitopes to the new variant. Our simulations suggest that these new variant-specific responses could dominate following subsequent vaccination or infection with either the currently circulating or future variants. We suggest a two-dose strategy for determining if the vaccine needs updating and for vaccinating high-risk individuals.
Collapse
Affiliation(s)
- Rajat Desikan
- Clinical Pharmacology Modeling & Simulation, GlaxoSmithKline (GSK), Gunnels Wood Rd, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
- These authors contributed equally
| | - Susanne L. Linderman
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Carl Davis
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Veronika Zarnitsyna
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- These authors contributed equally
| |
Collapse
|
6
|
Garg AK, Mittal S, Padmanabhan P, Desikan R, Dixit NM. Increased B Cell Selection Stringency In Germinal Centers Can Explain Improved COVID-19 Vaccine Efficacies With Low Dose Prime or Delayed Boost. Front Immunol 2021; 12:776933. [PMID: 34917089 PMCID: PMC8669483 DOI: 10.3389/fimmu.2021.776933] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022] Open
Abstract
The efficacy of COVID-19 vaccines appears to depend in complex ways on the vaccine dosage and the interval between the prime and boost doses. Unexpectedly, lower dose prime and longer prime-boost intervals have yielded higher efficacies in clinical trials. To elucidate the origins of these effects, we developed a stochastic simulation model of the germinal center (GC) reaction and predicted the antibody responses elicited by different vaccination protocols. The simulations predicted that a lower dose prime could increase the selection stringency in GCs due to reduced antigen availability, resulting in the selection of GC B cells with higher affinities for the target antigen. The boost could relax this selection stringency and allow the expansion of the higher affinity GC B cells selected, improving the overall response. With a longer dosing interval, the decay in the antigen with time following the prime could further increase the selection stringency, amplifying this effect. The effect remained in our simulations even when new GCs following the boost had to be seeded by memory B cells formed following the prime. These predictions offer a plausible explanation of the observed paradoxical effects of dosage and dosing interval on vaccine efficacy. Tuning the selection stringency in the GCs using prime-boost dosages and dosing intervals as handles may help improve vaccine efficacies.
Collapse
Affiliation(s)
- Amar K. Garg
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Soumya Mittal
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| |
Collapse
|
7
|
Robert PA, Arulraj T, Meyer-Hermann M. Ymir: A 3D structural affinity model for multi-epitope vaccine simulations. iScience 2021; 24:102979. [PMID: 34485861 PMCID: PMC8405928 DOI: 10.1016/j.isci.2021.102979] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 07/10/2021] [Accepted: 08/11/2021] [Indexed: 11/05/2022] Open
Abstract
Vaccine development is challenged by the hierarchy of immunodominance between target antigen epitopes and the emergence of antigenic variants by pathogen mutation. The strength and breadth of antibody responses relies on selection and mutation in the germinal center and on the structural similarity between antigens. Computational methods for assessing the breadth of germinal center responses to multivalent antigens are critical to speed up vaccine development. Yet, such methods have poorly reflected the 3D antigen structure and antibody breadth. Here, we present Ymir, a new 3D-lattice-based framework that calculates in silico antibody-antigen affinities. Key physiological properties naturally emerge from Ymir such as affinity jumps, cross-reactivity, and differential epitope accessibility. We validated Ymir by replicating known features of germinal center dynamics. We show that combining antigens with mutated but structurally related epitopes enhances vaccine breadth. Ymir opens a new avenue for understanding vaccine potency based on the structural relationship between vaccine antigens.
Collapse
Affiliation(s)
- Philippe A. Robert
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany
| | - Theinmozhi Arulraj
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
- Centre for Individualised Infection Medicine (CIIM), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| |
Collapse
|
8
|
Meyer-Hermann M. A molecular theory of germinal center B cell selection and division. Cell Rep 2021; 36:109552. [PMID: 34433043 DOI: 10.1016/j.celrep.2021.109552] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/06/2021] [Accepted: 07/27/2021] [Indexed: 01/30/2023] Open
Abstract
The selection of B cells (BCs) in germinal centers (GCs) is pivotal to the generation of high-affinity antibodies and memory BCs, but it lacks global understanding. Based on the idea of a single Tfh-cell signal that controls BC selection and division, experiments appear contradictory. Here, we use the current knowledge on the molecular pathways of GC BCs to develop a theory of GC BC selection and division based on the dynamics of molecular factors. This theory explains the seemingly contradictory experiments by the separation of signals for BC fate decision from signals controlling the number of BC divisions. Three model variants are proposed and experiments are predicted that allow one to distinguish those. Understanding information processing in molecular BC states is critical for targeted immune interventions, and the proposed theory implies that selection and division can be controlled independently in GC reactions.
Collapse
Affiliation(s)
- Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, Braunschweig 38106, Germany; Centre for Individualised Infection Medicine (CIIM), Hannover, Germany; Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany.
| |
Collapse
|
9
|
Ding C, Patel D, Ma Y, Mann JFS, Wu J, Gao Y. Employing Broadly Neutralizing Antibodies as a Human Immunodeficiency Virus Prophylactic & Therapeutic Application. Front Immunol 2021; 12:697683. [PMID: 34354709 PMCID: PMC8329590 DOI: 10.3389/fimmu.2021.697683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/05/2021] [Indexed: 11/18/2022] Open
Abstract
Despite the discovery that the human immunodeficiency virus 1 (HIV-1) is the pathogen of acquired immunodeficiency syndrome (AIDS) in 1983, there is still no effective anti-HIV-1 vaccine. The major obstacle to the development of HIV-1 vaccine is the extreme diversity of viral genome sequences. Nonetheless, a number of broadly neutralizing antibodies (bNAbs) against HIV-1 have been made and identified in this area. Novel strategies based on using these bNAbs as an efficacious preventive and/or therapeutic intervention have been applied in clinical. In this review, we summarize the recent development of bNAbs and its application in HIV-1 acquisition prevention as well as discuss the innovative approaches being used to try to convey protection within individuals at risk and being treated for HIV-1 infection.
Collapse
Affiliation(s)
- Chengchao Ding
- The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Darshit Patel
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Yunjing Ma
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Jamie F S Mann
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Jianjun Wu
- Department of AIDS Research, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yong Gao
- The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.,Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| |
Collapse
|
10
|
Arulraj T, Binder SC, Meyer-Hermann M. In Silico Analysis of the Longevity and Timeline of Individual Germinal Center Reactions in a Primary Immune Response. Cells 2021; 10:cells10071736. [PMID: 34359906 PMCID: PMC8306527 DOI: 10.3390/cells10071736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022] Open
Abstract
Germinal centers (GCs) are transient structures in the secondary lymphoid organs, where B cells undergo affinity maturation to produce high affinity memory and plasma cells. The lifetime of GC responses is a critical factor limiting the extent of affinity maturation and efficiency of antibody responses. While the average lifetime of overall GC reactions in a lymphoid organ is determined experimentally, the lifetime of individual GCs has not been monitored due to technical difficulties in longitudinal analysis. In silico analysis of the contraction phase of GC responses towards primary immunization with sheep red blood cells suggested that if individual GCs had similar lifetimes, the data would be consistent only when new GCs were formed until a very late phase after immunization. Alternatively, there could be a large variation in the lifetime of individual GCs suggesting that both long and short-lived GCs might exist in the same lymphoid organ. Simulations predicted that such differences in the lifetime of GCs could arise due to variations in antigen availability and founder cell composition. These findings identify the potential factors limiting GC lifetime and contribute to an understanding of overall GC responses from the perspective of individual GCs in a primary immune response.
Collapse
Affiliation(s)
- Theinmozhi Arulraj
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany; (T.A.); (S.C.B.)
| | - Sebastian C. Binder
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany; (T.A.); (S.C.B.)
| | - Michael Meyer-Hermann
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany; (T.A.); (S.C.B.)
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Correspondence:
| |
Collapse
|
11
|
Arulraj T, Binder SC, Robert PA, Meyer-Hermann M. Germinal Centre Shutdown. Front Immunol 2021; 12:705240. [PMID: 34305944 PMCID: PMC8293096 DOI: 10.3389/fimmu.2021.705240] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022] Open
Abstract
Germinal Centres (GCs) are transient structures in secondary lymphoid organs, where affinity maturation of B cells takes place following an infection. While GCs are responsible for protective antibody responses, dysregulated GC reactions are associated with autoimmune disease and B cell lymphoma. Typically, ‘normal’ GCs persist for a limited period of time and eventually undergo shutdown. In this review, we focus on an important but unanswered question – what causes the natural termination of the GC reaction? In murine experiments, lack of antigen, absence or constitutive T cell help leads to premature termination of the GC reaction. Consequently, our present understanding is limited to the idea that GCs are terminated due to a decrease in antigen access or changes in the nature of T cell help. However, there is no direct evidence on which biological signals are primarily responsible for natural termination of GCs and a mechanistic understanding is clearly lacking. We discuss the present understanding of the GC shutdown, from factors impacting GC dynamics to changes in cellular interactions/dynamics during the GC lifetime. We also address potential missing links and remaining questions in GC biology, to facilitate further studies to promote a better understanding of GC shutdown in infection and immune dysregulation.
Collapse
Affiliation(s)
- Theinmozhi Arulraj
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sebastian C Binder
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Philippe A Robert
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Immunology, University of Oslo, Oslo, Norway
| | - Michael Meyer-Hermann
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
12
|
Effective inactivated influenza vaccine for the elderly using a single-stranded RNA-based adjuvant. Sci Rep 2021; 11:11981. [PMID: 34099809 PMCID: PMC8184738 DOI: 10.1038/s41598-021-91445-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
There is an unmet need for new influenza vaccine strategies that compensate for impaired vaccine responses in elderly individuals. Here, we evaluated the effectiveness of a single-stranded RNA (ssRNA) as an adjuvant to enhance the efficacy of inactivated influenza vaccine (IIV) in mouse models. Immunization with the ssRNA along with IIV reduced viral titers as well as pathological and inflammatory scores in the lungs after influenza challenge in aged mice. ssRNA induced balanced Th1/Th2 responses with an increase in IgA titers. Moreover, the ssRNA adjuvant markedly increased the frequency of influenza HA-specific T cells and IFN-γ production along with the expression of genes related to innate and adaptive immune systems that could overcome immunosenescence in aged mice. Our findings indicate that ssRNA is an efficient vaccine adjuvant that boosts cellular and humoral immunity in aged mice, demonstrating its potential as a novel adjuvant for currently available influenza virus vaccines for elderly individuals.
Collapse
|
13
|
Cizmeci D, Lofano G, Rossignol E, Dugast AS, Kim D, Cavet G, Nguyen N, Tan YC, Seaman MS, Alter G, Julg B. Distinct clonal evolution of B-cells in HIV controllers with neutralizing antibody breadth. eLife 2021; 10:62648. [PMID: 33843586 PMCID: PMC8041465 DOI: 10.7554/elife.62648] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/02/2021] [Indexed: 01/16/2023] Open
Abstract
A minor subset of individuals infected with HIV-1 develop antibody neutralization breadth during the natural course of the infection, often linked to chronic, high-level viremia. Despite significant efforts, vaccination strategies have been unable to induce similar neutralization breadth and the mechanisms underlying neutralizing antibody induction remain largely elusive. Broadly neutralizing antibody responses can also be found in individuals who control HIV to low and even undetectable plasma levels in the absence of antiretroviral therapy, suggesting that high antigen exposure is not a strict requirement for neutralization breadth. We therefore performed an analysis of paired heavy and light chain B-cell receptor (BCR) repertoires in 12,591 HIV-1 envelope-specific single memory B-cells to determine alterations in the BCR immunoglobulin gene repertoire and B-cell clonal expansions that associate with neutralizing antibody breadth in 22 HIV controllers. We found that the frequency of genomic mutations in IGHV and IGLV was directly correlated with serum neutralization breadth. The repertoire of the most mutated antibodies was dominated by a small number of large clones with evolutionary signatures suggesting that these clones had reached peak affinity maturation. These data demonstrate that even in the setting of low plasma HIV antigenemia, similar to what a vaccine can potentially achieve, BCR selection for extended somatic hypermutation and clonal evolution can occur in some individuals suggesting that host-specific factors might be involved that could be targeted with future vaccine strategies.
Collapse
Affiliation(s)
- Deniz Cizmeci
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Giuseppe Lofano
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Evan Rossignol
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | | | | | - Guy Cavet
- Atreca Inc, Redwood City, United States
| | | | | | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, United States
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Boris Julg
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| |
Collapse
|
14
|
Garg AK, Desikan R, Dixit NM. Preferential Presentation of High-Affinity Immune Complexes in Germinal Centers Can Explain How Passive Immunization Improves the Humoral Response. Cell Rep 2020; 29:3946-3957.e5. [PMID: 31851925 PMCID: PMC7116025 DOI: 10.1016/j.celrep.2019.11.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/12/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Passive immunization (PI) with external antibodies has been used classically for rapid but temporary alleviation of disease. Transcending this role, recent studies have shown PI to induce lasting improvements in natural antibody production, suggesting that PI could become a powerful tool to engineer humoral responses. We propose a mechanism with which PI can alter the humoral response. Antigen-specific B cells evolve and get selected in germinal centers (GCs) on the basis of their ability to acquire antigen from antibody-antigen complexes presented in GCs. When external antibodies of high affinity for antigen are used, they form the majority of the complexes in GCs, letting only B cells with even higher affinities be selected. Using an in silico GC reaction model, we show that this mechanism explains the improved humoral responses following PI. The model also synthesizes several independent experimental observations, indicating the robustness of the mechanism, and proposes tunable handles to optimize PI.
Collapse
Affiliation(s)
- Amar K Garg
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India; Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India.
| |
Collapse
|
15
|
Follicular T-cell subsets in HIV infection: recent advances in pathogenesis research. Curr Opin HIV AIDS 2020; 14:71-76. [PMID: 30585797 DOI: 10.1097/coh.0000000000000525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW T cells within B-cell follicles of secondary lymphoid tissues play key roles in HIV immunopathogenesis. This review highlights recent findings and identifies gaps in current knowledge. RECENT FINDINGS B-cell follicles are major sites of virus replication and demonstrate significant impairments in the generation of humoral immunity in HIV infection. Follicular T helper cells (Tfh), follicular T regulatory cells (Tfr) and follicular CD8 T cells (fCD8) play key roles in HIV immunopathogenesis. Tfh and more recently Tfr are highly permissive to HIV, and may serve as reservoirs of HIV in treated infection. Virus-specific CD8 T cells are less abundant in B-cell follicles than extrafollicular regions, but their effector mechanisms remain an area of significant controversy. Impairments in Tfh likely contribute to impaired humoral immunity and potential mechanisms include B-cell counter-regulatory mechanisms, Tfr suppression and diminished repertoire breadth. A better understanding of the roles of Tfh, Tfr and fCD8 in HIV immunopathogenesis is critical to the development of effective HIV vaccines and cure strategies. SUMMARY Tfh, Tfr and fCD8 contribute to HIV persistence and impaired humoral immunity. A better understanding of their roles could facilitate vaccine development and HIV cure strategies.
Collapse
|
16
|
Mathematical model of broadly reactive plasma cell production. Sci Rep 2020; 10:3935. [PMID: 32127549 PMCID: PMC7054388 DOI: 10.1038/s41598-020-60316-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/04/2020] [Indexed: 11/18/2022] Open
Abstract
Strain-specific plasma cells are capable of producing neutralizing antibodies that are essential for clearance of challenging pathogens. These neutralizing antibodies also function as a main defense against disease establishment in a host. However, when a rapidly mutating pathogen infects a host, successful control of the invasion requires shifting the production of plasma cells from strain-specific to broadly reactive. In this study, we develop a mathematical model of germinal center dynamics and use it to predict the events that lead to improved breadth of the plasma cell response. We examine scenarios that lead to germinal centers that are composed of B-cells that come from a single strain-specific clone, a single broadly reactive clone or both clones. We find that the initial B-cell clonal composition, T-follicular helper cell signaling, increased rounds of productive somatic hypermutation, and B-cell selection strength are among the mechanisms differentiating between strain-specific and broadly reactive plasma cell production during infections. Understanding the contribution of these factors to emergence of breadth may assist in boosting broadly reactive plasma cells production.
Collapse
|
17
|
Dash PK, Kevadiya BD, Su H, Banoub MG, Gendelman HE. Pathways towards human immunodeficiency virus elimination. EBioMedicine 2020; 53:102667. [PMID: 32114397 PMCID: PMC7047153 DOI: 10.1016/j.ebiom.2020.102667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/17/2022] Open
Abstract
Antiretroviral therapy (ART) suppresses human immunodeficiency virus (HIV) infection. Research seeking to transform viral suppression into elimination has generated novel immune, chemical and molecular antiviral agents. However, none, to date, have excised latent integrated proviral DNA or removed infected cells from infected persons. These efforts included, but are not limited to, broadly neutralizing antibodies, "shock" and "kill" latency-reversing agents, innate immune regulators, and sequential long-acting antiretroviral nanoformulated prodrugs and CRISPR-Cas9 gene editing. While, the latter, enabled the complete excision of latent HIV-1 from the host genome success was so far limited. We contend that improvements in antiretroviral delivery, potency, agent specificity, or combinatorial therapies can provide a pathway towards complete HIV elimination.
Collapse
Affiliation(s)
- Prasanta K Dash
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Hang Su
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Mary G Banoub
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA.
| |
Collapse
|
18
|
Neutralizing Antibody Induction by HIV-1 Envelope Glycoprotein SOSIP Trimers on Iron Oxide Nanoparticles May Be Impaired by Mannose Binding Lectin. J Virol 2020; 94:JVI.01883-19. [PMID: 31852794 PMCID: PMC7158715 DOI: 10.1128/jvi.01883-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/12/2019] [Indexed: 01/23/2023] Open
Abstract
We covalently attached human immunodeficiency virus type 1 (HIV-1) Env SOSIP trimers to iron oxide nanoparticles (IO-NPs) to create a particulate immunogen for neutralizing antibody (NAb) induction. The attached trimers, ∼20 per particle, retained native-like antigenicity, judged by reactivity with NAbs and non-NAbs. Bivalent (BG505 and B41) trimer IO-NPs were made, as were IO-NPs displaying B41 trimers carrying a PADRE T-cell helper epitope (TCHE). We immunized mice with B41 soluble or IO-NP trimers after PADRE peptide priming. After two immunizations, IO-NP presentation and the TCHE tag independently and substantially increased anti-trimer antibody responses, but titer differences waned after two further doses. Notable and unexpected findings were that autologous NAbs to the N289 glycan hole epitope were consistently induced in mice given soluble but not IO-NP trimers. Various recombinant mannose binding lectins (MBLs) and MBLs in sera of both murine and human origin bound to soluble and IO-NP trimers. MBL binding occluded the autologous NAb epitope on the B41 IO-NP trimers, which may contribute to its poor immunogenicity. The exposure of a subset of broadly active NAb epitopes was also impaired by MBL binding, which could have substantial implications for the utility of trimer-bearing nanoparticles in general and perhaps also for soluble Env proteins.IMPORTANCE Recombinant trimeric SOSIP proteins are vaccine components intended to induce neutralizing antibodies (NAbs) that prevent cells from infection by human immunodeficiency virus type 1 (HIV-1). A way to increase the strength of antibody responses to these proteins is to present them on the surface of nanoparticles (NPs). We chemically attached about 20 SOSIP trimers to NPs made of iron oxide (IO). The resulting IO-NP trimers had appropriate properties when we studied them in the laboratory but, unexpectedly, were less able to induce NAbs than nonattached trimers when used to immunize mice. We found that mannose binding lectins, proteins naturally present in the serum of mice and other animals, bound strongly to the soluble and IO-NP trimers, blocking access to antibody epitopes in a way that may impede the development of NAb responses. These findings should influence how trimer-bearing NPs of various designs are made and used.
Collapse
|
19
|
Verma A, Schmidt BA, Elizaldi SR, Nguyen NK, Walter KA, Beck Z, Trinh HV, Dinasarapu AR, Lakshmanappa YS, Rane NN, Matyas GR, Rao M, Shen X, Tomaras GD, LaBranche CC, Reimann KA, Foehl DH, Gach JS, Forthal DN, Kozlowski PA, Amara RR, Iyer SS. Impact of T h1 CD4 Follicular Helper T Cell Skewing on Antibody Responses to an HIV-1 Vaccine in Rhesus Macaques. J Virol 2020; 94:e01737-19. [PMID: 31827000 PMCID: PMC7158739 DOI: 10.1128/jvi.01737-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Generating durable humoral immunity through vaccination depends upon effective interactions of follicular helper T (Tfh) cells with germinal center (GC) B cells. Th1 polarization of Tfh cells is an important process shaping the success of Tfh-GC B cell interactions by influencing costimulatory and cytokine-dependent Tfh help to B cells. However, the question remains as to whether adjuvant-dependent modulation of Tfh cells enhances HIV-1 vaccine-induced antienvelope (anti-Env) antibody responses. We investigated whether an HIV-1 vaccine platform designed to increase the number of Th1-polarized Tfh cells enhances the magnitude and quality of anti-Env antibodies. Utilizing a novel interferon-induced protein 10 (IP-10)-adjuvanted HIV-1 DNA prime followed by a monophosphoryl lipid A and QS-21 (MPLA+QS-21)-adjuvanted Env protein boost (DIP-10 PALFQ) in macaques, we observed higher anti-Env serum IgG titers with greater cross-clade reactivity, specificity for V1V2, and effector functions than in macaques primed with DNA lacking IP-10 and boosted with MPLA-plus-alum-adjuvanted Env protein (DPALFA) The DIP-10 PALFQ vaccine regimen elicited higher anti-Env IgG1 and lower IgG4 antibody levels in serum, showing for the first time that adjuvants can dramatically impact the IgG subclass profile in macaques. The DIP-10 PALFQ regimen also increased vaginal and rectal IgA antibodies to a greater extent. Within lymph nodes, we observed augmented GC B cell responses and the promotion of Th1 gene expression profiles in GC Tfh cells. The frequency of GC Tfh cells correlated with both the magnitude and avidity of anti-Env serum IgG. Together, these data suggest that adjuvant-induced stimulation of Th1-Tfh cells is an effective strategy for enhancing the magnitude and quality of anti-Env antibody responses.IMPORTANCE The results of the RV144 trial demonstrated that vaccination could prevent HIV transmission in humans and that longevity of anti-Env antibodies may be key to this protection. Efforts to improve upon the prime-boost vaccine regimen used in RV144 have indicated that booster immunizations can increase serum anti-Env antibody titers but only transiently. Poor antibody durability hampers efforts to develop an effective HIV-1 vaccine. This study was designed to identify the specific elements involved in the immunological mechanism necessary to produce robust HIV-1-specific antibodies in rhesus macaques. By clearly defining immune-mediated pathways that improve the magnitude and functionality of the anti-HIV-1 antibody response, we will have the foundation necessary for the rational development of an HIV-1 vaccine.
Collapse
Affiliation(s)
- Anil Verma
- The Center for Immunology and Infectious Diseases, UC Davis, Davis, California, USA
| | - Brian A Schmidt
- The Center for Immunology and Infectious Diseases, UC Davis, Davis, California, USA
| | - Sonny R Elizaldi
- The Center for Immunology and Infectious Diseases, UC Davis, Davis, California, USA
- Graduate Group in Immunology, UC Davis, Davis, California, USA
| | - Nancy K Nguyen
- The Center for Immunology and Infectious Diseases, UC Davis, Davis, California, USA
| | - Korey A Walter
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Zoltan Beck
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
- U.S. Military HIV Research Program, Laboratory of Adjuvant and Antigen Research, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Hung V Trinh
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
- U.S. Military HIV Research Program, Laboratory of Adjuvant and Antigen Research, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ashok R Dinasarapu
- Emory Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | | | - Niharika N Rane
- The Center for Immunology and Infectious Diseases, UC Davis, Davis, California, USA
| | - Gary R Matyas
- U.S. Military HIV Research Program, Laboratory of Adjuvant and Antigen Research, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Laboratory of Adjuvant and Antigen Research, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Keith A Reimann
- Nonhuman Primate Reagent Resource, MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, USA
| | - David H Foehl
- Nonhuman Primate Reagent Resource, MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, USA
| | - Johannes S Gach
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, School of Medicine, UC Irvine, Irvine, California, USA
| | - Donald N Forthal
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, School of Medicine, UC Irvine, Irvine, California, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, School of Medicine, UC Irvine, Irvine, California, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Smita S Iyer
- The Center for Immunology and Infectious Diseases, UC Davis, Davis, California, USA
- California National Primate Research Center, School of Veterinary Medicine, UC Davis, Davis, California, USA
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, UC Davis, Davis, California, USA
| |
Collapse
|
20
|
|
21
|
Meyer-Hermann M. Injection of Antibodies against Immunodominant Epitopes Tunes Germinal Centers to Generate Broadly Neutralizing Antibodies. Cell Rep 2019; 29:1066-1073.e5. [DOI: 10.1016/j.celrep.2019.09.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/19/2019] [Accepted: 09/18/2019] [Indexed: 12/28/2022] Open
|
22
|
Arulraj T, Binder SC, Robert PA, Meyer-Hermann M. Synchronous Germinal Center Onset Impacts the Efficiency of Antibody Responses. Front Immunol 2019; 10:2116. [PMID: 31555300 PMCID: PMC6742702 DOI: 10.3389/fimmu.2019.02116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 08/22/2019] [Indexed: 12/25/2022] Open
Abstract
The germinal center reaction is an important target for modulating antibody responses. Antibody production from germinal centers is regulated by a negative feedback mechanism termed antibody feedback. By imposing antibody feedback, germinal centers can interact and regulate the output of other germinal centers. Using an agent-based model of the germinal center reaction, we studied the impact of antibody feedback on kinetics and efficiency of a germinal center. Our simulations predict that high feedback of antibodies from germinal centers reduces the production of plasma cells and subsequently the efficiency of the germinal center reaction by promoting earlier termination. Affinity maturation is only weakly improved by increased antibody feedback and ultimately interrupted because of premature termination of the reaction. The model predicts that the asynchronous onset and changes in number of germinal centers could alter the efficiency of antibody response due to changes in feedback by soluble antibodies. Consequently, late initialized germinal centers have a compromised output due to higher antibody feedback from the germinal centers formed earlier. The results demonstrate potential effects of germinal center intercommunication and highlight the importance of understanding germinal center interactions for optimizing the antibody response, in particular, in the elderly and in the context of vaccination.
Collapse
Affiliation(s)
- Theinmozhi Arulraj
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sebastian C Binder
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Centre for Individualized Infection Medicine (CIIM), Hanover, Germany
| | - Philippe A Robert
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Centre for Individualized Infection Medicine (CIIM), Hanover, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
23
|
Martínez L, Milanič M, Malaina I, Álvarez C, Pérez MB, M. de la Fuente I. Weighted lambda superstrings applied to vaccine design. PLoS One 2019; 14:e0211714. [PMID: 30735507 PMCID: PMC6368308 DOI: 10.1371/journal.pone.0211714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/19/2019] [Indexed: 11/23/2022] Open
Abstract
We generalize the notion of λ-superstrings, presented in a previous paper, to the notion of weighted λ-superstrings. This generalization entails an important improvement in the applications to vaccine designs, as it allows epitopes to be weighted by their immunogenicities. Motivated by these potential applications of constructing short weighted λ-superstrings to vaccine design, we approach this problem in two ways. First, we formalize the problem as a combinatorial optimization problem (in fact, as two polynomially equivalent problems) and develop an integer programming (IP) formulation for solving it optimally. Second, we describe a model that also takes into account good pairwise alignments of the obtained superstring with the input strings, and present a genetic algorithm that solves the problem approximately. We apply both algorithms to a set of 169 strings corresponding to the Nef protein taken from patiens infected with HIV-1. In the IP-based algorithm, we take the epitopes and the estimation of the immunogenicities from databases of experimental epitopes. In the genetic algorithm we take as candidate epitopes all 9-mers present in the 169 strings and estimate their immunogenicities using a public bioinformatics tool. Finally, we used several bioinformatic tools to evaluate the properties of the candidates generated by our method, which indicated that we can score high immunogenic λ-superstrings that at the same time present similar conformations to the Nef virus proteins.
Collapse
Affiliation(s)
- Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Basque Center for Applied Mathematics BCAM, Bilbao, Spain
- * E-mail:
| | - Martin Milanič
- University of Primorska, UP IAM and UP FAMNIT, Koper, Slovenia
| | - Iker Malaina
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Carmen Álvarez
- IDIVAL Valdecilla Biomedical Research Institute, Santander, Spain
| | - Martín-Blas Pérez
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Ildefonso M. de la Fuente
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Department of Nutrition, CEBAS-CSIC Institute, Murcia, Spain
| |
Collapse
|
24
|
Nandagopal P, Bhattacharya J, Srikrishnan AK, Goyal R, Ravichandran Swathirajan C, Patil S, Saravanan S, Deshpande S, Vignesh R, Solomon SS, Singla N, Mukherjee J, Murugavel KG. Broad neutralization response in a subset of HIV-1 subtype C-infected viraemic non-progressors from southern India. J Gen Virol 2018; 99:379-392. [PMID: 29458681 DOI: 10.1099/jgv.0.001016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Broadly neutralizing antibodies (bnAbs) have been considered to be potent therapeutic tools and potential vaccine candidates to enable protection against various clades of human immunodeficiency virus (HIV). The generation of bnAbs has been associated with enhanced exposure to antigen, high viral load and low CD4+ T cell counts, among other factors. However, only limited data are available on the generation of bnAbs in viraemic non-progressors that demonstrate moderate to high viraemia. Further, since HIV-1 subtype C viruses account for more than 50 % of global HIV infections, the identification of bnAbs with novel specificities is crucial to enable the development of potent tools to aid in HIV therapy and prevention. In the present study, we analysed and compared the neutralization potential of responses in 70 plasma samples isolated from ART-naïve HIV-1 subtype C-infected individuals with various disease progression profiles against a panel of 30 pseudoviruses. Among the seven samples that exhibited a neutralization breadth of ≥70 %, four were identified as 'elite neutralizers', and three of these were from viraemic non-progressors while the fourth was from a typical progressor. Analysis of the neutralization specificities revealed that none of the four elite neutralizers were reactive to epitopes in the membrane proximal external region (MPER), CD4-binding site and V1V2 or V3 glycan. However, two of the four elite neutralizers exhibited enhanced sensitivity towards viruses lacking N332 glycan, indicating high neutralization potency. Overall, our findings indicate that the identification of potent neutralization responses with distinct epitope specificities is possible from the as yet unexplored Indian population, which has a high prevalence of HIV-1 subtype C infection.
Collapse
Affiliation(s)
| | - Jayanta Bhattacharya
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | | | - Rajat Goyal
- International AIDS Vaccine Initiative (IAVI), New Delhi, India
| | | | - Shilpa Patil
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | | | - Suprit Deshpande
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Ramachandran Vignesh
- YRG Center for AIDS Research and Education, Chennai, India.,Laboratory-based Department, UniKL-Royal College of Medicine Perak (UniKL-RCMP), Universiti Kuala Lumpur, Greentown, Ipoh 30450, Malaysia
| | - Sunil Suhas Solomon
- YRG Center for AIDS Research and Education, Chennai, India.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nikhil Singla
- International AIDS Vaccine Initiative (IAVI), New Delhi, India
| | | | | |
Collapse
|