1
|
Purcell RA, Theisen RM, Arnold KB, Chung AW, Selva KJ. Polyfunctional antibodies: a path towards precision vaccines for vulnerable populations. Front Immunol 2023; 14:1183727. [PMID: 37600816 PMCID: PMC10433199 DOI: 10.3389/fimmu.2023.1183727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/30/2023] [Indexed: 08/22/2023] Open
Abstract
Vaccine efficacy determined within the controlled environment of a clinical trial is usually substantially greater than real-world vaccine effectiveness. Typically, this results from reduced protection of immunologically vulnerable populations, such as children, elderly individuals and people with chronic comorbidities. Consequently, these high-risk groups are frequently recommended tailored immunisation schedules to boost responses. In addition, diverse groups of healthy adults may also be variably protected by the same vaccine regimen. Current population-based vaccination strategies that consider basic clinical parameters offer a glimpse into what may be achievable if more nuanced aspects of the immune response are considered in vaccine design. To date, vaccine development has been largely empirical. However, next-generation approaches require more rational strategies. We foresee a generation of precision vaccines that consider the mechanistic basis of vaccine response variations associated with both immunogenetic and baseline health differences. Recent efforts have highlighted the importance of balanced and diverse extra-neutralising antibody functions for vaccine-induced protection. However, in immunologically vulnerable populations, significant modulation of polyfunctional antibody responses that mediate both neutralisation and effector functions has been observed. Here, we review the current understanding of key genetic and inflammatory modulators of antibody polyfunctionality that affect vaccination outcomes and consider how this knowledge may be harnessed to tailor vaccine design for improved public health.
Collapse
Affiliation(s)
- Ruth A. Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Robert M. Theisen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Kelly B. Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Amy W. Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Kevin J. Selva
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
2
|
Bharadwaj P, Shrestha S, Pongracz T, Concetta C, Sharma S, Le Moine A, de Haan N, Murakami N, Riella LV, Holovska V, Wuhrer M, Marchant A, Ackerman ME. Afucosylation of HLA-specific IgG1 as a potential predictor of antibody pathogenicity in kidney transplantation. Cell Rep Med 2022; 3:100818. [PMID: 36384101 PMCID: PMC9729883 DOI: 10.1016/j.xcrm.2022.100818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/23/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Antibody-mediated rejection (AMR) is the leading cause of graft failure. While donor-specific antibodies (DSAs) are associated with a higher risk of AMR, not all patients with DSAs develop rejection, suggesting that the characteristics of alloantibodies determining their pathogenicity remain undefined. Using human leukocyte antigen (HLA)-A2-specific antibodies as a model, we apply systems serology tools to investigate qualitative features of immunoglobulin G (IgG) alloantibodies including Fc-glycosylation patterns and FcγR-binding properties. Levels of afucosylated anti-A2 antibodies are elevated in seropositive patients, especially those with AMR, suggesting potential cytotoxicity via FcγRIII-mediated mechanisms. Afucosylation of both glycoengineered monoclonal and naturally glycovariant polyclonal serum IgG specific to HLA-A2 drives potentiated binding to, slower dissociation from, and enhanced signaling through FcγRIII, a receptor widely expressed on innate effector cells, and greater cytotoxicity against HLA-A2+ cells mediated by natural killer (NK) cells. Collectively, these results suggest that afucosylated DSA may be a biomarker of AMR and contribute to pathogenesis.
Collapse
Affiliation(s)
- Pranay Bharadwaj
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Sweta Shrestha
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Tamas Pongracz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Catalano Concetta
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium,Department of Nephrology, Dialysis and Renal Transplantation, Hôpital Erasme, Université libre de Bruxelles, Bruxelles, Belgium
| | - Shilpee Sharma
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Alain Le Moine
- Department of Nephrology, Dialysis and Renal Transplantation, Hôpital Erasme, Université libre de Bruxelles, Bruxelles, Belgium
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Naoka Murakami
- Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonardo V. Riella
- Division of Nephrology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Vanda Holovska
- HLA Laboratory, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB), Hôpital Erasme ULB, Brussels, Belgium
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnaud Marchant
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA,Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA,Corresponding author
| |
Collapse
|
3
|
Abstract
PURPOSE OF REVIEW The quest for HIV-1 cure could take advantage of the study of rare individuals that control viral replication spontaneously (elite controllers) or after an initial course of antiretroviral therapy (posttreatment controllers, PTCs). In this review, we will compare back-to-back the immunological and virological features underlying viral suppression in elite controllers and PTCs, and explore their possible contributions to the HIV-1 cure research. RECENT FINDINGS HIV-1 control in elite controllers shows hallmarks of an effective antiviral response, favored by genetic background and possibly associated to residual immune activation. The immune pressure in elite controllers might select against actively transcribing intact proviruses, allowing the persistence of a small and poorly inducible reservoir. Evidence on PTCs is less abundant but preliminary data suggest that antiviral immune responses may be less pronounced. Therefore, these patients may rely on distinct mechanisms, not completely elucidated to date, suppressing HIV-1 transcription and replication. SUMMARY PTCs and elite controllers may control HIV replication using distinct pathways, the elucidation of which may contribute to design future interventional strategies aiming to achieve a functional cure.
Collapse
|
4
|
Lin LY, Carapito R, Su B, Moog C. Fc receptors and the diversity of antibody responses to HIV infection and vaccination. Genes Immun 2022; 23:149-156. [PMID: 35688931 PMCID: PMC9388370 DOI: 10.1038/s41435-022-00175-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022]
Abstract
The development of an effective vaccine against HIV is desperately needed. The successive failures of HIV vaccine efficacy trials in recent decades have shown the difficulty of inducing an appropriate protective immune response to fight HIV. Different correlates of antibody parameters associated with a decreased risk of HIV-1 acquisition have been identified. However, these parameters are difficult to reproduce and improve, possibly because they have an intricate and combined action. Here, we describe the numerous antibody (Ab) functions associated with HIV-1 protection and report the interrelated parameters regulating their complex functions. Indeed, besides neutralizing and Fc-mediated activity, additional factors such as Ab type, concentration and kinetics of induction, and Fc-receptor expression and binding capacity also influence the protective effect conferred by Abs. As these parameters were described to be associated with ethnicity, age and sex, these additional factors must be considered for the development of an effective immune response. Therefore, future vaccine designs need to consider these multifaceted Ab functions together with the demographic attributes of the patient populations.
Collapse
Affiliation(s)
- Li-Yun Lin
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Institut thématique interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Institut thématique interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Christiane Moog
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Institut thématique interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France. .,Vaccine Research Institute (VRI), Créteil, France.
| |
Collapse
|
5
|
Bernard NF, Kant S, Kiani Z, Tremblay C, Dupuy FP. Natural Killer Cells in Antibody Independent and Antibody Dependent HIV Control. Front Immunol 2022; 13:879124. [PMID: 35720328 PMCID: PMC9205404 DOI: 10.3389/fimmu.2022.879124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Abstract
Infection with the human immunodeficiency virus (HIV), when left untreated, typically leads to disease progression towards acquired immunodeficiency syndrome. Some people living with HIV (PLWH) control their virus to levels below the limit of detection of standard viral load assays, without treatment. As such, they represent examples of a functional HIV cure. These individuals, called Elite Controllers (ECs), are rare, making up <1% of PLWH. Genome wide association studies mapped genes in the major histocompatibility complex (MHC) class I region as important in HIV control. ECs have potent virus specific CD8+ T cell responses often restricted by protective MHC class I antigens. Natural Killer (NK) cells are innate immune cells whose activation state depends on the integration of activating and inhibitory signals arising from cell surface receptors interacting with their ligands on neighboring cells. Inhibitory NK cell receptors also use a subset of MHC class I antigens as ligands. This interaction educates NK cells, priming them to respond to HIV infected cell with reduced MHC class I antigen expression levels. NK cells can also be activated through the crosslinking of the activating NK cell receptor, CD16, which binds the fragment crystallizable portion of immunoglobulin G. This mode of activation confers NK cells with specificity to HIV infected cells when the antigen binding portion of CD16 bound immunoglobulin G recognizes HIV Envelope on infected cells. Here, we review the role of NK cells in antibody independent and antibody dependent HIV control.
Collapse
Affiliation(s)
- Nicole F. Bernard
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Clinical Immunology, McGill University Health Centre, Montreal, QC, Canada
- *Correspondence: Nicole F. Bernard,
| | - Sanket Kant
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Zahra Kiani
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Department of Microbiology Infectiology and Immunology, University of Montreal, Montreal, QC, Canada
| | - Franck P. Dupuy
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| |
Collapse
|
6
|
Molinos-Albert LM, Lorin V, Monceaux V, Orr S, Essat A, Dufloo J, Schwartz O, Rouzioux C, Meyer L, Hocqueloux L, Sáez-Cirión A, Mouquet H, Prazuck T, Dieuleveult BD, Bani-Sadr F, Hentzien M, Berger JL, Kmiec I, Pichancourt G, Nasri S, Hittinger G, Lambry V, Beauey AC, Pialoux G, Palacios C, Siguier M, Adda A, Foucoin J, Weiss L, Karmochkine M, Meghadecha M, Ptak M, Salmon-Ceron D, Blanche P, Piétri MP, Molina JM, Taulera O, Lascoux-Combe C, Ponscarme D, Bertaut JD, Makhloufi D, Godinot M, Artizzu V, Yazdanpanah Y, Matheron S, Godard C, Julia Z, Bernard L, Bastides F, Bourgault O, Jacomet C, Goncalves E, Meybeck A, Huleux T, Cornavin P, Debab Y, Théron D, Miailhes P, Cotte L, Pailhes S, Ogoudjobi S, Viard JP, Dulucq MJ, Bodard L, Churaqui F, Guimard T, Laine L. Transient viral exposure drives functionally-coordinated humoral immune responses in HIV-1 post-treatment controllers. Nat Commun 2022; 13:1944. [PMID: 35410989 PMCID: PMC9001681 DOI: 10.1038/s41467-022-29511-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 03/21/2022] [Indexed: 12/11/2022] Open
Abstract
AbstractHIV-1 post-treatment controllers are rare individuals controlling HIV-1 infection for years after antiretroviral therapy interruption. Identification of immune correlates of control in post-treatment controllers could aid in designing effective HIV-1 vaccine and remission strategies. Here, we perform comprehensive immunoprofiling of the humoral response to HIV-1 in long-term post-treatment controllers. Global multivariate analyses combining clinico-virological and humoral immune data reveal distinct profiles in post-treatment controllers experiencing transient viremic episodes off therapy compared to those stably aviremic. Virally-exposed post-treatment controllers display stronger HIV-1 humoral responses, and develop more frequently Env-specific memory B cells and cross-neutralizing antibodies. Both are linked to short viremic exposures, which are also accompanied by an increase in blood atypical memory B cells and activated subsets of circulating follicular helper T cells. Still, most humoral immune variables only correlate with Th2-like circulating follicular helper T cells. Thus, post-treatment controllers form a heterogeneous group with two distinct viral behaviours and associated immune signatures. Post-treatment controllers stably aviremic present “silent” humoral profiles, while those virally-exposed develop functionally robust HIV-specific B-cell and antibody responses, which may participate in controlling infection.
Collapse
|
7
|
Natarajan H, Xu S, Crowley AR, Butler SE, Weiner JA, Bloch EM, Littlefield K, Benner SE, Shrestha R, Ajayi O, Wieland-Alter W, Sullivan D, Shoham S, Quinn TC, Casadevall A, Pekosz A, Redd AD, Tobian AAR, Connor RI, Wright PF, Ackerman ME. Antibody attributes that predict the neutralization and effector function of polyclonal responses to SARS-CoV-2. BMC Immunol 2022; 23:7. [PMID: 35172720 PMCID: PMC8851712 DOI: 10.1186/s12865-022-00480-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND While antibodies can provide significant protection from SARS-CoV-2 infection and disease sequelae, the specific attributes of the humoral response that contribute to immunity are incompletely defined. METHODS We employ machine learning to relate characteristics of the polyclonal antibody response raised by natural infection to diverse antibody effector functions and neutralization potency with the goal of generating both accurate predictions of each activity based on antibody response profiles as well as insights into antibody mechanisms of action. RESULTS To this end, antibody-mediated phagocytosis, cytotoxicity, complement deposition, and neutralization were accurately predicted from biophysical antibody profiles in both discovery and validation cohorts. These models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion. CONCLUSIONS Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions.
Collapse
Affiliation(s)
- Harini Natarajan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Shiwei Xu
- Program in Quantitative Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Andrew R Crowley
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Savannah E Butler
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Joshua A Weiner
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kirsten Littlefield
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sarah E Benner
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ruchee Shrestha
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Olivia Ajayi
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Wendy Wieland-Alter
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - David Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shmuel Shoham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas C Quinn
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew D Redd
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ruth I Connor
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Peter F Wright
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Margaret E Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA.
- Program in Quantitative Biological Sciences, Dartmouth College, Hanover, NH, USA.
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.
| |
Collapse
|
8
|
Cheng HD, Dowell KG, Bailey-Kellogg C, Goods BA, Love JC, Ferrari G, Alter G, Gach J, Forthal DN, Lewis GK, Greene K, Gao H, Montefiori DC, Ackerman ME. Diverse antiviral IgG effector activities are predicted by unique biophysical antibody features. Retrovirology 2021; 18:35. [PMID: 34717659 PMCID: PMC8557579 DOI: 10.1186/s12977-021-00579-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/20/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The critical role of antibody Fc-mediated effector functions in immune defense has been widely reported in various viral infections. These effector functions confer cellular responses through engagement with innate immune cells. The precise mechanism(s) by which immunoglobulin G (IgG) Fc domain and cognate receptors may afford protection are poorly understood, however, in the context of HIV/SHIV infections. Many different in vitro assays have been developed and utilized to measure effector functions, but the extent to which these assays capture distinct antibody activities has not been fully elucidated. RESULTS In this study, six Fc-mediated effector function assays and two biophysical antibody profiling assays were performed on a common set of samples from HIV-1 infected and vaccinated subjects. Biophysical antibody profiles supported robust prediction of diverse IgG effector functions across distinct Fc-mediated effector function assays. While a number of assays showed correlated activities, supervised machine learning models indicated unique antibody features as primary contributing factors to the associated effector functions. Additional experiments established the mechanistic relevance of relationships discovered using this unbiased approach. CONCLUSIONS In sum, this study provides better resolution on the diversity and complexity of effector function assays, offering a clearer perspective into this family of antibody mechanisms of action to inform future HIV-1 treatment and vaccination strategies.
Collapse
Affiliation(s)
- Hao D. Cheng
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA ,grid.254880.30000 0001 2179 2404Molecular and Cellular Biology Program, Dartmouth College, 14 Engineering Dr., Hanover, NH 03755 USA
| | - Karen G. Dowell
- grid.254880.30000 0001 2179 2404Department of Computer Science, Dartmouth College, Hanover, 03755 USA
| | - Chris Bailey-Kellogg
- grid.254880.30000 0001 2179 2404Department of Computer Science, Dartmouth College, Hanover, 03755 USA
| | - Brittany A. Goods
- grid.116068.80000 0001 2341 2786Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,grid.116068.80000 0001 2341 2786Department of Biological Engineering, Koch Institute at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - J. Christopher Love
- grid.116068.80000 0001 2341 2786Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,grid.116068.80000 0001 2341 2786Department of Biological Engineering, Koch Institute at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Guido Ferrari
- grid.189509.c0000000100241216Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA ,grid.189509.c0000000100241216Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27719 USA
| | - Galit Alter
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Johannes Gach
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, Irvine School of Medicine, University California, Irvine, CA 92697 USA
| | - Donald N. Forthal
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, Irvine School of Medicine, University California, Irvine, CA 92697 USA
| | - George K. Lewis
- grid.411024.20000 0001 2175 4264Division of Vaccine Research, Institute of Human Virology, University Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Kelli Greene
- grid.189509.c0000000100241216Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA
| | - Hongmei Gao
- grid.189509.c0000000100241216Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA
| | - David C. Montefiori
- grid.189509.c0000000100241216Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA ,grid.189509.c0000000100241216Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27719 USA
| | - Margaret E. Ackerman
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA ,grid.254880.30000 0001 2179 2404Molecular and Cellular Biology Program, Dartmouth College, 14 Engineering Dr., Hanover, NH 03755 USA
| |
Collapse
|
9
|
Tan ZC, Murphy MC, Alpay HS, Taylor SD, Meyer AS. Tensor-structured decomposition improves systems serology analysis. Mol Syst Biol 2021; 17:e10243. [PMID: 34487431 PMCID: PMC8420856 DOI: 10.15252/msb.202110243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 01/04/2023] Open
Abstract
Systems serology provides a broad view of humoral immunity by profiling both the antigen-binding and Fc properties of antibodies. These studies contain structured biophysical profiling across disease-relevant antigen targets, alongside additional measurements made for single antigens or in an antigen-generic manner. Identifying patterns in these measurements helps guide vaccine and therapeutic antibody development, improve our understanding of diseases, and discover conserved regulatory mechanisms. Here, we report that coupled matrix-tensor factorization (CMTF) can reduce these data into consistent patterns by recognizing the intrinsic structure of these data. We use measurements from two previous studies of HIV- and SARS-CoV-2-infected subjects as examples. CMTF outperforms standard methods like principal components analysis in the extent of data reduction while maintaining equivalent prediction of immune functional responses and disease status. Under CMTF, model interpretation improves through effective data reduction, separation of the Fc and antigen-binding effects, and recognition of consistent patterns across individual measurements. Data reduction also helps make prediction models more replicable. Therefore, we propose that CMTF is an effective general strategy for data exploration in systems serology.
Collapse
Affiliation(s)
- Zhixin Cyrillus Tan
- Bioinformatics Interdepartmental ProgramUniversity of California, Los AngelesLos AngelesCAUSA
| | - Madeleine C Murphy
- Computational and Systems BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Hakan S Alpay
- Department of Computer ScienceUniversity of California, Los AngelesLos AngelesCAUSA
| | - Scott D Taylor
- Department of BioengineeringUniversity of California, Los AngelesLos AngelesCAUSA
| | - Aaron S Meyer
- Bioinformatics Interdepartmental ProgramUniversity of California, Los AngelesLos AngelesCAUSA
- Department of BioengineeringUniversity of California, Los AngelesLos AngelesCAUSA
- Jonsson Comprehensive Cancer CenterUniversity of California, Los AngelesLos AngelesCAUSA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchUniversity of California, Los AngelesLos AngelesCAUSA
| |
Collapse
|
10
|
Natarajan H, Xu S, Crowley AR, Butler SE, Weiner JA, Bloch EM, Littlefield K, Benner SE, Shrestha R, Ajayi O, Wieland-alter W, Sullivan D, Shoham S, Quinn TC, Casadevall A, Pekosz A, Redd AD, Tobian AA, Connor RI, Wright PF, Ackerman ME. Antibody Attributes that Predict the Neutralization and Effector Function of Polyclonal Responses to SARS-CoV-2.. [PMID: 34401890 PMCID: PMC8366811 DOI: 10.1101/2021.08.06.21261710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
While antibodies provide significant protection from SARS-CoV-2 infection and disease sequelae, the specific attributes of the humoral response that contribute to immunity are incompletely defined. In this study, we employ machine learning to relate characteristics of the polyclonal antibody response raised by natural infection to diverse antibody effector functions and neutralization potency with the goal of generating both accurate predictions of each activity based on antibody response profiles as well as insights into antibody mechanisms of action. To this end, antibody-mediated phagocytosis, cytotoxicity, complement deposition, and neutralization were accurately predicted from biophysical antibody profiles in both discovery and validation cohorts. These predictive models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion. Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions.
Collapse
|
11
|
Abstract
Glycans play important roles in the biology of infectious diseases. Although glycans are expressed on both the pathogens and the host, the functions and dynamics of the host glycome during infection are not well understood. Recent years have witnessed new discoveries on the host glycome respsonse to infection, as well as related mechanisms and their implications. Herein, we present a brief review on the latest findings in this field and put them in the context of host immunity.
Collapse
Affiliation(s)
- Rui Qin
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
| |
Collapse
|
12
|
Moritz CP, Tholance Y, Stoevesandt O, Ferraud K, Camdessanché JP, Antoine JC. CIDP Antibodies Target Junction Proteins and Identify Patient Subgroups: An Autoantigenomic Approach. Neurol Neuroimmunol Neuroinflamm 2021; 8:8/2/e944. [PMID: 33408168 PMCID: PMC7862091 DOI: 10.1212/nxi.0000000000000944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/29/2020] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To discover systemic characteristics in the repertoires of targeted autoantigens in chronic inflammatory demyelinating polyneuropathy (CIDP), we detected the entire autoantigen repertoire of patients and controls and analyzed them systematically. METHODS We screened 43 human serum samples, of which 22 were from patients with CIDP, 12 from patients with other neuropathies, and 9 from healthy controls via HuProt Human Proteome microarrays testing about 16,000 distinct human bait proteins. Autoantigen repertoires were analyzed via bioinformatical autoantigenomic approaches: principal component analysis, analysis of the repertoire sizes in disease groups and clinical subgroups, and overrepresentation analyses using Gene Ontology and PantherDB. RESULTS The autoantigen repertoires enabled the identification of a subgroup of 10/22 patients with CIDP with a younger age at onset and a higher frequency of mixed motor and sensory CIDP. IV immunoglobulin therapy responders targeted 3 times more autoantigens than nonresponders. No CIDP-specific autoantibody is present in all patients; however, anchoring junction components were significantly targeted by 86.4% of patients with CIDP. There are potential novel CIDP-specific autoantigens such as the myelination- or axo-glial structure-related proteins actin-related protein 2/3 complex subunit 1B, band 4.1-like protein 2, cadherin-15, cytohesin-1, epidermal growth factor receptor, ezrin, and radixin. CONCLUSIONS The repertoire of targeted autoantigens of patients with CIDP differs in a systematic degree from those of controls. Systematic autoantigenomic approaches can help to understand the disease and to discover novel bioinformatical tools and novel autoantigen panels to improve diagnosis, treatment, prognosis, or patient stratification.
Collapse
Affiliation(s)
- Christian P Moritz
- From the Department of Neurology (C.P.M., K.F., J.-P.C., J.-C.A.), and Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne; Synaptopathies and Autoantibodies (C.P.M., Y.T., J.-P.C., J.-C.A.), Institut NeuroMyoGène, INSERM U1217/CNRS UMR 5310, University of Lyon, University Jean-Monnet, Saint-Étienne, France; and Cambridge Protein Arrays Ltd. (O.S.), Babraham Research Campus, United Kingdom.
| | - Yannick Tholance
- From the Department of Neurology (C.P.M., K.F., J.-P.C., J.-C.A.), and Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne; Synaptopathies and Autoantibodies (C.P.M., Y.T., J.-P.C., J.-C.A.), Institut NeuroMyoGène, INSERM U1217/CNRS UMR 5310, University of Lyon, University Jean-Monnet, Saint-Étienne, France; and Cambridge Protein Arrays Ltd. (O.S.), Babraham Research Campus, United Kingdom
| | - Oda Stoevesandt
- From the Department of Neurology (C.P.M., K.F., J.-P.C., J.-C.A.), and Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne; Synaptopathies and Autoantibodies (C.P.M., Y.T., J.-P.C., J.-C.A.), Institut NeuroMyoGène, INSERM U1217/CNRS UMR 5310, University of Lyon, University Jean-Monnet, Saint-Étienne, France; and Cambridge Protein Arrays Ltd. (O.S.), Babraham Research Campus, United Kingdom
| | - Karine Ferraud
- From the Department of Neurology (C.P.M., K.F., J.-P.C., J.-C.A.), and Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne; Synaptopathies and Autoantibodies (C.P.M., Y.T., J.-P.C., J.-C.A.), Institut NeuroMyoGène, INSERM U1217/CNRS UMR 5310, University of Lyon, University Jean-Monnet, Saint-Étienne, France; and Cambridge Protein Arrays Ltd. (O.S.), Babraham Research Campus, United Kingdom
| | - Jean-Philippe Camdessanché
- From the Department of Neurology (C.P.M., K.F., J.-P.C., J.-C.A.), and Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne; Synaptopathies and Autoantibodies (C.P.M., Y.T., J.-P.C., J.-C.A.), Institut NeuroMyoGène, INSERM U1217/CNRS UMR 5310, University of Lyon, University Jean-Monnet, Saint-Étienne, France; and Cambridge Protein Arrays Ltd. (O.S.), Babraham Research Campus, United Kingdom
| | - Jean-Christophe Antoine
- From the Department of Neurology (C.P.M., K.F., J.-P.C., J.-C.A.), and Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne; Synaptopathies and Autoantibodies (C.P.M., Y.T., J.-P.C., J.-C.A.), Institut NeuroMyoGène, INSERM U1217/CNRS UMR 5310, University of Lyon, University Jean-Monnet, Saint-Étienne, France; and Cambridge Protein Arrays Ltd. (O.S.), Babraham Research Campus, United Kingdom
| |
Collapse
|
13
|
Das J, Devadhasan A, Linde C, Broge T, Sassic J, Mangano M, O'Keefe S, Suscovich T, Streeck H, Irrinki A, Pohlmeyer C, Min-Oo G, Lin S, Weiner JA, Cihlar T, Ackerman ME, Julg B, Deeks S, Lauffenburger DA, Alter G. Mining for humoral correlates of HIV control and latent reservoir size. PLoS Pathog 2020; 16:e1008868. [PMID: 33048992 DOI: 10.1371/journal.ppat.1008868] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 08/06/2020] [Indexed: 11/19/2022] Open
Abstract
While antiretroviral therapy (ART) has effectively revolutionized HIV care, the virus is never fully eliminated. Instead, immune dysfunction, driven by persistent non-specific immune activation, ensues and progressively leads to premature immunologic aging. Current biomarkers monitoring immunologic changes encompass generic inflammatory biomarkers, that may also change with other infections or disease states, precluding the antigen-specific monitoring of HIV-infection associated changes in disease. Given our growing appreciation of the significant changes in qualitative and quantitative properties of disease-specific antibodies in HIV infection, we used a systems approach to explore humoral profiles associated with HIV control. We found that HIV-specific antibody profiles diverge by spontaneous control of HIV, treatment status, viral load and reservoir size. Specifically, HIV-specific antibody profiles representative of changes in viral load were largely quantitative, reflected by differential HIV-specific antibody levels and Fc-receptor binding. Conversely, HIV-specific antibody features that tracked with reservoir size exhibited a combination of quantitative and qualitative changes marked by more distinct subclass selection profiles and unique HIV-specific Fc-glycans. Our analyses suggest that HIV-specific antibody Fc-profiles provide antigen-specific resolution on both cell free and cell-associated viral loads, pointing to potentially novel biomarkers to monitor reservoir activity. Current combination antiretroviral therapy (ART) regimens have reversed the death sentence once associated with an HIV diagnosis. However, the virus is never fully eliminated. Rather, latently infected cells with integrated virus (latent reservoir) persist and the virus rebounds rapidly upon discontinuation of therapy. Further, even for those on ART, immune dysfunction, driven by persistent non-specific immune activation, ensues and progressively leads to premature immunologic aging. Current biomarkers monitoring these changes are non-specific–they focus on generic inflammatory changes that may also track with other infections or disease states. In this manuscript, we used an unbiased analytical systems approach to identify antigen-specific biomarkers of HIV disease state/treatment status, active viremia and the latent reservoir. By virtue of them being antigen-specific, these are robust context-specific biomarkers of HIV disease progression, viremia and reservoir size. Our framework highlights the strength of using systems approaches in identifying humoral biomarkers, and can be used in other contexts to identify antigen-specific correlates of infectious disease outcome.
Collapse
|
14
|
Natarajan H, Crowley AR, Butler SE, Xu S, Weiner JA, Bloch EM, Littlefield K, Wieland-Alter W, Connor RI, Wright PF, Benner SE, Bonny TS, Laeyendecker O, Sullivan D, Shoham S, Quinn TC, Larman HB, Casadevall A, Pekosz A, Redd AD, Tobian AA, Ackerman ME. SARS-CoV-2 antibody signatures robustly predict diverse antiviral functions relevant for convalescent plasma therapy. medRxiv 2020:2020.09.16.20196154. [PMID: 32995801 PMCID: PMC7523138 DOI: 10.1101/2020.09.16.20196154] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Convalescent plasma has emerged as a promising COVID-19 treatment. However, the humoral factors that contribute to efficacy are poorly understood. This study functionally and phenotypically profiled plasma from eligible convalescent donors. In addition to viral neutralization, convalescent plasma contained antibodies capable of mediating such Fc-dependent functions as complement activation, phagocytosis and antibody-dependent cellular cytotoxicity against SARS-CoV-2. These activities expand the antiviral functions associated with convalescent plasma and together with neutralization efficacy, could be accurately and robustly from antibody phenotypes. These results suggest that high-throughput profiling could be used to screen donors and plasma may provide benefits beyond neutralization.
Collapse
Affiliation(s)
- Harini Natarajan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Andrew R. Crowley
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Savannah E. Butler
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Shiwei Xu
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Joshua A. Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Evan M. Bloch
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kirsten Littlefield
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wendy Wieland-Alter
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Ruth I. Connor
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Peter F. Wright
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Sarah E. Benner
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tania S. Bonny
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Oliver Laeyendecker
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shmuel Shoham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas C. Quinn
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - H. Benjamin Larman
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew D. Redd
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aaron A.R. Tobian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| |
Collapse
|
15
|
Jennewein MF, Mabuka J, Papia CL, Boudreau CM, Dong KL, Ackerman ME, Ndung'u T, Alter G. Tracking the Trajectory of Functional Humoral Immune Responses Following Acute HIV Infection. Front Immunol 2020; 11:1744. [PMID: 32849622 PMCID: PMC7426367 DOI: 10.3389/fimmu.2020.01744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Increasing evidence points to a role for antibody-mediated effector functions in preventing and controlling HIV infection. However, less is known about how these antibody effector functions evolve following infection. Moreover, how the humoral immune response is naturally tuned to recruit the antiviral activity of the innate immune system, and the extent to which these functions aid in the control of infection, are poorly understood. Using plasma samples from 10 hyper-acute HIV-infected South African women, identified in Fiebig stage I (the FRESH cohort), systems serology was performed to evaluate the functional and biophysical properties of gp120-, gp41-, and p24- specific antibody responses during the first year of infection. Significant changes were observed in both the functional and biophysical characteristics of the humoral immune response following acute HIV infection. Antibody Fc-functionality increased over the course of infection, with increases in antibody-mediated phagocytosis, NK activation, and complement deposition occurring in an antigen-specific manner. Changes in both antibody subclass and antibody Fc-glycosylation drove the evolution of antibody effector activity, highlighting natural modifications in the humoral immune response that may enable the directed recruitment of the innate immune system to target and control HIV. Moreover, enhanced antibody functionality, particularly gp120-specific polyfunctionality, was tied to improvements in clinical course of infection, supporting a role for functional antibodies in viral control.
Collapse
Affiliation(s)
- Madeleine F Jennewein
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
| | - Jennifer Mabuka
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States.,Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cassidy L Papia
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
| | - Carolyn M Boudreau
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
| | - Krista L Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
| | | | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States.,Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Max Planck Institute for Infection Biology, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
| |
Collapse
|
16
|
Abstract
PURPOSE OF REVIEW Rare patients naturally control HIV replication without antiretroviral therapy. Understanding the mechanisms implicated in natural HIV control will inform the development of immunotherapies against HIV. Elite controllers are known for developing efficient antiviral T-cell responses, but recent findings suggest that antibody responses also play a significant role in HIV control. We review the key studies that uncovered a potent memory B-cell response and highly functional anti-HIV antibodies in elite controllers, and explore the mechanisms that may account for the distinct properties of their humoral response. RECENT FINDINGS Elite controllers maintain a large HIV-specific memory B-cell pool that is sustained by efficient T follicular helper function. Neutralizing antibody rarely show high titers in controllers, but seem capable, at least in certain cases, of neutralizing contemporaneous viral strains. In addition, elite controllers display a unique HIV-specific antibody profile in terms of isotype, antigen specificity, and glycosylation pattern, resulting in polyfunctional antibody effector functions that may promote infected cell lysis and prime effectors of the antiviral immune response. SUMMARY Lessons from elite controller studies argue for the importance of integrating the many parameters defining a polyfunctional antibody response when evaluating candidate vaccines and immunotherapeutic approaches directed at HIV.
Collapse
|
17
|
Pittala S, Morrison KS, Ackerman ME. Systems serology for decoding infection and vaccine-induced antibody responses to HIV-1. Curr Opin HIV AIDS 2019; 14:253-64. [PMID: 31033729 DOI: 10.1097/COH.0000000000000558] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW Experimental and analytical advances have enabled systematic, high-resolution studies of humoral immune responses, and are beginning to define mechanisms of immunity to HIV. RECENT FINDINGS High-throughput, information-rich experimental and analytical methods, whether genomic, proteomic, or transcriptomic, have firmly established their value across a diversity of fields. Consideration of these tools as trawlers in 'fishing expeditions' has faded as 'data-driven discovery' has come to be valued as an irreplaceable means to develop fundamental understanding of biological systems. Collectively, studies of HIV-1 infection and vaccination including functional, biophysical, and biochemical humoral profiling approaches have provided insights into the phenotypic characteristics of individual and pools of antibodies. Relating these measures to clinical status, protection/efficacy outcomes, and cellular profiling data using machine learning has offered the possibility of identifying unanticipated mechanisms of action and gaining insights into fundamental immunological processes that might otherwise be difficult to decipher. SUMMARY Recent evidence establishes that systematic data collection and application of machine learning approaches can identify humoral immune correlates that are generalizable across distinct HIV-1 immunogens and vaccine regimens and translatable between model organisms and the clinic. These outcomes provide a strong rationale supporting the utility and further expansion of these approaches both in support of vaccine development and more broadly in defining mechanisms of immunity.
Collapse
|
18
|
Abstract
PURPOSE OF REVIEW Although the goal of preventive HIV vaccine design is primarily the induction of broadly neutralizing antibodies (bNAbs), recent evidence suggests that a protective response will also benefit from Fc effector functions. Here, we provide an update on the antibody response to HIV infection, including both Fab and Fc-mediated antibody responses. We also highlight recent studies showing the interplay between these functions, focusing primarily on studies published in the last year. RECENT FINDINGS Identification and characterization of bNAb donors continues to provide insights into viral factors that are potentially translatable to vaccine design. Improved and more diverse measures of Fc effector function, and modulators thereof, are enabling a deeper understanding of their role in infection. New data providing mechanistic links between the innate and adaptive humoral immune responses are creating exciting opportunities for vaccine strategies, with the aim of eliciting a polyfunctional protective response. SUMMARY New insights into the overall humoral response to HIV infection are defining diverse and synergistic mechanisms required for antibody protection from HIV through vaccination.
Collapse
|
19
|
Abstract
PURPOSE OF REVIEW The review recalls recent findings regarding the induction of vaccinal effects by HIV-1 broadly neutralizing antibodies (bNAbs) and highlights potential therapeutic strategies to exploit such immunomodulatory properties. RECENT FINDINGS Studies in different animal models have shown that mAbs can generate long-lasting protective immunity. Induction of this vaccinal effect by HIV-1 bNAbs has also been more recently reported in animal models of HIV-1 infection. Notably, bNAbs treatment of macaques infected with the chimeric simian-human immunodeficiency virus (SHIV) improved both humoral and cellular adaptive immune responses that contributed to disease control. Importantly, this concept has been extended to HIV-1-infected patients as enhancement of humoral responses was recently reported in HIV-1 patients treated with bNAbs. Studies aiming at elucidating the mechanisms underlying these immunomodulatory properties of bNAbs have identified a role for immune complexes in shaping immune responses against HIV-1. They also highlight different Fc (fragment crystallizable) region effector functions that might be required for the enhancement of HIV-1 immune responses upon bNAbs treatment. SUMMARY HIV-1 bNAbs can elicit protective adaptive immune responses through mechanisms involving multiple cellular and molecular actors of the immune system. Harnessing these mechanisms will be crucial to achieve protective immunity against HIV-1 infection by bNAbs.
Collapse
|
20
|
Goldberg BS, Ackerman ME. Antibody-mediated complement activation in pathology and protection. Immunol Cell Biol 2020; 98:305-317. [PMID: 32142167 DOI: 10.1111/imcb.12324] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 01/10/2023]
Abstract
Antibody-dependent complement activity is associated not only with autoimmune morbidity, but also with antitumor efficacy. In infectious disease, both recombinant monoclonal antibodies and polyclonal antibodies generated in natural adaptive responses can mediate complement activity to protective, therapeutic or disease-enhancing effect. Recent advances have contributed to the structural resolution of molecular complexes involved in antibody-mediated complement activation, defining the avid nature of participating interactions and pointing to how antibody isotype, subclass, hinge flexibility, glycosylation state, amino acid sequence and the contextual nature of the cognate antigen/epitope are all factors that can determine complement activity through impact on antibody multimerization and subsequent recruitment of complement component 1q. Beyond the efficiency of activation, complement activation products interact with various cell types that mediate immune adherence, trafficking, immune education and innate functions. Similarly, depending on the anatomical location and extent of activation, complement can support homeostatic restoration or be leveraged by pathogens or neoplasms to enhance infection or promote tumorigenic microenvironments, respectively. Advances in means to suppress complement activation by intravenous immunoglobulin (IVIG), IVIG mimetics and complement-intervening antibodies represent proven and promising exploratory therapeutic strategies, while antibody engineering has likewise offered frameworks to enhance, eliminate or isolate complement activation to interrogate in vivo mechanisms of action. Such strategies promise to support the optimization of antibody-based drugs that are able to tackle emerging and difficult-to-treat diseases by improving our understanding of the synergistic and antagonistic relationships between antibody mechanisms mediated by Fc receptors, direct binding and the products of complement activation.
Collapse
Affiliation(s)
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA.,Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| |
Collapse
|
21
|
Chu TH, Crowley AR, Backes I, Chang C, Tay M, Broge T, Tuyishime M, Ferrari G, Seaman MS, Richardson SI, Tomaras GD, Alter G, Leib D, Ackerman ME. Hinge length contributes to the phagocytic activity of HIV-specific IgG1 and IgG3 antibodies. PLoS Pathog 2020; 16:e1008083. [PMID: 32092122 PMCID: PMC7058349 DOI: 10.1371/journal.ppat.1008083] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 03/05/2020] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
Antibody functions such as neutralization require recognition of antigen by the Fab region, while effector functions are additionally mediated by interactions of the Fc region with soluble factors and cellular receptors. The efficacy of individual antibodies varies based on Fab domain characteristics, such as affinity for antigen and epitope-specificity, and on Fc domain characteristics that include isotype, subclass, and glycosylation profile. Here, a series of HIV-specific antibody subclass and hinge variants were constructed and tested to define those properties associated with differential effector function. In the context of the broadly neutralizing CD4 binding site-specific antibody VRC01 and the variable loop (V3) binding antibody 447-52D, hinge truncation and extension had a considerable impact on the magnitude of phagocytic activity of both IgG1 and IgG3 subclasses. The improvement in phagocytic potency of antibodies with extended hinges could not be attributed to changes in either intrinsic antigen or antibody receptor affinity. This effect was specific to phagocytosis and was generalizable to different phagocytes, at different effector cell to target ratios, for target particles of different size and composition, and occurred across a range of antibody concentrations. Antibody dependent cellular cytotoxicity and neutralization were generally independent of hinge length, and complement deposition displayed variable local optima. In vivo stability testing showed that IgG molecules with altered hinges can exhibit similar biodistribution and pharmacokinetic profiles as IgG1. Overall, these results suggest that when high phagocytic activity is desirable, therapeutic antibodies may benefit from being formatted as human IgG3 or engineered IgG1 forms with elongated hinges.
Collapse
Affiliation(s)
- Thach H. Chu
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Andrew R. Crowley
- The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Iara Backes
- The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Cheryl Chang
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Matthew Tay
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Thomas Broge
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Marina Tuyishime
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael S. Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Simone I. Richardson
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - David Leib
- The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
- The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| |
Collapse
|
22
|
Moritz CP, Paul S, Stoevesandt O, Tholance Y, Camdessanché JP, Antoine JC. Autoantigenomics: Holistic characterization of autoantigen repertoires for a better understanding of autoimmune diseases. Autoimmun Rev 2020; 19:102450. [DOI: 10.1016/j.autrev.2019.102450] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
|
23
|
Keshavjee S, Amanullah F, Cattamanchi A, Chaisson R, Dobos KM, Fox GJ, Gendelman HE, Gordon R, Hesseling A, Le Van H, Kampmann B, Kana B, Khuller G, Lewinsohn DM, Lewinsohn DA, Lin PL, Lu LL, Maartens G, Owen A, Protopopova M, Rengarajan J, Rubin E, Salgame P, Schurr E, Seddon JA, Swindells S, Tobin DM, Udwadia Z, Walzl G, Srinivasan S, Rustomjee R, Nahid P. Moving toward Tuberculosis Elimination. Critical Issues for Research in Diagnostics and Therapeutics for Tuberculosis Infection. Am J Respir Crit Care Med 2020; 199:564-571. [PMID: 30335466 DOI: 10.1164/rccm.201806-1053pp] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Salmaan Keshavjee
- 1 Harvard Medical School, Boston, Massachusetts.,2 Harvard Medical School Center for Global Health Delivery-Dubai, Dubai, United Arab Emirates
| | | | - Adithya Cattamanchi
- 4 University of California San Francisco, Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Richard Chaisson
- 5 Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Gregory J Fox
- 7 University of Sydney, Sydney, New South Wales, Australia
| | | | - Richard Gordon
- 9 South African Medical Research Council, Cape Town, Western Cape, South Africa
| | | | - Hoi Le Van
- 11 National Lung Hospital, Hanoi, Vietnam.,12 National TB Program in Vietnam, Hanoi, Vietnam
| | - Beate Kampmann
- 13 London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bavesh Kana
- 14 University of Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa.,15 Centre for the AIDS Programme of Research in South Africa, CAPRISA, Durban, South Africa
| | - Gopal Khuller
- 16 Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - David M Lewinsohn
- 17 Oregon Health & Science University, Portland, Oregon.,18 Portland VA Medical Center, Portland, Oregon
| | | | - Philiana Ling Lin
- 19 University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Lenette Lin Lu
- 20 Massachusetts General Hospital, Boston, Massachusetts
| | - Gary Maartens
- 21 Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Owen
- 22 University of Liverpool, Liverpool, England
| | - Marina Protopopova
- 23 Division of AIDS, National Institute of Allergy and Infectious Diseases, NIH, Department of Health and Human Services, Rockville, Maryland
| | | | - Eric Rubin
- 25 Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | | | - James A Seddon
- 13 London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - David M Tobin
- 28 Duke University School of Medicine, Durham, North Carolina; and
| | - Zarir Udwadia
- 29 Hinduja Hospital & Research Center, Mumbai, India
| | - Gerhard Walzl
- 30 Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa.,14 University of Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
| | - Sudha Srinivasan
- 23 Division of AIDS, National Institute of Allergy and Infectious Diseases, NIH, Department of Health and Human Services, Rockville, Maryland
| | - Roxana Rustomjee
- 23 Division of AIDS, National Institute of Allergy and Infectious Diseases, NIH, Department of Health and Human Services, Rockville, Maryland
| | - Payam Nahid
- 4 University of California San Francisco, Zuckerberg San Francisco General Hospital, San Francisco, California
| |
Collapse
|
24
|
Abstract
Antibodies serve as the primary correlate of protection following most clinically approved vaccines and are thought to confer protection in part through their ability to block (neutralize) infection. Increasingly, studies have shown that beyond their blocking activities, the ability of antibodies to leverage the innate immune response may serve a vital role in protection from infection. Specifically, antibodies can drive phagocytosis, complement activation, and cellular cytotoxicity by interacting with Fc-receptors found on all innate immune cells. Measuring the capacity of antibodies to induce these functions has become critical for the identification of correlates of protection in large-scale vaccine trials. Therefore, there is a growing need to develop robust, high throughput assays able to interrogate the functional capacity of innate immune recruiting antibodies. However, in many instances, only small sample volumes are available. Nevertheless, profiling antibody functions across many pathogen-associated antigens or across global intra-pathogen variants is in high demand, making sample sparing approaches to perform this antibody evaluation critical. Here we describe the development of an approach to interrogate the functional activity of antibodies in serum against up to 5 antigen targets simultaneously. A single bead-based cellular assay was adapted to accommodate 5 different fluorescently colored beads, allowing for the concurrent investigation of antibody responses directed against multiple antigens in a single well. The multiplexed assay was as sensitive, specific, and accurate as the single antigen assay and robustly able to assess functional differences mediated by antibodies across different samples. These findings show multiplexing allows for accurate and more efficient analysis of antibody-mediated effector profiles.
Collapse
Affiliation(s)
| | | | - Galit Alter
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| |
Collapse
|
25
|
Abstract
PURPOSE OF REVIEW In humans, only one independent immunologic correlate of reduced risk of HIV infection has been identified: a robust antibody (Ab) response to the V1V2 domain of the gp120 envelope (Env) protein. In recent years, the presence and level of V1V2-specific Abs has also been correlated with protection from SIV and SHIV infections. Here, we review the multitude of studies showing the in-vivo protective effects of V1V2 Abs and review their immunologic characteristics and antiviral functions. RECENT FINDINGS Structural and immunologic studies have defined four epitope families in the V1V2 domain: one epitope family, V2q, which preferentially presents as a quaternary structure of the Env trimer, and another epitope family (V2qt) which requires the quaternary trimeric Env structure; these two epitope types are recognized by two families of monoclonal Abs (mAbs)-V2q-specific and V2qt-specific mAbs-which display broad and potent neutralizing activity. A third epitope family, V2i, is present as a discontinuous conformational structure that overlays the α4β7 integrin binding motif, and a fourth epitope family (V2p) exists on V2 peptides. Antibodies specific for V2i and V2p epitopes display only poor neutralizing activity but effectively mediate other antiviral activities and have been correlated with control of and/or protection from HIV, SIV and SHIV. Notably, V2q and V2qt Abs have not been induced by any vaccines, but V2p and V2i Abs have been readily induced with various vaccines in nonhuman primates and humans. SUMMARY The correlation of vaccine-induced V2p and V2i Abs with protection from HIV, SIV and SHIV suggests that these Ab types are extremely important to induce with prophylactic vaccines.
Collapse
Affiliation(s)
- Susan Zolla-Pazner
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai
| | - Raymond Alvarez
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Svenja Weiss
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai
| |
Collapse
|
26
|
Naegeli A, Bratanis E, Karlsson C, Shannon O, Kalluru R, Linder A, Malmström J, Collin M. Streptococcus pyogenes evades adaptive immunity through specific IgG glycan hydrolysis. J Exp Med 2019; 216:1615-1629. [PMID: 31092533 PMCID: PMC6605743 DOI: 10.1084/jem.20190293] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/19/2022] Open
Abstract
EndoS from Streptococcus pyogenes hydrolyzes the functionally important glycan on the Fc portion of IgG during infections in humans. In mice with IgG mediated immunity against the M1 protein on the bacteria, EndoS is a virulence factor. Streptococcus pyogenes (Group A streptococcus; GAS) is a human pathogen causing diseases from uncomplicated tonsillitis to life-threatening invasive infections. GAS secretes EndoS, an endoglycosidase that specifically cleaves the conserved N-glycan on IgG antibodies. In vitro, removal of this glycan impairs IgG effector functions, but its relevance to GAS infection in vivo is unclear. Using targeted mass spectrometry, we characterized the effects of EndoS on host IgG glycosylation during the course of infections in humans. Substantial IgG glycan hydrolysis occurred at the site of infection and systemically in the severe cases. We demonstrated decreased resistance to phagocytic killing of GAS lacking EndoS in vitro and decreased virulence in a mouse model of invasive infection. This is the first described example of specific bacterial IgG glycan hydrolysis during infection and thereby verifies the hypothesis that EndoS modifies antibodies in vivo. This mechanisms of immune evasion could have implications for treatment of severe GAS infections and for future efforts at vaccine development.
Collapse
Affiliation(s)
- Andreas Naegeli
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Eleni Bratanis
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Christofer Karlsson
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Oonagh Shannon
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Raja Kalluru
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Adam Linder
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Johan Malmström
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Mattias Collin
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| |
Collapse
|
27
|
Shapiro SZ. Lessons for general vaccinology research from attempts to develop an HIV vaccine. Vaccine 2019; 37:3400-8. [PMID: 30979571 DOI: 10.1016/j.vaccine.2019.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 01/12/2023]
Abstract
In the past when large investments have been made in tackling narrow scientific challenges, the enormous expansion in our knowledge in one small area has had a spill-over effect on research and treatment of other diseases. The large investment in HIV vaccine development in recent years has the potential for such an effect on vaccine development for other diseases. HIV vaccine developers have experienced repeated failure using the standard approaches to vaccine development. This has forced them to consider immune responses in greater depth and detail. It has led to a recognition of the importance of epitopic specificity in both antibody and T cell responses. Also, it has led to an understanding of the importance of affinity maturation in antibody responses and the quality of T cell responses in T cell-mediated immunity. It has advanced the development of many novel vaccine vectors and vehicles that are now available for use in other vaccines. Further, it has focused attention on the impact of research funding mechanisms and community engagement on vaccine development. These developments and considerations have implications for vaccinology more generally. Some suggestions are made for investigators working on other "hard-to-develop" vaccines.
Collapse
|
28
|
Bing X, Bunea F, Royer M, Das J. Latent Model-Based Clustering for Biological Discovery. iScience 2019; 14:125-135. [PMID: 30954780 PMCID: PMC6449745 DOI: 10.1016/j.isci.2019.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/26/2018] [Accepted: 03/18/2019] [Indexed: 11/27/2022] Open
Abstract
LOVE, a robust, scalable latent model-based clustering method for biological discovery, can be used across a range of datasets to generate both overlapping and non-overlapping clusters. In our formulation, a cluster comprises variables associated with the same latent factor and is determined from an allocation matrix that indexes our latent model. We prove that the allocation matrix and corresponding clusters are uniquely defined. We apply LOVE to biological datasets (gene expression, serological responses measured from HIV controllers and chronic progressors, vaccine-induced humoral immune responses) resulting in meaningful biological output. For all three datasets, the clusters generated by LOVE remain stable across tuning parameters. Finally, we compared LOVE's performance to that of 13 state-of-the-art methods using previously established benchmarks and found that LOVE outperformed these methods across datasets. Our results demonstrate that LOVE can be broadly used across large-scale biological datasets to generate accurate and meaningful overlapping and non-overlapping clusters. LOVE is a robust, scalable, and versatile latent model-based clustering method Has theoretical guarantees, and can generate overlapping and non-overlapping clusters Generates meaningful clusters from datasets spanning a range of biological domains Using established benchmarks, outperforms 13 state-of-the-art methods across datasets
Collapse
|