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Abu-Shmais AA, Vukovich MJ, Wasdin PT, Suresh YP, Marinov TM, Rush SA, Gillespie RA, Sankhala RS, Choe M, Joyce MG, Kanekiyo M, McLellan JS, Georgiev IS. Antibody sequence determinants of viral antigen specificity. mBio 2024:e0156024. [PMID: 39264172 DOI: 10.1128/mbio.01560-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/13/2024] [Indexed: 09/13/2024] Open
Abstract
Throughout life, humans experience repeated exposure to viral antigens through infection and vaccination, resulting in the generation of diverse, antigen-specific antibody repertoires. A paramount feature of antibodies that enables their critical contributions in counteracting recurrent and novel pathogens, and consequently fostering their utility as valuable targets for therapeutic and vaccine development, is the exquisite specificity displayed against their target antigens. Yet, there is still limited understanding of the determinants of antibody-antigen specificity, particularly as a function of antibody sequence. In recent years, experimental characterization of antibody repertoires has led to novel insights into fundamental properties of antibody sequences but has been largely decoupled from at-scale antigen specificity analysis. Here, using the LIBRA-seq technology, we generated a large data set mapping antibody sequence to antigen specificity for thousands of B cells, by screening the repertoires of a set of healthy individuals against 20 viral antigens representing diverse pathogens of biomedical significance. Analysis uncovered virus-specific patterns in variable gene usage, gene pairing, somatic hypermutation, as well as the presence of convergent antiviral signatures across multiple individuals, including the presence of public antibody clonotypes. Notably, our results showed that, for B-cell receptors originating from different individuals but leveraging an identical combination of heavy and light chain variable genes, there is a specific CDRH3 identity threshold above which B cells appear to exclusively share the same antigen specificity. This finding provides a quantifiable measure of the relationship between antibody sequence and antigen specificity and further defines experimentally grounded criteria for defining public antibody clonality.IMPORTANCEThe B-cell compartment of the humoral immune system plays a critical role in the generation of antibodies upon new and repeated pathogen exposure. This study provides an unprecedented level of detail on the molecular characteristics of antibody repertoires that are specific to each of the different target pathogens studied here and provides empirical evidence in support of a 70% CDRH3 amino acid identity threshold in pairs of B cells encoded by identical IGHV:IGL(K)V genes, as a means of defining public clonality and therefore predicting B-cell antigen specificity in different individuals. This is of exceptional importance when leveraging public clonality as a method to annotate B-cell receptor data otherwise lacking antigen specificity information. Understanding the fundamental rules of antibody-antigen interactions can lead to transformative new approaches for the development of antibody therapeutics and vaccines against current and emerging viruses.
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Affiliation(s)
- Alexandra A Abu-Shmais
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Matthew J Vukovich
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Perry T Wasdin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yukthi P Suresh
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Toma M Marinov
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Scott A Rush
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rajeshwer S Sankhala
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Misook Choe
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - M Gordon Joyce
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Ortiz AM, Brenchley JM. Untangling the role of the microbiome across the stages of HIV disease. Curr Opin HIV AIDS 2024; 19:221-227. [PMID: 38935047 PMCID: PMC11305932 DOI: 10.1097/coh.0000000000000870] [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] [Indexed: 06/28/2024]
Abstract
PURPOSE OF REVIEW The primate microbiome consists of bacteria, eukaryotes, and viruses that dynamically shape and respond to host health and disease. Understanding how the symbiotic relationship between the host and microbiome responds to HIV has implications for therapeutic design. RECENT FINDINGS Advances in microbiome identification technologies have expanded our ability to identify constituents of the microbiome and to infer their functional capacity. The dual use of these technologies and animal models has allowed interrogation into the role of the microbiome in lentiviral acquisition, vaccine efficacy, and the response to antiretrovirals. Lessons learned from such studies are now being harnessed to design microbiome-based interventions. SUMMARY Previous studies considering the role of the microbiome in people living with HIV largely described viral acquisition as an intrusion on the host:microbiome interface. Re-framing this view to consider HIV as a novel, albeit unwelcome, component of the microbiome may better inform the research and development of pre and postexposure prophylaxes.
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Affiliation(s)
- Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland, USA
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3
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Rossouw C, Ryan FJ, Lynn DJ. The role of the gut microbiota in regulating responses to vaccination: current knowledge and future directions. FEBS J 2024. [PMID: 39102299 DOI: 10.1111/febs.17241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/13/2024] [Accepted: 07/24/2024] [Indexed: 08/07/2024]
Abstract
Antigen-specific B and T cell responses play a critical role in vaccine-mediated protection against infectious diseases, but these responses are highly variable between individuals and vaccine immunogenicity is frequently sub-optimal in infants, the elderly and in people living in low- and middle-income countries. Although many factors such as nutrition, age, sex, genetics, environmental exposures, and infections may all contribute to variable vaccine immunogenicity, mounting evidence indicates that the gut microbiota is an important and targetable factor shaping optimal immune responses to vaccination. In this review, we discuss evidence from human, preclinical and experimental studies supporting a role for a healthy gut microbiota in mediating optimal vaccine immunogenicity, including the immunogenicity of COVID-19 vaccines. Furthermore, we provide an overview of the potential mechanisms through which this could occur and discuss strategies that could be used to target the microbiota to boost vaccine immunogenicity where it is currently sub-optimal.
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Affiliation(s)
- Charné Rossouw
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
| | - Feargal J Ryan
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
| | - David J Lynn
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
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4
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Liu Y, Zhou J, Yang Y, Chen X, Chen L, Wu Y. Intestinal Microbiota and Its Effect on Vaccine-Induced Immune Amplification and Tolerance. Vaccines (Basel) 2024; 12:868. [PMID: 39203994 PMCID: PMC11359036 DOI: 10.3390/vaccines12080868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
This review provides the potential of intestinal microbiota in vaccine design and application, exploring the current insights into the interplay between the intestinal microbiota and the immune system, with a focus on its intermediary function in vaccine efficacy. It summarizes families and genera of bacteria that are part of the intestinal microbiota that may enhance or diminish vaccine efficacy and discusses the foundational principles of vaccine sequence design and the application of gut microbial characteristics in vaccine development. Future research should further investigate the use of multi-omics technologies to elucidate the interactive mechanisms between intestinal microbiota and vaccine-induced immune responses, aiming to optimize and improve vaccine design.
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Affiliation(s)
- Yixin Liu
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China;
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China; (J.Z.); (L.C.)
| | - Jianfeng Zhou
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China; (J.Z.); (L.C.)
| | - Yushang Yang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China; (J.Z.); (L.C.)
| | - Xiangzheng Chen
- Department of Liver Surgery & Liver Transplantation, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Longqi Chen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China; (J.Z.); (L.C.)
| | - Yangping Wu
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China;
- State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Chengdu 610041, China
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Opriessnig T, Halbur P, Bayne J, Rawal G, Tong H, Mou K, Li G, Zhang D, Zhang J, Muwonge A. Exploratory application of a cannulation model in recently weaned pigs to monitor longitudinal changes in the enteric microbiome across varied porcine reproductive and respiratory syndrome virus (PRRSV) infection statuses. Front Vet Sci 2024; 11:1422012. [PMID: 39100768 PMCID: PMC11294941 DOI: 10.3389/fvets.2024.1422012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Introduction The enteric microbiome and its possible modulation to improve feed conversion or vaccine efficacy is gaining more attention in pigs. Weaning pigs from their dam, along with many routine procedures, is stressful. A better understanding of the impact of this process on the microbiome may be important for improving pig production. The objective of this study was to develop a weaner pig cannulation model, thus allowing ileum content collection from the same pig over time for 16S rRNA sequencing under different porcine reproductive and respiratory syndrome virus (PRRSV) infection statuses. Methods A total of 15 3-week-old pigs underwent abdominal surgery and were fitted with an ileum cannula, with ileum contents collected over time. In this pilot study, treatment groups included a NEG-CONTROL group (no vaccination, no PRRSV challenge), a POS-CONTROL group (no vaccination, challenged with PRRSV), a VAC-PRRSV group (vaccinated, challenged with PRRSV), a VAC-PRO-PRRSV group (vaccinated, supplemented with a probiotic, challenged with PRRSV), and a VAC-ANTI-PRRSV group (vaccinated, administered an antibiotic, challenged with PRRSV). We assessed the microbiome over time and measured anti-PRRSV serum antibodies, PRRSV load in serum and nasal samples, and the severity of lung lesions. Results Vaccination was protective against PRRSV challenge, irrespective of other treatments. All vaccinated pigs mounted an immune response to PRRSV within 1 week after vaccination. A discernible impact of treatment on the diversity, structure, and taxonomic abundance of the enteric microbiome among the groups was not observed. Instead, significant influences on the ileum microbiome were observed in relation to time and treatment. Discussion The cannulation model described in this pilot study has the potential to be useful in studying the impact of weaning, vaccination, disease challenge, and antimicrobial administration on the enteric microbiome and its impact on pig health and production. Remarkably, despite the cannulation procedures, all vaccinated pigs exhibited robust immune responses and remained protected against PRRSV challenge, as evidenced by the development of anti-PRRSV serum antibodies and viral shedding data.
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Affiliation(s)
- Tanja Opriessnig
- Department of Vaccines and Diagnostics, Moredun Research Institute, Penicuik, United Kingdom
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Patrick Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Jenna Bayne
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Gaurav Rawal
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Hao Tong
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Kathy Mou
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Danyang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Adrian Muwonge
- The Digital One Health Laboratory, Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
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Biswas S, Kuwata T, Yamauchi S, Okazaki K, Kaku Y, Hasan MZ, Morioka H, Matsushita S. Idiotopes of antibodies against HIV-1 CD4-induced epitope shared with those against microorganisms. Immunology 2024; 171:534-548. [PMID: 38102962 DOI: 10.1111/imm.13742] [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: 09/22/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023] Open
Abstract
Induction of antibodies (Abs) against the conformational CD4-induced (CD4i) epitope is frequent in HIV-1 infection. However, the mechanism of development of anti-CD4i Abs is unclear. We used anti-idiotypic (aID) monoclonal Abs (mAbs) of anti-CD4i mAbs to isolate anti-CD4i mAbs from infected subjects and track the causative antigens. One anti-aID mAb sorted from infected subjects by aID mAbs had the characteristics of anti-CD4i Abs, including IGHV1-69 usage and ability to bind to HIV-1 Env enhanced by sCD4. Critical amino acid sequences for the binding of six anti-aID mAbs, with shared idiotope to anti-CD4i mAbs, were analysed by phage display. The identified amino acid sequences showed similarity to proteins from human microbiota and infectious agents. Peptides synthesized from Caudoviricetes sp and Vibrio vulnificus based on the identified sequences were reactive to most anti-aID and some anti-CD4i mAbs. These results suggest that anti-CD4i Abs may evolve from B cells primed by microorganisms.
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Affiliation(s)
- Shashwata Biswas
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takeo Kuwata
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Soichiro Yamauchi
- Department of Analytical and Biophysical Chemistry, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kyo Okazaki
- Department of Analytical and Biophysical Chemistry, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yu Kaku
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Md Zahid Hasan
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Shuzo Matsushita
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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Potchen NB, Johnson AM, Hager K, Graham J, Van P, Lyn-Kew KH, Warrier L, Talavera IC, Lund JM, Kublin JG. Oral tolerance to systemic vaccination remains intact without RORγt expression in regulatory T cells. iScience 2023; 26:108504. [PMID: 38125026 PMCID: PMC10730369 DOI: 10.1016/j.isci.2023.108504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/29/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Many promising vaccine candidates and licensed vaccines lead to variable immune responses within humans. Studies suggest that environmental exposures in the gastrointestinal tract could contribute to a reduction in vaccine efficacy via immune tolerance at this site; this is partly achieved by a high abundance of regulatory T cells (Tregs). It is unclear if Treg subsets regulate systemic vaccine responses following oral antigen pre-exposure. Here, we implemented a conditional knock-out mouse model of RORγt+ Tregs to examine the role of these cells in mediating this process. Following oral exposure to the model antigen ovalbumin (OVA) prior to immunization, we found similar induction of vaccine-induced antibody responses in mice lacking RORγt expression in Tregs compared to sufficient controls. Use of various adjuvants led to distinct findings. Our data suggest that expression of RORγt+ within Tregs is not required to regulate tolerance to systemic vaccination following oral antigen exposure.
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Affiliation(s)
- Nicole B. Potchen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Andrew M.F. Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kevin Hager
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jessica Graham
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Phuong Van
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Katelyn H. Lyn-Kew
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lakshmi Warrier
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Irene Cruz Talavera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Jennifer M. Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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Nyangahu DD, Happel AU, Wendoh J, Kiravu A, Wang Y, Feng C, Plumlee C, Cohen S, Brown BP, Djukovic D, Ganief T, Gasper M, Raftery D, Blackburn JM, Allbritton NL, Gray CM, Paik J, Urdahl KB, Jaspan HB. Bifidobacterium infantis associates with T cell immunity in human infants and is sufficient to enhance antigen-specific T cells in mice. SCIENCE ADVANCES 2023; 9:eade1370. [PMID: 38064556 PMCID: PMC10708209 DOI: 10.1126/sciadv.ade1370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Bacille Calmette-Guerin (BCG) vaccine can elicit good TH1 responses in neonates. We hypothesized that the pioneer gut microbiota affects vaccine T cell responses. Infants who are HIV exposed but uninfected (iHEU) display an altered immunity to vaccination. BCG-specific immune responses were analyzed at 7 weeks of age in iHEU, and responses were categorized as high or low. Bifidobacterium longum subsp. infantis was enriched in the stools of high responders, while Bacteroides thetaiotaomicron was enriched in low responders at time of BCG vaccination. Neonatal germ-free or SPF mice orally gavaged with live B. infantis exhibited significantly higher BCG-specific T cells compared with pups gavaged with B. thetaiotaomicron. B. infantis and B. thetaiotaomicron differentially affected stool metabolome and colonic transcriptome. Human colonic epithelial cells stimulated with B. infantis induced a unique gene expression profile versus B. thetaiotaomicron. We thus identified a causal role of B. infantis in early-life antigen-specific immunity.
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Affiliation(s)
- Donald D. Nyangahu
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Anna-Ursula Happel
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Jerome Wendoh
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Agano Kiravu
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Yuli Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Colin Feng
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Courtney Plumlee
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Sara Cohen
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Bryan P. Brown
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Danijel Djukovic
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA
| | - Tariq Ganief
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Division of Chemical and Systems Biology, University of Cape Town, Cape Town, South Africa
| | - Melanie Gasper
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA
| | - Jonathan M. Blackburn
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Division of Chemical and Systems Biology, University of Cape Town, Cape Town, South Africa
| | | | - Clive M. Gray
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
- Biomedical Research Institute, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Jisun Paik
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
| | - Kevin B. Urdahl
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, School of Medicine, University of Washington, Seattle WA, USA
| | - Heather B. Jaspan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
- Department of Pediatrics, School of Medicine, University of Washington, Seattle WA, USA
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9
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Jiang D, Goswami R, Dennis M, Heimsath H, Kozlowski PA, Ardeshir A, Van Rompay KKA, De Paris K, Permar SR, Surana NK. Sutterella and its metabolic pathways positively correlate with vaccine-elicited antibody responses in infant rhesus macaques. Front Immunol 2023; 14:1283343. [PMID: 38124733 PMCID: PMC10731017 DOI: 10.3389/fimmu.2023.1283343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction It is becoming clearer that the microbiota helps drive responses to vaccines; however, little is known about the underlying mechanism. In this study, we aimed to identify microbial features that are associated with vaccine immunogenicity in infant rhesus macaques. Methods We analyzed 16S rRNA gene sequencing data of 215 fecal samples collected at multiple timepoints from 64 nursery-reared infant macaques that received various HIV vaccine regimens. PERMANOVA tests were performed to determine factors affecting composition of the gut microbiota throughout the first eight months of life in these monkeys. We used DESeq2 to identify differentially abundant bacterial taxa, PICRUSt2 to impute metagenomic information, and mass spectrophotometry to determine levels of fecal short-chain fatty acids and bile acids. Results Composition of the early-life gut microbial communities in nursery-reared rhesus macaques from the same animal care facility was driven by age, birth year, and vaccination status. We identified a Sutterella and a Rodentibacter species that positively correlated with vaccine-elicited antibody responses, with the Sutterella species exhibiting more robust findings. Analysis of Sutterella-related metagenomic data revealed five metabolic pathways that significantly correlated with improved antibody responses following HIV vaccination. Given these pathways have been associated with short-chain fatty acids and bile acids, we quantified the fecal concentration of these metabolites and found several that correlated with higher levels of HIV immunogen-elicited plasma IgG. Discussion Our findings highlight an intricate bidirectional relationship between the microbiota and vaccines, where multiple aspects of the vaccination regimen modulate the microbiota and specific microbial features facilitate vaccine responses. An improved understanding of this microbiota-vaccine interplay will help develop more effective vaccines, particularly those that are tailored for early life.
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Affiliation(s)
- Danting Jiang
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, United States
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, United States
| | - Ria Goswami
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, United States
| | - Maria Dennis
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, United States
| | - Holly Heimsath
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Pamela A. Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Amir Ardeshir
- California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Koen K. A. Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Kristina De Paris
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Sallie R. Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, United States
| | - Neeraj K. Surana
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, United States
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, United States
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10
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Johnson AMF, Hager K, Alameh MG, Van P, Potchen N, Mayer-Blackwell K, Fiore-Gartland A, Minot S, Lin PJC, Tam YK, Weissman D, Kublin JG. The Regulation of Nucleic Acid Vaccine Responses by the Microbiome. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1680-1692. [PMID: 37850965 PMCID: PMC10656434 DOI: 10.4049/jimmunol.2300196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Nucleic acid vaccines, including both RNA and DNA platforms, are key technologies that have considerable promise in combating both infectious disease and cancer. However, little is known about the extrinsic factors that regulate nucleic acid vaccine responses and which may determine their effectiveness. The microbiome is recognized as a significant regulator of immune development and response, whose role in regulating some traditional vaccine platforms has recently been discovered. Using germ-free and specific pathogen-free mouse models in combination with different protein, DNA, and mRNA vaccine regimens, we demonstrate that the microbiome is a significant regulator of nucleic acid vaccine immunogenicity. Although the presence of the microbiome enhances CD8+ T cell responses to mRNA lipid nanoparticle immunization, the microbiome suppresses Ig and CD4+ T cell responses to DNA-prime, DNA-protein-boost immunization, indicating contrasting roles for the microbiome in the regulation of these different nucleic acid vaccine platforms. In the case of mRNA lipid nanoparticle vaccination, germ-free mice display reduced dendritic cell/macrophage activation that may underlie the deficient vaccine response. Our study identifies the microbiome as a relevant determinant of nucleic acid vaccine response with implications for continued therapeutic development and deployment of these vaccines.
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Affiliation(s)
- Andrew M. F. Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Kevin Hager
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | - Phuong Van
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Nicole Potchen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | | | - Samuel Minot
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | | | - Drew Weissman
- Penn Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
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11
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Bondareva M, Budzinski L, Durek P, Witkowski M, Angermair S, Ninnemann J, Kreye J, Letz P, Ferreira-Gomes M, Semin I, Guerra GM, Momsen Reincke S, Sánchez-Sendin E, Yilmaz S, Sempert T, Heinz GA, Tizian C, Raftery M, Schönrich G, Matyushkina D, Smirnov IV, Govorun VM, Schrezenmeier E, Stefanski AL, Dörner T, Zocche S, Viviano E, Klement N, Sehmsdorf KJ, Lunin A, Chang HD, Drutskaya M, Kozlovskaya L, Treskatsch S, Radbruch A, Diefenbach A, Prüss H, Enghard P, Mashreghi MF, Kruglov AA. Cross-regulation of antibody responses against the SARS-CoV-2 Spike protein and commensal microbiota via molecular mimicry. Cell Host Microbe 2023; 31:1866-1881.e10. [PMID: 37944493 DOI: 10.1016/j.chom.2023.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 07/11/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
The commensal microflora provides a repertoire of antigens that illicit mucosal antibodies. In some cases, these antibodies can cross-react with host proteins, inducing autoimmunity, or with other microbial antigens. We demonstrate that the oral microbiota can induce salivary anti-SARS-CoV-2 Spike IgG antibodies via molecular mimicry. Anti-Spike IgG antibodies in the saliva correlated with enhanced abundance of Streptococcus salivarius 1 month after anti-SARS-CoV-2 vaccination. Several human commensal bacteria, including S. salivarius, were recognized by SARS-CoV-2-neutralizing monoclonal antibodies and induced cross-reactive anti-Spike antibodies in mice, facilitating SARS-CoV-2 clearance. A specific S. salivarius protein, RSSL-01370, contains regions with homology to the Spike receptor-binding domain, and immunization of mice with RSSL-01370 elicited anti-Spike IgG antibodies in the serum. Additionally, oral S. salivarius supplementation enhanced salivary anti-Spike antibodies in vaccinated individuals. Altogether, these data show that distinct species of the human microbiota can express molecular mimics of SARS-CoV-2 Spike protein, potentially enhancing protective immunity.
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Affiliation(s)
- Marina Bondareva
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Belozersky Institute of Physico-Chemical Biology and Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Lisa Budzinski
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Pawel Durek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Mario Witkowski
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charité-Universitätsmedizin Berlin, 12203 Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Stefan Angermair
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Anesthesiology and Intensive Care Medicine, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Justus Ninnemann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Jakob Kreye
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Philine Letz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Marta Ferreira-Gomes
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Iaroslav Semin
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Belozersky Institute of Physico-Chemical Biology and Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Gabriela Maria Guerra
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - S Momsen Reincke
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Elisa Sánchez-Sendin
- German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Selin Yilmaz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Toni Sempert
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Gitta Anne Heinz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Caroline Tizian
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charité-Universitätsmedizin Berlin, 12203 Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Martin Raftery
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Günther Schönrich
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Daria Matyushkina
- Scientific Research Institute for Systems Biology and Medicine, Scientific Driveway, 18, 117246 Moscow, Russia
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Vadim M Govorun
- Scientific Research Institute for Systems Biology and Medicine, Scientific Driveway, 18, 117246 Moscow, Russia
| | - Eva Schrezenmeier
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Department of Nephrology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Anna-Luisa Stefanski
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Dörner
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Silvia Zocche
- Departments of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité University Medicine, 10117 Berlin, Germany
| | - Edoardo Viviano
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Physiology, Center for Space Medicine and Extreme Environments Berlin, 10117 Berlin, Germany
| | - Nele Klement
- Department of Nephrology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Katharina Johanna Sehmsdorf
- Department of Nephrology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Alexander Lunin
- Chumakov Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences (Institute of Poliomyelitis), 108819 Moscow, Russia
| | - Hyun-Dong Chang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Marina Drutskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Liubov Kozlovskaya
- Chumakov Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences (Institute of Poliomyelitis), 108819 Moscow, Russia; Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Sascha Treskatsch
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Anesthesiology and Intensive Care Medicine, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Diefenbach
- Berlin Institute of Health (BIH), 10178 Berlin, Germany; Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charité-Universitätsmedizin Berlin, 12203 Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Philipp Enghard
- Department of Nephrology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany
| | - Andrey A Kruglov
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117 Berlin, Germany; Belozersky Institute of Physico-Chemical Biology and Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Biological Faculty, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
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12
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Ponziani FR, Coppola G, Rio P, Caldarelli M, Borriello R, Gambassi G, Gasbarrini A, Cianci R. Factors Influencing Microbiota in Modulating Vaccine Immune Response: A Long Way to Go. Vaccines (Basel) 2023; 11:1609. [PMID: 37897011 PMCID: PMC10611107 DOI: 10.3390/vaccines11101609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Vaccine immunogenicity still represents an unmet need in specific populations, such as people from developing countries and "edge populations". Both intrinsic and extrinsic factors, such as the environment, age, and dietary habits, influence cellular and humoral immune responses. The human microbiota represents a potential key to understanding how these factors impact the immune response to vaccination, with its modulation being a potential step to address vaccine immunogenicity. The aim of this narrative review is to explore the intricate interactions between the microbiota and the immune system in response to vaccines, highlighting the state of the art in gut microbiota modulation as a novel therapeutic approach to enhancing vaccine immunogenicity and laying the foundation for future, more solid data for its translation to the clinical practice.
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Affiliation(s)
| | | | | | | | | | | | | | - Rossella Cianci
- Department of Translational Medicine and Surgery, Catholic University, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy (G.C.); (P.R.); (M.C.); (R.B.); (G.G.); (A.G.)
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13
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Planchais C, Molinos-Albert LM, Rosenbaum P, Hieu T, Kanyavuz A, Clermont D, Prazuck T, Lefrou L, Dimitrov JD, Hüe S, Hocqueloux L, Mouquet H. HIV-1 treatment timing shapes the human intestinal memory B-cell repertoire to commensal bacteria. Nat Commun 2023; 14:6326. [PMID: 37816704 PMCID: PMC10564866 DOI: 10.1038/s41467-023-42027-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
HIV-1 infection causes severe alterations of gut mucosa, microbiota and immune system, which can be curbed by early antiretroviral therapy. Here, we investigate how treatment timing affects intestinal memory B-cell and plasmablast repertoires of HIV-1-infected humans. We show that only class-switched memory B cells markedly differ between subjects treated during the acute and chronic phases of infection. Intestinal memory B-cell monoclonal antibodies show more prevalent polyreactive and commensal bacteria-reactive clones in late- compared to early-treated individuals. Mirroring this, serum IgA polyreactivity and commensal-reactivity are strongly increased in late-treated individuals and correlate with intestinal permeability and systemic inflammatory markers. Polyreactive blood IgA memory B cells, many of which egressed from the gut, are also substantially enriched in late-treated individuals. Our data establish gut and systemic B-cell polyreactivity to commensal bacteria as hallmarks of chronic HIV-1 infection and suggest that initiating treatment early may limit intestinal B-cell abnormalities compromising HIV-1 humoral response.
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Affiliation(s)
- Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Luis M Molinos-Albert
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036, Barcelona, Spain
| | - Pierre Rosenbaum
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Thierry Hieu
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Alexia Kanyavuz
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006, Paris, France
| | - Dominique Clermont
- Collection of the Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Thierry Prazuck
- Service des Maladies Infectieuses et Tropicales, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Laurent Lefrou
- Service d'Hépato-Gastro-Entérologie, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006, Paris, France
| | - Sophie Hüe
- INSERM U955-Équipe 16, Université Paris-Est Créteil, Faculté de Médecine, 94000, Créteil, France
| | - Laurent Hocqueloux
- Service des Maladies Infectieuses et Tropicales, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France.
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14
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Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
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Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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15
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Ji H, Jiang Z, Wei C, Ma Y, Zhao J, Wang F, Zhao B, Wang D, Tang D. Intratumoural microbiota: from theory to clinical application. Cell Commun Signal 2023; 21:164. [PMID: 37381018 DOI: 10.1186/s12964-023-01134-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/22/2023] [Indexed: 06/30/2023] Open
Abstract
Cancer is a major cause of high morbidity and mortality worldwide. Several environmental, genetic and lifestyle factors are associated with the development of cancer in humans and result in suboptimal treatment. The human microbiota has been implicated in the pathophysiological process of cancer and has been used as a diagnostic, prognostic and risk assessment tool in cancer management. Notably, both extratumoural and intratumoural microbiota are important components of the tumor microenvironment, subtly influencing tumorigenesis, progression, treatment and prognosis. The potential oncogenic mechanisms of action of the intratumoural microbiota include induction of DNA damage, influence on cell signaling pathways and impairment of immune responses. Some naturally occurring or genetically engineered microorganisms can specifically accumulate and replicate in tumors and then initiate various anti-tumor programs, ultimately promoting the therapeutic effect of tumor microbiota and reducing the toxic and side effects of conventional tumor treatments, which may be conducive to the pursuit of accurate cancer treatment. In this review, we summarise evidence revealing the impact of the intratumoural microbiota on cancer occurrence and progress and potential therapeutic and diagnostic applications, which may be a promising novel strategy to inhibit tumor development and enhance therapeutic efficacy. Video Abstract.
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Affiliation(s)
- Hao Ji
- Clinical Medical College, Yangzhou University, Yangzhou, 225000, Jiangsu Province, China
| | - Zhengting Jiang
- Clinical Medical College, Yangzhou University, Yangzhou, 225000, Jiangsu Province, China
| | - Chen Wei
- Clinical Medical College, Yangzhou University, Yangzhou, 225000, Jiangsu Province, China
| | - Yichao Ma
- Clinical Medical College, Yangzhou University, Yangzhou, 225000, Jiangsu Province, China
| | - Jiahao Zhao
- Clinical Medical College, Yangzhou University, Yangzhou, 225000, Jiangsu Province, China
| | - Fei Wang
- Clinical Medical College, Dalian Medical University, Dalian, 116044, Liaoning Province, China
| | - Bin Zhao
- Clinical Medical College, Dalian Medical University, Dalian, 116044, Liaoning Province, China
| | - Daorong Wang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, 225000, China
| | - Dong Tang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, 225000, China.
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16
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Huang B, Wang J, Li L. Recent five-year progress in the impact of gut microbiota on vaccination and possible mechanisms. Gut Pathog 2023; 15:27. [PMID: 37308966 DOI: 10.1186/s13099-023-00547-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/17/2023] [Indexed: 06/14/2023] Open
Abstract
Vaccine is the most effective way to prevent the spread of communicable diseases, but the immune response induced by it varies greatly between individuals and populations in different regions of the world. Current studies have identified the composition and function of the gut microbiota as key factors in modulating the immune response to vaccination. This article mainly reviews the differences in gut microbiota among different groups of vaccinated people and animals, explores the possible mechanism of vaccine immunity affected by gut microbiota, and reviews the strategies for targeting gut microbiota to improve vaccine efficacy.
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Affiliation(s)
- Biqing Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University school of medicine, Hangzhou, China
- Research Units of Infectious disease and Microecology, Chinese Academy of Medical Sciences & Peking Union Medical College, Hangzhou, China
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University school of medicine, Hangzhou, China.
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University school of medicine, Hangzhou, China.
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17
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Haynes BF, Wiehe K, Borrow P, Saunders KO, Korber B, Wagh K, McMichael AJ, Kelsoe G, Hahn BH, Alt F, Shaw GM. Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies. Nat Rev Immunol 2023; 23:142-158. [PMID: 35962033 PMCID: PMC9372928 DOI: 10.1038/s41577-022-00753-w] [Citation(s) in RCA: 113] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
After nearly four decades of research, a safe and effective HIV-1 vaccine remains elusive. There are many reasons why the development of a potent and durable HIV-1 vaccine is challenging, including the extraordinary genetic diversity of HIV-1 and its complex mechanisms of immune evasion. HIV-1 envelope glycoproteins are poorly recognized by the immune system, which means that potent broadly neutralizing antibodies (bnAbs) are only infrequently induced in the setting of HIV-1 infection or through vaccination. Thus, the biology of HIV-1-host interactions necessitates novel strategies for vaccine development to be designed to activate and expand rare bnAb-producing B cell lineages and to select for the acquisition of critical improbable bnAb mutations. Here we discuss strategies for the induction of potent and broad HIV-1 bnAbs and outline the steps that may be necessary for ultimate success.
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Affiliation(s)
- Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Kshitij Wagh
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Immunology, Duke University of School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederick Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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18
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Pilewski KA, Wall S, Richardson SI, Manamela NP, Clark K, Hermanus T, Binshtein E, Venkat R, Sautto GA, Kramer KJ, Shiakolas AR, Setliff I, Salas J, Mapengo RE, Suryadevara N, Brannon JR, Beebout CJ, Parks R, Raju N, Frumento N, Walker LM, Fechter EF, Qin JS, Murji AA, Janowska K, Thakur B, Lindenberger J, May AJ, Huang X, Sammour S, Acharya P, Carnahan RH, Ross TM, Haynes BF, Hadjifrangiskou M, Crowe JE, Bailey JR, Kalams S, Morris L, Georgiev IS. Functional HIV-1/HCV cross-reactive antibodies isolated from a chronically co-infected donor. Cell Rep 2023; 42:112044. [PMID: 36708513 PMCID: PMC10372200 DOI: 10.1016/j.celrep.2023.112044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/30/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
Despite prolific efforts to characterize the antibody response to human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) mono-infections, the response to chronic co-infection with these two ever-evolving viruses is poorly understood. Here, we investigate the antibody repertoire of a chronically HIV-1/HCV co-infected individual using linking B cell receptor to antigen specificity through sequencing (LIBRA-seq). We identify five HIV-1/HCV cross-reactive antibodies demonstrating binding and functional cross-reactivity between HIV-1 and HCV envelope glycoproteins. All five antibodies show exceptional HCV neutralization breadth and effector functions against both HIV-1 and HCV. One antibody, mAb688, also cross-reacts with influenza and coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We examine the development of these antibodies using next-generation sequencing analysis and lineage tracing and find that somatic hypermutation established and enhanced this reactivity. These antibodies provide a potential future direction for therapeutic and vaccine development against current and emerging infectious diseases. More broadly, chronic co-infection represents a complex immunological challenge that can provide insights into the fundamental rules that underly antibody-antigen specificity.
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Affiliation(s)
- Kelsey A Pilewski
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Steven Wall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Simone I Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Nelia P Manamela
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Kaitlyn Clark
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tandile Hermanus
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rohit Venkat
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Giuseppe A Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Kevin J Kramer
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrea R Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ian Setliff
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jordan Salas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rutendo E Mapengo
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Naveen Suryadevara
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John R Brannon
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Connor J Beebout
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rob Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Nagarajan Raju
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicole Frumento
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lauren M Walker
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Juliana S Qin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Amyn A Murji
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Bhishem Thakur
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | | | - Aaron J May
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Xiao Huang
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Salam Sammour
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Biochemistry, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Barton F Haynes
- Departments of Medicine and Immunology, Duke University, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Justin R Bailey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Spyros Kalams
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lynn Morris
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Computer Science, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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19
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Johnson AMF, Hager K, Alameh MG, Van P, Potchen N, Mayer-Blackwell K, Fiore-Gartland A, Minot S, Lin PJC, Tam YK, Weissman D, Kublin JG. The Regulation of Nucleic Acid Vaccine Responses by the Microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.18.529093. [PMID: 36824851 PMCID: PMC9949122 DOI: 10.1101/2023.02.18.529093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Nucleic acid vaccines, including both RNA and DNA platforms, are key technologies that have considerable promise in combating both infectious disease and cancer. However, little is known about the extrinsic factors that regulate nucleic acid vaccine responses and which may determine their effectiveness. The microbiome is recognized as a significant regulator of immune development and response, whose role in regulating some traditional vaccine platforms has recently been discovered. Using germ-free and specific-pathogen-free mouse models in combination with different protein, DNA, and mRNA vaccine regimens, we demonstrate that the microbiome is a significant regulator of nucleic acid vaccine immunogenicity. While the presence of the microbiome enhances CD8+ T cell responses to mRNA lipid nanoparticle (LNP) immunization, the microbiome suppresses immunoglobulin and CD4+ T cell responses to DNA-prime, DNA-protein-boost immunization, indicating contrasting roles for the microbiome in the regulation of these different nucleic acid vaccine platforms. In the case of mRNA-LNP vaccination, germ-free mice display reduced dendritic cell/macrophage activation that may underlie the deficient vaccine response. Our study identifies the microbiome as a relevant determinant of nucleic acid vaccine response with implications for their continued therapeutic development and deployment.
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20
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Mayer-Blackwell K, Johnson AM, Potchen N, Minot SS, Heptinstall J, Seaton K, Sawant S, Shen X, Tomaras GD, Fiore-Gartland A, Kublin JG. Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines. Front Immunol 2022; 13:983313. [PMID: 36311720 PMCID: PMC9597301 DOI: 10.3389/fimmu.2022.983313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Many participants in HIV-1 vaccine trials, who have not previously been exposed to or vaccinated against HIV-1, display serum immunoglobulin antibodies that bind the gp41 region of HIV-1 envelope prior to vaccination. Previous studies have hypothesized that these pre-existing antibodies may be cross-reactive and may skew future vaccine responses. In 12 large studies conducted by the HIV Vaccine Trial Network (HVTN) (n=1470 individuals), we find wide variation among participants in the pre-vaccine levels of gp41-reactive antibodies as measured by the binding antibody multiplex assay (BAMA). In the absence of exposure to the gp41 immunogen, anti-gp41 IgG levels were temporally stable over 26-52 weeks in repeated measures of placebo recipients. The analysis revealed that the geometric mean of pre-vaccine anti-gp41 IgG response was greater among participants in South Africa compared with participants in the United States. With gene-level metagenomic sequencing of pre-vaccination fecal samples collected from participants in one trial (HVTN 106), we detected positive associations between pre-vaccine anti-gp41 IgG and abundance of genes from multiple taxa in the Eubacteriales order. The genes most strongly associated with higher baseline anti-gp41 IgG mapped to a clade containing Blautia wexlerae and closely related strains. In trials with vaccine products containing the full or partial portion of gp41 immunogen alongside a gp120 immunogen, we did not find evidence that individuals with higher baseline anti-gp41 IgG had different levels of anti-gp120 IgG after vaccination compared to individuals with lower pre-vaccine anti-gp41 levels (pooled estimate of standardized mean difference -0.01 with a 95% CI [-0.37; 0.34]).
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Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Andrew M. Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Nicole Potchen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Simon S. Minot
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jack Heptinstall
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Kelly Seaton
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Sheetal Sawant
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Xiaoying Shen
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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21
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Huang Y, Zhang Y, Seaton KE, De Rosa S, Heptinstall J, Carpp LN, Randhawa AK, McKinnon LR, McLaren P, Viegas E, Gray GE, Churchyard G, Buchbinder SP, Edupuganti S, Bekker LG, Keefer MC, Hosseinipour MC, Goepfert PA, Cohen KW, Williamson BD, McElrath MJ, Tomaras GD, Thakar J, Kobie JJ. Baseline host determinants of robust human HIV-1 vaccine-induced immune responses: A meta-analysis of 26 vaccine regimens. EBioMedicine 2022; 84:104271. [PMID: 36179551 PMCID: PMC9520208 DOI: 10.1016/j.ebiom.2022.104271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/27/2022] [Accepted: 09/02/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The identification of baseline host determinants that associate with robust HIV-1 vaccine-induced immune responses could aid HIV-1 vaccine development. We aimed to assess both the collective and relative performance of baseline characteristics in classifying individual participants in nine different Phase 1-2 HIV-1 vaccine clinical trials (26 vaccine regimens, conducted in Africa and in the Americas) as High HIV-1 vaccine responders. METHODS This was a meta-analysis of individual participant data, with studies chosen based on participant-level (vs. study-level summary) data availability within the HIV-1 Vaccine Trials Network. We assessed the performance of 25 baseline characteristics (demographics, safety haematological measurements, vital signs, assay background measurements) and estimated the relative importance of each characteristic in classifying 831 participants as High (defined as within the top 25th percentile among positive responders or above the assay upper limit of quantification) versus Non-High responders. Immune response outcomes included HIV-1-specific serum IgG binding antibodies and Env-specific CD4+ T-cell responses assessed two weeks post-last dose, all measured at central HVTN laboratories. Three variable importance approaches based on SuperLearner ensemble machine learning were considered. FINDINGS Overall, 30.1%, 50.5%, 36.2%, and 13.9% of participants were categorized as High responders for gp120 IgG, gp140 IgG, gp41 IgG, and Env-specific CD4+ T-cell vaccine-induced responses, respectively. When including all baseline characteristics, moderate performance was achieved for the classification of High responder status for the binding antibody responses, with cross-validated areas under the ROC curve (CV-AUC) of 0.72 (95% CI: 0.68, 0.76) for gp120 IgG, 0.73 (0.69, 0.76) for gp140 IgG, and 0.67 (95% CI: 0.63, 0.72) for gp41 IgG. In contrast, the collection of all baseline characteristics yielded little improvement over chance for predicting High Env-specific CD4+ T-cell responses [CV-AUC: 0.53 (0.48, 0.58)]. While estimated variable importance patterns differed across the three approaches, female sex assigned at birth, lower height, and higher total white blood cell count emerged as significant predictors of High responder status across multiple immune response outcomes using Approach 1. Of these three baseline variables, total white blood cell count ranked highly across all three approaches for predicting vaccine-induced gp41 and gp140 High responder status. INTERPRETATION The identified features should be studied further in pursuit of intervention strategies to improve vaccine responses and may be adjusted for in analyses of immune response data to enhance statistical power. FUNDING National Institute of Allergy and Infectious Diseases (UM1AI068635 to YH, UM1AI068614 to GDT, UM1AI068618 to MJM, and UM1 AI069511 to MCK), the Duke CFAR P30 AI064518 to GDT, and National Institute of Dental and Craniofacial Research (R01DE027245 to JJK). This work was also supported by the Bill and Melinda Gates Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funding sources.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America; Department of Global Health, University of Washington, Seattle, WA, United States of America.
| | - Yuanyuan Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Kelly E Seaton
- Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Stephen De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Jack Heptinstall
- Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - April Kaur Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Lyle R McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MN, Canada; JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MN, Canada; Centre for the AIDS Program of Research in South Africa (CAPRISA), Durban, South Africa
| | - Paul McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MN, Canada; JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MN, Canada
| | - Edna Viegas
- Instituto Nacional de Saúde, Maputo, Mozambique
| | - Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; South African Medical Research Council, Cape Town, South Africa
| | - Gavin Churchyard
- Aurum Institute, Johannesburg, South Africa; School of Public Health, University of Witwatersrand, Johannesburg, South Africa
| | - Susan P Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, United States of America; Department of Medicine and Department of Epidemiology, University of California, San Francisco, CA, United States of America
| | - Srilatha Edupuganti
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Michael C Keefer
- Department of Medicine, Infectious Diseases Division, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| | - Mina C Hosseinipour
- University of North Carolina Project, Lilongwe, Malawi; Department of Medicine, Institution for Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Paul A Goepfert
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Brian D Williamson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America; Kaiser Permanente Washington Health Research Institute, Seattle, WA, United States of America
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Georgia D Tomaras
- Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| | - James J Kobie
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America.
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22
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Jia L, Weng S, Wu J, Tian X, Zhang Y, Wang X, Wang J, Yan D, Wang W, Fang F, Zhu Z, Qiu C, Zhang W, Xu Y, Wan Y. Preexisting antibodies targeting SARS-CoV-2 S2 cross-react with commensal gut bacteria and impact COVID-19 vaccine induced immunity. Gut Microbes 2022; 14:2117503. [PMID: 36100957 PMCID: PMC9481142 DOI: 10.1080/19490976.2022.2117503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The origins of preexisting SARS-CoV-2 cross-reactive antibodies and their potential impacts on vaccine efficacy have not been fully clarified. In this study, we demonstrated that S2 was the prevailing target of the preexisting S protein cross-reactive antibodies in both healthy human and SPF mice. A dominant antibody epitope was identified on the connector domain of S2 (1147-SFKEELDKYFKNHT-1160, P144), which could be recognized by preexisting antibodies in both human and mouse. Through metagenomic sequencing and fecal bacteria transplant, we demonstrated that the generation of S2 cross-reactive antibodies was associated with commensal gut bacteria. Furthermore, six P144 reactive monoclonal antibodies were isolated from naïve SPF mice and were proven to cross-react with commensal gut bacteria collected from both human and mouse. A variety of cross-reactive microbial proteins were identified using LC-MS, of which E. coli derived HSP60 and HSP70 proteins were confirmed to be able to bind to one of the isolated monoclonal antibodies. Mice with high levels of preexisting S2 cross-reactive antibodies mounted higher S protein specific binding antibodies, especially against S2, after being immunized with a SARS-CoV-2 S DNA vaccine. Similarly, we found that levels of preexisting S2 and P144-specific antibodies correlated positively with RBD binding antibody titers after two doses of inactivated SARS-CoV-2 vaccination in human. Collectively, our study revealed an alternative origin of preexisting S2-targeted antibodies and disclosed a previously neglected aspect of the impact of gut microbiota on host anti-SARS-CoV-2 immunity.
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Affiliation(s)
- Liqiu Jia
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shufeng Weng
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China,Ying Xu State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Xiangxiang Tian
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
| | - Yifan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
| | - Xuyang Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Department of Immunology, School of Basic Medical, Jiamusi University, Jiamusi, China
| | - Dongmei Yan
- Department of Immunology, School of Basic Medical, Jiamusi University, Jiamusi, China
| | - Wanhai Wang
- Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
| | - Fang Fang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhaoqin Zhu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Zhaoqin Zhu Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chao Qiu
- Institutes of Biomedical Sciences & Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, China,Chao Qiu Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China,State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China,Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China,Wenhong Zhang Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Xu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,Ying Xu State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Yanmin Wan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China,State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,Department of Radiology, Shanghai Public Health Clinical Center, Shanghai, China,CONTACT Yanmin Wan Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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23
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Jones ST, Guo K, Cooper EH, Dillon SM, Wood C, Nguyen DH, Shen G, Barrett BS, Frank DN, Kroehl M, Janoff EN, Kechris K, Wilson CC, Santiago ML. Altered Immunoglobulin Repertoire and Decreased IgA Somatic Hypermutation in the Gut during Chronic HIV-1 Infection. J Virol 2022; 96:e0097622. [PMID: 35938870 PMCID: PMC9472609 DOI: 10.1128/jvi.00976-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 11/27/2022] Open
Abstract
Humoral immune perturbations contribute to pathogenic outcomes in persons with HIV-1 infection (PWH). Gut barrier dysfunction in PWH is associated with microbial translocation and alterations in microbial communities (dysbiosis), and IgA, the most abundant immunoglobulin (Ig) isotype in the gut, is involved in gut homeostasis by interacting with the microbiome. We determined the impact of HIV-1 infection on the antibody repertoire in the gastrointestinal tract by comparing Ig gene utilization and somatic hypermutation (SHM) in colon biopsies from PWH (n = 19) versus age and sex-matched controls (n = 13). We correlated these Ig parameters with clinical, immunological, microbiome and virological data. Gene signatures of enhanced B cell activation were accompanied by skewed frequencies of multiple Ig Variable genes in PWH. PWH showed decreased frequencies of SHM in IgA and possibly IgG, with a substantial loss of highly mutated IgA sequences. The decline in IgA SHM in PWH correlated with gut CD4+ T cell loss and inversely correlated with mucosal inflammation and microbial translocation. Diminished gut IgA SHM in PWH was driven by transversion mutations at A or T deoxynucleotides, suggesting a defect not at the AID/APOBEC3 deamination step but at later stages of IgA SHM. These results expand our understanding of humoral immune perturbations in PWH that could have important implications in understanding mucosal immune defects in individuals with chronic HIV-1 infection. IMPORTANCE The gut is a major site of early HIV-1 replication and pathogenesis. Extensive CD4+ T cell depletion in this compartment results in a compromised epithelial barrier that facilitates the translocation of microbes into the underlying lamina propria and systemic circulation, resulting in chronic immune activation. To date, the consequences of microbial translocation on the mucosal humoral immune response (or vice versa) remains poorly integrated into the panoply of mucosal immune defects in PWH. We utilized next-generation sequencing approaches to profile the Ab repertoire and ascertain frequencies of somatic hypermutation in colon biopsies from antiretroviral therapy-naive PWH versus controls. Our findings identify perturbations in the Ab repertoire of PWH that could contribute to development or maintenance of dysbiosis. Moreover, IgA mutations significantly decreased in PWH and this was associated with adverse clinical outcomes. These data may provide insight into the mechanisms underlying impaired Ab-dependent gut homeostasis during chronic HIV-1 infection.
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Affiliation(s)
- Sean T. Jones
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Emily H. Cooper
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Stephanie M. Dillon
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Cheyret Wood
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - David H. Nguyen
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Guannan Shen
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bradley S. Barrett
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Miranda Kroehl
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Edward N. Janoff
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA
| | - Katerina Kechris
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Cara C. Wilson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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24
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Association between Recent Usage of Antibiotics and Immunogenicity within Six Months after COVID-19 Vaccination. Vaccines (Basel) 2022; 10:vaccines10071122. [PMID: 35891286 PMCID: PMC9318721 DOI: 10.3390/vaccines10071122] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Gut microbiota can be associated with COVID-19 vaccine immunogenicity. We investigated whether recent antibiotic use influences BNT162b2 vaccine immunogenicity. Methods: BNT162b2 recipients from three centers were prospectively recruited. Outcomes of interest were seroconversion of neutralising antibody (NAb) at day 21, 56 and 180 after first dose. We calculated the adjusted odds ratio (aOR) of seroconversion with antibiotic usage (defined as ever use of any antibiotics within six months before first dose of vaccine) by adjusting for covariates including age, sex, smoking, alcohol, and comorbidities. Results: Of 316 BNT162b2 recipients (100 [31.6%] male; median age: 50.1 [IQR: 40.0–57.0] years) recruited, 29 (9.2%) were antibiotic users. There was a trend of lower seroconversion rates in antibiotic users than non-users at day 21 (82.8% vs. 91.3%; p = 0.14) and day 56 (96.6% vs. 99.3%; p = 0.15), but not at day 180 (93.3% vs. 94.1%). A multivariate analysis showed that recent antibiotic usage was associated with a lower seroconversion rate at day 21 (aOR 0.26;95% CI: 0.08–0.96). Other factors associated with a lower seroconversion rate after first dose of the BNT162b2 vaccine included age ≥ 60 years (aOR: 0.34;95% CI: 0.13–0.95) and male sex (aOR: 0.14, 95% CI: 0.05–0.34). There were no significant factors associated with seroconversion after two doses of BNT16b2, including antibiotic use (aOR: 0.03;95% CI: 0.001–1.15). Conclusions: Recent antibiotic use may be associated with a lower seroconversion rate at day 21 (but not day 56 or 180) among BNT162b2 recipients. Further long-term follow-up data with a larger sample size is needed to reach a definite conclusion on how antibiotics influence immunogenicity and the durability of the vaccine response.
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25
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Harris JE. The repeated setbacks of HIV vaccine development laid the groundwork for SARS-CoV-2 vaccines. HEALTH POLICY AND TECHNOLOGY 2022; 11:100619. [PMID: 35340773 PMCID: PMC8935961 DOI: 10.1016/j.hlpt.2022.100619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The decades-long effort to produce a workable HIV vaccine has hardly been a waste of public and private resources. To the contrary, the scientific know-how acquired along the way has served as the critical foundation for the development of vaccines against the novel, pandemic SARS-CoV-2 virus. We retell the real-world story of HIV vaccine research - with all its false leads and missteps - in a way that sheds light on the current state of the art of antiviral vaccines. We find that HIV-related R&D had more than a general spillover effect. In fact, the repeated failures of phase 2 and 3 clinical trials of HIV vaccine candidates have served as a critical stimulus to the development of successful vaccine technologies today. We rebut the counterargument that HIV vaccine development has been no more than a blind alley, and that recently developed vaccines against COVID-19 are really descendants of successful vaccines against Ebola, MERS, and SARS. These successful vaccines likewise owe much to the vicissitudes of HIV vaccine development. We then discuss how the failures of HIV vaccine development have taught us how adapt SARS-CoV-2 vaccines to immune escape from emerging variants. Finally, we inquire whether recent advances in the development of vaccines against SARS-CoV-2 might in turn further the development of an HIV vaccine - what we describe as a reverse spillover effect.
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Affiliation(s)
- Jeffrey E Harris
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Eisner Health, Los Angeles, CA 90015, USA
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26
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Klasse PJ, Moore JP. Reappraising the Value of HIV-1 Vaccine Correlates of Protection Analyses. J Virol 2022; 96:e0003422. [PMID: 35384694 PMCID: PMC9044961 DOI: 10.1128/jvi.00034-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2022] [Indexed: 01/09/2023] Open
Abstract
With the much-debated exception of the modestly reduced acquisition reported for the RV144 efficacy trial, HIV-1 vaccines have not protected humans against infection, and a vaccine of similar design to that tested in RV144 was not protective in a later trial, HVTN 702. Similar vaccine regimens have also not consistently protected nonhuman primates (NHPs) against viral acquisition. Conversely, experimental vaccines of different designs have protected macaques from viral challenges but then failed to protect humans, while many other HIV-1 vaccine candidates have not protected NHPs. While efficacy varies more in NHPs than humans, vaccines have failed to protect in the most stringent NHP model. Intense investigations have aimed to identify correlates of protection (CoPs), even in the absence of net protection. Unvaccinated animals and humans vary vastly in their susceptibility to infection and in their innate and adaptive responses to the vaccines; hence, merely statistical associations with factors that do not protect are easily found. Systems biological analyses, including artificial intelligence, have identified numerous candidate CoPs but with no clear consistency within or between species. Proposed CoPs sometimes have only tenuous mechanistic connections to immune protection. In contrast, neutralizing antibodies (NAbs) are a central mechanistic CoP for vaccines that succeed against other viruses, including SARS-CoV-2. No HIV-1 vaccine candidate has yet elicited potent and broadly active NAbs in NHPs or humans, but narrow-specificity NAbs against the HIV-1 isolate corresponding to the immunogen do protect against infection by the autologous virus. Here, we analyze why so many HIV-1 vaccines have failed, summarize the outcomes of vaccination in NHPs and humans, and discuss the value and pitfalls of hunting for CoPs other than NAbs. We contrast the failure to find a consistent CoP for HIV-1 vaccines with the identification of NAbs as the principal CoP for SARS-CoV-2.
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Affiliation(s)
- P. J. Klasse
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
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27
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Geanes ES, LeMaster C, Fraley ER, Khanal S, McLennan R, Grundberg E, Selvarangan R, Bradley T. Cross-reactive antibodies elicited to conserved epitopes on SARS-CoV-2 spike protein after infection and vaccination. Sci Rep 2022; 12:6496. [PMID: 35444221 PMCID: PMC9019795 DOI: 10.1038/s41598-022-10230-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is a novel betacoronavirus that caused coronavirus disease 2019 and has resulted in millions of deaths worldwide. Novel coronavirus infections in humans have steadily become more common. Understanding antibody responses to SARS-CoV-2, and identifying conserved, cross-reactive epitopes among coronavirus strains could inform the design of vaccines and therapeutics with broad application. Here, we determined that individuals with previous SARS-CoV-2 infection or vaccinated with the Pfizer-BioNTech BNT162b2 vaccine produced antibody responses that cross-reacted with related betacoronaviruses. Moreover, we designed a peptide-conjugate vaccine with a conserved SARS-CoV-2 S2 spike epitope, immunized mice and determined cross-reactive antibody binding to SARS-CoV-2 and other related coronaviruses. This conserved spike epitope also shared sequence homology to proteins in commensal gut microbiota and could prime immune responses in humans. Thus, SARS-CoV-2 conserved epitopes elicit cross-reactive immune responses to both related coronaviruses and host bacteria that could serve as future targets for broad coronavirus therapeutics and vaccines.
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Affiliation(s)
- Eric S Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elizabeth R Fraley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Rangaraj Selvarangan
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA. .,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA. .,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA. .,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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28
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Cook JD, Khondker A, Lee JE. Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies. Commun Biol 2022; 5:291. [PMID: 35361878 PMCID: PMC8971491 DOI: 10.1038/s42003-022-03235-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/08/2022] [Indexed: 12/17/2022] Open
Abstract
The early humoral immune response to acute HIV-1 infection is largely non-neutralizing. The principal target of these antibodies is the primary immunodominant region (PID) on the gp41 fusion protein. The PID is a highly conserved 15-residue region displayed on the surface of HIV-1 virions. In this study, we analyzed the humoral determinants of HIV-1 gp41 PID binding using biophysical, structural, and computational methods. In complex with a patient-derived near-germline antibody fragment, the PID motif adopts an elongated random coil, whereas the PID bound to affinity-matured Fab adopts a strand-turn-helix conformation. Molecular dynamics simulations showed that the PID is structurally plastic suggesting that the PID can form an ensemble of structural states recognized by various non-neutralizing antibodies, facilitating HIV-1 immunodominance observed in acute and chronic HIV-1 infections. An improved understanding of how the HIV-1 gp41 PID misdirects the early humoral response should guide the development of an effective HIV-1 vaccine. The 15-amino-acid primary immunodominant (PID) region on HIV-1 gp41 adopts an ensemble of conformational states. This conformational plasticity is suggested to misdirect the early humoral immune response.
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Affiliation(s)
- Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Adree Khondker
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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29
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Huettner I, Krumm SA, Serna S, Brzezicka K, Monaco S, Walpole S, van Diepen A, Allan F, Hicks T, Kimuda S, Emery AM, Landais E, Hokke CH, Angulo J, Reichardt N, Doores KJ. Cross-reactivity of glycan-reactive HIV-1 broadly neutralizing antibodies with parasite glycans. Cell Rep 2022; 38:110611. [PMID: 35354052 PMCID: PMC10073069 DOI: 10.1016/j.celrep.2022.110611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/26/2022] [Accepted: 03/11/2022] [Indexed: 11/03/2022] Open
Abstract
The HIV-1 Envelope glycoprotein (Env) is the sole target for broadly neutralizing antibodies (bnAbs). Env is heavily glycosylated with host-derived N-glycans, and many bnAbs bind to, or are dependent upon, Env glycans for neutralization. Although glycan-binding bnAbs are frequently detected in HIV-infected individuals, attempts to elicit them have been unsuccessful because of the poor immunogenicity of Env N-glycans. Here, we report cross-reactivity of glycan-binding bnAbs with self- and non-self N-glycans and glycoprotein antigens from different life-stages of Schistosoma mansoni. Using the IAVI Protocol C HIV infection cohort, we examine the relationship between S. mansoni seropositivity and development of bnAbs targeting glycan-dependent epitopes. We show that the unmutated common ancestor of the N332/V3-specific bnAb lineage PCDN76, isolated from an HIV-infected donor with S. mansoni seropositivity, binds to S. mansoni cercariae while lacking reactivity to gp120. Overall, these results present a strategy for elicitation of glycan-reactive bnAbs which could be exploited in HIV-1 vaccine development.
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Affiliation(s)
- Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Stefanie A Krumm
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sonia Serna
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Katarzyna Brzezicka
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Angela van Diepen
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Fiona Allan
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, UK
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Simon Kimuda
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Aidan M Emery
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, UK
| | - Elise Landais
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Cornelis H Hokke
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK; Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Niels Reichardt
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain; CIBER-BBN, Paseo Miramón 182, 20009 San Sebastian, Spain
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK.
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30
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Lorin V, Fernández I, Masse-Ranson G, Bouvin-Pley M, Molinos-Albert LM, Planchais C, Hieu T, Péhau-Arnaudet G, Hrebík D, Girelli-Zubani G, Fiquet O, Guivel-Benhassine F, Sanders RW, Walker BD, Schwartz O, Scheid JF, Dimitrov JD, Plevka P, Braibant M, Seaman MS, Bontems F, Di Santo JP, Rey FA, Mouquet H. Epitope convergence of broadly HIV-1 neutralizing IgA and IgG antibody lineages in a viremic controller. J Exp Med 2022; 219:213042. [PMID: 35230385 PMCID: PMC8932546 DOI: 10.1084/jem.20212045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a viremic controller, two of which comprised only IgG+ or IgA+ blood memory B cells; the third combined both IgG and IgA clonal variants. 7-269 bNAb in the IgA-only lineage displayed the highest neutralizing capacity despite limited somatic mutation, and delayed viral rebound in humanized mice. bNAbs in all three lineages targeted the N332 glycan supersite. The 2.8-Å resolution cryo-EM structure of 7-269-BG505 SOSIP.664 complex showed a similar pose as 2G12, on an epitope mainly composed of sugar residues comprising the N332 and N295 glycans. Binding and cryo-EM structural analyses showed that antibodies from the two other lineages interact mostly with glycans N332 and N386. Hence, multiple B cell lineages of IgG and IgA bNAbs focused on a unique HIV-1 site of vulnerability can codevelop in HIV-1 viremic controllers.
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Affiliation(s)
- Valérie Lorin
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Ignacio Fernández
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre national de la recherche scientifique URA3015, Paris, France
| | - Guillemette Masse-Ranson
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Mélanie Bouvin-Pley
- Université de Tours, Institut national de la santé et de la recherche médicale U1259, Tours, France
| | - Luis M Molinos-Albert
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Thierry Hieu
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Gérard Péhau-Arnaudet
- Imagopole, Plate-Forme de Microscopie Ultrastructurale and UMR 3528, Institut Pasteur, Paris, France
| | - Dominik Hrebík
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Giulia Girelli-Zubani
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Oriane Fiquet
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Florence Guivel-Benhassine
- Centre national de la recherche scientifique URA3015, Paris, France.,Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA.,Partners AIDS Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Olivier Schwartz
- Centre national de la recherche scientifique URA3015, Paris, France.,Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Johannes F Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, Institut national de la santé et de la recherche médicale, Sorbonne Université, Université de Paris, Paris, France
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martine Braibant
- Université de Tours, Institut national de la santé et de la recherche médicale U1259, Tours, France
| | | | - François Bontems
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Institut de Chimie des Substances Naturelles, Centre national de la recherche scientifique, Université Paris Saclay, Gif-sur-Yvette, France
| | - James P Di Santo
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Félix A Rey
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre national de la recherche scientifique URA3015, Paris, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
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31
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Traxinger BR, Richert-Spuhler LE, Lund JM. Mucosal tissue regulatory T cells are integral in balancing immunity and tolerance at portals of antigen entry. Mucosal Immunol 2022; 15:398-407. [PMID: 34845322 PMCID: PMC8628059 DOI: 10.1038/s41385-021-00471-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/19/2021] [Accepted: 11/03/2021] [Indexed: 02/04/2023]
Abstract
Foxp3+ regulatory T cells (Tregs) are a subset of CD4+ T cells that exert suppressive control over other immune cells. Tregs are critical for preventing systemic autoimmunity and maintaining peripheral tolerance, and yet they also assist in orchestration of immunity to pathogenic insult, wherein they limit collateral immunopathology and assist in facilitating a fine balance between immune tolerance and effector activity. Tregs have been extensively studied in lymphoid tissues, and a growing body of work has characterized phenotypically distinct Tregs localized in various nonlymphoid tissue compartments. These tissue Tregs can perform location-specific, alternative functions, highlighting their dynamic, context-dependent roles. Tregs have also been identified in mucosal tissues where specialized physiological functions are paramount, including helping the host to respond appropriately to pathogenic versus innocuous antigens that are abundant at mucosal portals of antigen entry. As in other tissue Treg compartments, mucosal Tregs in the respiratory, gastrointestinal, and genitourinary tracts are distinct from circulating counterparts and can carry out mucosa-specific functions as well as classic suppressive functions that are the hallmark of Tregs. In this review, we summarize current knowledge regarding mucosal Tregs in both health and disease.
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Affiliation(s)
- Brianna R Traxinger
- Department of Global Health, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laura E Richert-Spuhler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jennifer M Lund
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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32
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Moysi E, Paris RM, Le Grand R, Koup RA, Petrovas C. Human lymph node immune dynamics as driver of vaccine efficacy: an understudied aspect of immune responses. Expert Rev Vaccines 2022; 21:633-644. [PMID: 35193447 DOI: 10.1080/14760584.2022.2045198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION During the last century, changes in hygiene, sanitation, and the advent of childhood vaccination have resulted in profound reductions in mortality from infectious diseases. Despite this success, infectious diseases remain an enigmatic public health threat, where effective vaccines for influenza, human immunodeficiency virus (HIV), tuberculosis, and malaria, among others remain elusive. AREA COVERED In addition to the immune evasion tactics employed by complex pathogens, our understanding of immunopathogenesis and the development of effective vaccines is also complexified by the inherent variability of human immune responses. Lymph nodes (LNs) are the anatomical sites where B cell responses develop. An important, but understudied component of immune response complexity is variation in LN immune dynamics and in particular variation in germinal center follicular helper T cells (Tfh) and B cells which can be impacted by genetic variation, aging, the microbiome and chronic infection. EXPERT OPINION This review describes the contribution of genetic variation, aging, microbiome and chronic infection on LN immune dynamics and associated Tfh responses and offers perspective on how inclusion of LN immune subset and cytoarchitecture analyses, along with peripheral blood biomarkers can supplement systems vaccinology or immunology approaches for the development of vaccines or other interventions to prevent infectious diseases.
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Affiliation(s)
- Eirini Moysi
- Tissue Analysis Core, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | | | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Constantinos Petrovas
- Tissue Analysis Core, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.,Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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33
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Lakhashe SK, Amacker M, Hariraju D, Vyas HK, Morrison KS, Weiner JA, Ackerman ME, Roy V, Alter G, Ferrari G, Montefiori DC, Tomaras GD, Sawant S, Yates NL, Gast C, Fleury S, Ruprecht RM. Cooperation Between Systemic and Mucosal Antibodies Induced by Virosomal Vaccines Targeting HIV-1 Env: Protection of Indian Rhesus Macaques Against Low-Dose Intravaginal SHIV Challenges. Front Immunol 2022; 13:788619. [PMID: 35273592 PMCID: PMC8902080 DOI: 10.3389/fimmu.2022.788619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
A virosomal vaccine inducing systemic/mucosal anti-HIV-1 gp41 IgG/IgA had previously protected Chinese-origin rhesus macaques (RMs) against vaginal SHIVSF162P3 challenges. Here, we assessed its efficacy in Indian-origin RMs by intramuscular priming/intranasal boosting (n=12/group). Group K received virosome-P1-peptide alone (harboring the Membrane Proximal External Region), Group L combined virosome-rgp41 plus virosome-P1, and Group M placebo virosomes. Vaccination induced plasma binding but no neutralizing antibodies. Five weeks after boosting, all RMs were challenged intravaginally with low-dose SHIVSF162P3 until persistent systemic infection developed. After SHIV challenge #7, six controls were persistently infected versus only one Group L animal (vaccine efficacy 87%; P=0.0319); Group K was not protected. After a 50% SHIV dose increase starting with challenge #8, protection in Group L was lost. Plasmas/sera were analyzed for IgG phenotypes and effector functions; the former revealed that protection in Group L was significantly associated with increased binding to FcγR2/3(A/B) across several time-points, as were some IgG measurements. Vaginal washes contained low-level anti-gp41 IgGs and IgAs, representing a 1-to-5-fold excess over the SHIV inoculum's gp41 content, possibly explaining loss of protection after the increase in challenge-virus dose. Virosomal gp41-vaccine efficacy was confirmed during the initial seven SHIV challenges in Indian-origin RMs when the SHIV inoculum had at least 100-fold more HIV RNA than acutely infected men's semen. Vaccine protection by virosome-induced IgG and IgA parallels the cooperation between systemically administered IgG1 and mucosally applied dimeric IgA2 monoclonal antibodies that as single-agents provided no/low protection - but when combined, prevented mucosal SHIV transmission in all passively immunized RMs.
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Affiliation(s)
| | - Mario Amacker
- Department of Pulmonary Medicine, Bern University Hospital, University of Bern, Bern, Switzerland,Mymetics SA, Epalinges, Switzerland
| | - Dinesh Hariraju
- Texas Biomedical Research Institute, San Antonio, TX, United States,New Iberia Research Center, University of Louisiana at Lafayette, Lafayette, LA, United States,Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Hemant K. Vyas
- Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Kyle S. Morrison
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Joshua A. Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States,Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
| | - Vicky Roy
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States,Massachusetts Consortium on Pathogen Readiness, Boston, MA, United States
| | - Guido Ferrari
- Department of Surgery, Duke University, Durham, NC, United States,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - David C. Montefiori
- Department of Surgery, Duke University, Durham, NC, United States,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Georgia D. Tomaras
- Department of Surgery, Duke University, Durham, NC, United States,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States,Department of Immunology, Duke University, Durham, NC, United States
| | - Sheetal Sawant
- Department of Surgery, Duke University, Durham, NC, United States
| | - Nicole L. Yates
- Department of Surgery, Duke University, Durham, NC, United States
| | | | | | - Ruth M. Ruprecht
- Texas Biomedical Research Institute, San Antonio, TX, United States,New Iberia Research Center, University of Louisiana at Lafayette, Lafayette, LA, United States,Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States,*Correspondence: Ruth M. Ruprecht,
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34
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Monocyte Gene and Molecular Expression Profiles Suggest Distinct Effector and Regulatory Functions in Beninese HIV Highly Exposed Seronegative Female Commercial Sex Workers. Viruses 2022; 14:v14020361. [PMID: 35215954 PMCID: PMC8878004 DOI: 10.3390/v14020361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 11/22/2022] Open
Abstract
We have previously reported that the female genital tract (FGT) of Beninese HIV highly-exposed seronegative (HESN) commercial sex workers (CSWs), presented elevated frequencies of a myeloid HLA-DR+CD14+CD11c+ population presenting “tolerogenic” monocyte derived dendritic cells (MoDC) features. In order to assess whether a differential profile of monocytes may be involved in the generation of these genital MoDCs, we have herein characterized the blood monocyte compartment of Beninese HESNs (HIV-uninfected ≥ 10 years CSWs) and relevant controls (HIV-uninfected 2.5–5 years CSWs herein termed “early HESNs”), HIV-infected CSWs, and low-risk HIV-uninfected women from the general population. Transcriptomic analyses by RNA-Seq of total sorted blood monocytes demonstrate that in comparison to the control groups, HESNs present increased expression levels of FCGR2C, FCAR, ITGAX, ITGAM, CR2, CD68, and CD163 genes, associated with effector functions. Moreover, we found increased expression levels of genes associated with protection/control against SHIV/HIV such as CCL3, CCL4, CCL5, BHLHE40, and TNFSF13, as well as with immune regulation such as IL-10, Ahr, CD83, and the orphan nuclear receptor (NR)4A1, NR4A2, and NR4A3. Through multicolor flow cytometry analyses, we noticed that the frequencies of intermediate and non-classical monocyte populations tended to be elevated in the blood of HESNs, and exhibited increased expression levels of effector CD16, CD11c, CD11b, as well as regulatory HLA-G, IL-10, and IFN-α markers when compared to HIV-uninfected women and/or HIV-infected CSWs. This profile is compatible with that previously reported in the FGT of HESNs, and likely confers an enormous advantage in their resistance to HIV infection.
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35
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Lynn DJ, Benson SC, Lynn MA, Pulendran B. Modulation of immune responses to vaccination by the microbiota: implications and potential mechanisms. Nat Rev Immunol 2022; 22:33-46. [PMID: 34002068 PMCID: PMC8127454 DOI: 10.1038/s41577-021-00554-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 02/05/2023]
Abstract
The need for highly effective vaccines that induce robust and long-lasting immunity has never been more apparent. However, for reasons that are still poorly understood, immune responses to vaccination are highly variable between different individuals and different populations. Furthermore, vaccine immunogenicity is frequently suboptimal in the very populations who are at most risk from infectious disease, including infants, the elderly, and those living in low-income and middle-income countries. Although many factors have the potential to influence vaccine immunogenicity and therefore vaccine effectiveness, increasing evidence from clinical studies and animal models now suggests that the composition and function of the gut microbiota are crucial factors modulating immune responses to vaccination. In this Review, we synthesize this evidence, discuss the immunological mechanisms that potentially mediate these effects and consider the potential of microbiota-targeted interventions to optimize vaccine effectiveness.
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Affiliation(s)
- David J Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia.
| | - Saoirse C Benson
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Miriam A Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Bali Pulendran
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
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36
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Williams WB, Wiehe K, Saunders KO, Haynes BF. Strategies for induction of HIV-1 envelope-reactive broadly neutralizing antibodies. J Int AIDS Soc 2021; 24 Suppl 7:e25831. [PMID: 34806332 PMCID: PMC8606870 DOI: 10.1002/jia2.25831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/23/2021] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION A primary focus of HIV-1 vaccine development is the activation of B cell receptors for naïve or precursor broadly neutralizing antibodies (bnAbs), followed by expansion and maturation of bnAb B cell lineage intermediates leading to highly affinity-matured bnAbs. HIV-1 envelope (Env) encodes epitopes for bnAbs of different specificities. Design of immunogens to induce bnAb precursors of different specificities and mature them into bnAb status is a goal for HIV-1 vaccine development. We review vaccine strategies for bnAb lineages development and highlight the immunological barriers that these strategies must overcome to generate bnAbs. METHODS We provide perspectives based on published research articles and reviews. DISCUSSION The recent Antibody Mediated Protection (AMP) trial that tested the protective efficacy of one HIV-1 Env bnAb specificity demonstrated that relatively high levels of long-lasting serum titers of multiple specificities of bnAbs will be required for protection from HIV-1 transmission. Current vaccine efforts for induction of bnAb lineages are focused on immunogens designed to expand naïve HIV-1 bnAb precursor B cells following the recent success of vaccine-induction of bnAb precursor B cells in macaques and humans. BnAb precursor B cells serve as templates for priming-immunogen design. However, design of boosting immunogens for bnAb maturation requires knowledge of the optimal immunogen design and immunological environment for bnAb B cell lineage affinity maturation. BnAb lineages acquire rare genetic changes as mutations during B cell maturation. Moreover, the immunological environment that supports bnAb development during HIV-1 infection is perturbed with an altered B cell repertoire and dysfunctional immunoregulatory controls, suggesting that in normal settings, bnAb development will be disfavoured. Thus, strategies for vaccine induction of bnAbs must circumvent immunological barriers for bnAb development that normally constrain bnAb B cell affinity maturation. CONCLUSIONS A fully protective HIV-1 vaccine needs to induce durable high titers of bnAbs that can be generated by a sequential set of Env immunogens for expansion and maturation of bnAb B cell lineages in a permitted immunological environment. Moreover, multiple specificities of bnAbs will be required to be sufficiently broad to prevent the escape of HIV-1 strains during transmission.
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Affiliation(s)
- Wilton B. Williams
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin Wiehe
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin O. Saunders
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Barton F. Haynes
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
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37
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Liu Y, Budylowski P, Dong S, Li Z, Goroshko S, Leung LYT, Grunebaum E, Campisi P, Propst EJ, Wolter NE, Rini JM, Zia A, Ostrowski M, Ehrhardt GRA. SARS-CoV-2-Reactive Mucosal B Cells in the Upper Respiratory Tract of Uninfected Individuals. THE JOURNAL OF IMMUNOLOGY 2021; 207:2581-2588. [PMID: 34607939 DOI: 10.4049/jimmunol.2100606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/02/2021] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 is a respiratory pathogen that can cause severe disease in at-risk populations but results in asymptomatic infections or a mild course of disease in the majority of cases. We report the identification of SARS-CoV-2-reactive B cells in human tonsillar tissue obtained from children who were negative for coronavirus disease 2019 prior to the pandemic and the generation of mAbs recognizing the SARS-CoV-2 Spike protein from these B cells. These Abs showed reduced binding to Spike proteins of SARS-CoV-2 variants and did not recognize Spike proteins of endemic coronaviruses, but subsets reacted with commensal microbiota and exhibited SARS-CoV-2-neutralizing potential. Our study demonstrates pre-existing SARS-CoV-2-reactive Abs in various B cell populations in the upper respiratory tract lymphoid tissue that may lead to the rapid engagement of the pathogen and contribute to prevent manifestations of symptomatic or severe disease.
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Affiliation(s)
- Yanling Liu
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | | | - Shilan Dong
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sofiya Goroshko
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Leslie Y T Leung
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Eyal Grunebaum
- Division of Immunology and Allergy, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Paolo Campisi
- Department of Otolaryngology-Head & Neck Surgery, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Evan J Propst
- Department of Otolaryngology-Head & Neck Surgery, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Nikolas E Wolter
- Department of Otolaryngology-Head & Neck Surgery, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - James M Rini
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; and
| | - Amin Zia
- dYcode.bio, Toronto, Ontario, Canada
| | - Mario Ostrowski
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Götz R A Ehrhardt
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada;
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38
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Abstract
Purpose of Review Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models. Recent Findings Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Summary Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA.
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39
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Dong J, Zost SJ, Greaney AJ, Starr TN, Dingens AS, Chen EC, Chen RE, Case JB, Sutton RE, Gilchuk P, Rodriguez J, Armstrong E, Gainza C, Nargi RS, Binshtein E, Xie X, Zhang X, Shi PY, Logue J, Weston S, McGrath ME, Frieman MB, Brady T, Tuffy KM, Bright H, Loo YM, McTamney PM, Esser MT, Carnahan RH, Diamond MS, Bloom JD, Crowe JE. Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat Microbiol 2021; 6:1233-1244. [PMID: 34548634 PMCID: PMC8543371 DOI: 10.1038/s41564-021-00972-2] [Citation(s) in RCA: 187] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
Understanding the molecular basis for immune recognition of SARS-CoV-2 spike glycoprotein antigenic sites will inform the development of improved therapeutics. We determined the structures of two human monoclonal antibodies-AZD8895 and AZD1061-which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor-binding domain (RBD) of SARS-CoV-2 to define the genetic and structural basis of neutralization. AZD8895 forms an 'aromatic cage' at the heavy/light chain interface using germ line-encoded residues in complementarity-determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals. AZD1061 has an unusually long LCDR1; the HCDR3 makes interactions with the opposite face of the RBD from that of AZD8895. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the crucial binding residues of both antibodies and identified positions of concern with regards to virus escape from antibody-mediated neutralization. Both AZD8895 and AZD1061 have strong neutralizing activity against SARS-CoV-2 and variants of concern with antigenic substitutions in the RBD. We conclude that germ line-encoded antibody features enable recognition of the SARS-CoV-2 spike RBD and demonstrate the utility of the cocktail AZD7442 in neutralizing emerging variant viruses.
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MESH Headings
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antigenic Variation
- Binding Sites
- COVID-19/immunology
- COVID-19/virology
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/genetics
- Humans
- Mutation
- Protein Domains
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Jinhui Dong
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Adam S Dingens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine C Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica Rodriguez
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Erica Armstrong
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher Gainza
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rachel S Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xuping Xie
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - James Logue
- Department of Microbiology and Immunology, The University of Maryland, College Park, MD, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, The University of Maryland, College Park, MD, USA
| | - Marisa E McGrath
- Department of Microbiology and Immunology, The University of Maryland, College Park, MD, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, The University of Maryland, College Park, MD, USA
| | - Tyler Brady
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | - Kevin M Tuffy
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | - Helen Bright
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | - Yueh-Ming Loo
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | | | - Mark T Esser
- Microbial Sciences, AstraZeneca, Gaithersburg, MD, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
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40
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Tan CY, Ramirez ZE, Surana NK. A Modern-World View of Host-Microbiota-Pathogen Interactions. THE JOURNAL OF IMMUNOLOGY 2021; 207:1710-1718. [PMID: 34544813 DOI: 10.4049/jimmunol.2100215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/14/2021] [Indexed: 12/14/2022]
Abstract
The microbiota-the diverse set of commensal microbes that normally colonize humans-represents the first line of defense against infectious diseases. In this review, we summarize the direct and indirect mechanisms by which the microbiota modulates susceptibility to, and severity of, infections, with a focus on immunological mechanisms. Moreover, we highlight some of the ways that modern-world lifestyles have influenced the structure-function relationship between the microbiota and infectious diseases. Ultimately, understanding how the microbiota influences infectious risks will facilitate development of microbiota-derived therapeutics that bolster host defenses.
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Affiliation(s)
- Chin Yee Tan
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, NC.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC; and
| | - Zeni E Ramirez
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, NC.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC; and
| | - Neeraj K Surana
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, NC; .,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC; and.,Department of Immunology, Duke University School of Medicine, Durham, NC
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41
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Sobia P, Archary D. Preventive HIV Vaccines-Leveraging on Lessons from the Past to Pave the Way Forward. Vaccines (Basel) 2021; 9:vaccines9091001. [PMID: 34579238 PMCID: PMC8472969 DOI: 10.3390/vaccines9091001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Almost four decades on, since the 1980’s, with hundreds of HIV vaccine candidates tested in both non-human primates and humans, and several HIV vaccines trials later, an efficacious HIV vaccine continues to evade us. The enormous worldwide genetic diversity of HIV, combined with HIV’s inherent recombination and high mutation rates, has hampered the development of an effective vaccine. Despite the advent of antiretrovirals as pre-exposure prophylaxis and preventative treatment, which have shown to be effective, HIV infections continue to proliferate, highlighting the great need for a vaccine. Here, we provide a brief history for the HIV vaccine field, with the most recent disappointments and advancements. We also provide an update on current passive immunity trials, testing proof of the concept of the most clinically advanced broadly neutralizing monoclonal antibodies for HIV prevention. Finally, we include mucosal immunity, the importance of vaccine-elicited immune responses and the challenges thereof in the most vulnerable environment–the female genital tract and the rectal surfaces of the gastrointestinal tract for heterosexual and men who have sex with men transmissions, respectively.
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Affiliation(s)
- Parveen Sobia
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4001, South Africa
- Correspondence: ; Tel.: +27-(0)-31-655-0540
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42
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Pan C, Yue H, Zhu L, Ma GH, Wang HL. Prophylactic vaccine delivery systems against epidemic infectious diseases. Adv Drug Deliv Rev 2021; 176:113867. [PMID: 34280513 PMCID: PMC8285224 DOI: 10.1016/j.addr.2021.113867] [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: 03/30/2021] [Revised: 05/20/2021] [Accepted: 07/11/2021] [Indexed: 01/04/2023]
Abstract
Prophylactic vaccines have evolved from traditional whole-cell vaccines to safer subunit vaccines. However, subunit vaccines still face problems, such as poor immunogenicity and low efficiency, while traditional adjuvants are usually unable to meet specific response needs. Advanced delivery vectors are important to overcome these barriers; they have favorable safety and effectiveness, tunable properties, precise location, and immunomodulatory capabilities. Nevertheless, there has been no systematic summary of the delivery systems to cover a wide range of infectious pathogens. We herein summarized and compared the delivery systems for major or epidemic infectious diseases caused by bacteria, viruses, fungi, and parasites. We also included the newly licensed vaccines (e.g., COVID-19 vaccines) and those close to licensure. Furthermore, we highlighted advanced delivery systems with high efficiency, cross-protection, or long-term protection against epidemic pathogens, and we put forward prospects and thoughts on the development of future prophylactic vaccines.
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Affiliation(s)
- Chao Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, PR China
| | - Hua Yue
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, PR China
| | - Guang-Hui Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Heng-Liang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, PR China.
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43
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Chen EC, Gilchuk P, Zost SJ, Suryadevara N, Winkler ES, Cabel CR, Binshtein E, Chen RE, Sutton RE, Rodriguez J, Day S, Myers L, Trivette A, Williams JK, Davidson E, Li S, Doranz BJ, Campos SK, Carnahan RH, Thorne CA, Diamond MS, Crowe JE. Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals. Cell Rep 2021; 36:109604. [PMID: 34411541 PMCID: PMC8352653 DOI: 10.1016/j.celrep.2021.109604] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/13/2021] [Accepted: 08/04/2021] [Indexed: 01/02/2023] Open
Abstract
Unrelated individuals can produce genetically similar clones of antibodies, known as public clonotypes, which have been seen in responses to different infectious diseases, as well as healthy individuals. Here we identify 37 public clonotypes in memory B cells from convalescent survivors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or in plasmablasts from an individual after vaccination with mRNA-encoded spike protein. We identify 29 public clonotypes, including clones recognizing the receptor-binding domain (RBD) in the spike protein S1 subunit (including a neutralizing, angiotensin-converting enzyme 2 [ACE2]-blocking clone that protects in vivo) and others recognizing non-RBD epitopes that bind the S2 domain. Germline-revertant forms of some public clonotypes bind efficiently to spike protein, suggesting these common germline-encoded antibodies are preconfigured for avid recognition. Identification of large numbers of public clonotypes provides insight into the molecular basis of efficacy of SARS-CoV-2 vaccines and sheds light on the immune pressures driving the selection of common viral escape mutants.
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Affiliation(s)
- Elaine C Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Emma S Winkler
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Carly R Cabel
- Department of Cellular & Molecular Medicine, University of Arizona College of Medicine, Tucson, AZ 85724, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85724, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Rachel E Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jessica Rodriguez
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Samuel Day
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Luke Myers
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew Trivette
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | | | - Shuaizhi Li
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | | | - Samuel K Campos
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85724, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Curtis A Thorne
- Department of Cellular & Molecular Medicine, University of Arizona College of Medicine, Tucson, AZ 85724, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85724, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - James E Crowe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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44
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Shipley MM, Mangala Prasad V, Doepker LE, Dingens A, Ralph DK, Harkins E, Dhar A, Arenz D, Chohan V, Weight H, Mandaliya K, Bloom JD, Matsen FA, Lee KK, Overbaugh JM. Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection. eLife 2021; 10:68110. [PMID: 34263727 PMCID: PMC8376252 DOI: 10.7554/elife.68110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. BnAb QA013.2 bound initial and superinfecting viral Env, despite its probable naive progenitor only recognizing the superinfecting strain, suggesting both viruses influenced this lineage. A 4.15 Å cryo-EM structure of QA013.2 bound to native-like trimer showed recognition of V3 signatures (N301/N332 and GDIR). QA013.2 relies less on CDRH3 and more on framework and CDRH1 for affinity and breadth compared to other V3/glycan-specific bnAbs. Antigenic profiling revealed that viral escape was achieved by changes in the structurally-defined epitope and by mutations in V1. These results highlight shared and novel properties of QA013.2 relative to other V3/glycan-specific bnAbs in the setting of sequential, diverse antigens.
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Affiliation(s)
- Mackenzie M Shipley
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Vidya Mangala Prasad
- Department of Medicinal Chemistry, University of Washington, Seattle, United States
| | - Laura E Doepker
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Adam Dingens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Duncan K Ralph
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Elias Harkins
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Amrit Dhar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Dana Arenz
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Vrasha Chohan
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Haidyn Weight
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kishor Mandaliya
- Coast Provincial General Hospital, Women's Health Project, Mombasa, Kenya
| | - Jesse D Bloom
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, United States
| | - Julie M Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
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45
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Williams WB, Meyerhoff RR, Edwards RJ, Li H, Manne K, Nicely NI, Henderson R, Zhou Y, Janowska K, Mansouri K, Gobeil S, Evangelous T, Hora B, Berry M, Abuahmad AY, Sprenz J, Deyton M, Stalls V, Kopp M, Hsu AL, Borgnia MJ, Stewart-Jones GBE, Lee MS, Bronkema N, Moody MA, Wiehe K, Bradley T, Alam SM, Parks RJ, Foulger A, Oguin T, Sempowski GD, Bonsignori M, LaBranche CC, Montefiori DC, Seaman M, Santra S, Perfect J, Francica JR, Lynn GM, Aussedat B, Walkowicz WE, Laga R, Kelsoe G, Saunders KO, Fera D, Kwong PD, Seder RA, Bartesaghi A, Shaw GM, Acharya P, Haynes BF. Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell 2021; 184:2955-2972.e25. [PMID: 34019795 PMCID: PMC8135257 DOI: 10.1016/j.cell.2021.04.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/22/2021] [Accepted: 04/23/2021] [Indexed: 01/03/2023]
Abstract
Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA.
| | - R Ryan Meyerhoff
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - R J Edwards
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | | | | | | | | | - Bhavna Hora
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | | | | | | | | | - Megan Kopp
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | | | - Matthew S Lee
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Naomi Bronkema
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | | | - Thomas Oguin
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Michael Seaman
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - John Perfect
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - Geoffrey M Lynn
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Avidea Technologies, Inc., Baltimore, MD, USA
| | | | | | - Richard Laga
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27705, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA.
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46
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Lamptey H, Bonney EY, Adu B, Kyei GB. Are Fc Gamma Receptor Polymorphisms Important in HIV-1 Infection Outcomes and Latent Reservoir Size? Front Immunol 2021; 12:656894. [PMID: 34017334 PMCID: PMC8129575 DOI: 10.3389/fimmu.2021.656894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Fc gamma receptors (FcγR) are cell surface glycoproteins which trigger specific effector-cell responses when cross-linked with the Fc portions of immunoglobulin (IgG) antibodies. During HIV-1 infection, the course of disease progression, ART response, and viral reservoir size vary in different individuals. Several factors may account for these differences; however, Fc gamma receptor gene polymorphisms, which influence receptor binding to IgG antibodies, are likely to play a key role. FcγRIIa (CD32) was recently reported as a potential marker for latent HIV reservoir, however, this assertion is still inconclusive. Whether FcγR polymorphisms influence the size of the viral reservoir, remains an important question in HIV cure studies. In addition, potential cure or viral suppression methods such as broadly neutralizing antibody (bNAbs) may depend on FcγRs to control the virus. Here, we discuss the current evidence on the potential role played by FcγR polymorphisms in HIV-1 infection, treatment and vaccine trial outcomes. Importantly, we highlight contrasting findings that may be due to multiple factors and the relatively limited data from African populations. We recommend further studies especially in sub-Saharan Africa to confirm the role of FcγRIIa in the establishment of latent reservoir and to determine their influence in therapies involving bNAbs.
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Affiliation(s)
- Helena Lamptey
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Evelyn Y. Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Bright Adu
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - George B. Kyei
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Medicine, Washington University School of Medicine in St Louis, St. Louis, MO, United States
- Medical and Scientific Research Centre, University of Ghana Medical Centre, University of Ghana, Accra, Ghana
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47
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Chen EC, Gilchuk P, Zost SJ, Suryadevara N, Winkler ES, Cabel CR, Binshtein E, Sutton RE, Rodriguez J, Day S, Myers L, Trivette A, Williams JK, Davidson E, Li S, Doranz BJ, Campos SK, Carnahan RH, Thorne CA, Diamond MS, Crowe JE. Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33972937 DOI: 10.1101/2021.05.02.442326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Unrelated individuals can produce genetically similar clones of antibodies, known as public clonotypes, which have been seen in responses to different infectious diseases as well as healthy individuals. Here we identify 37 public clonotypes in memory B cells from convalescent survivors of SARS-CoV-2 infection or in plasmablasts from an individual after vaccination with mRNA-encoded spike protein. We identified 29 public clonotypes, including clones recognizing the receptor-binding domain (RBD) in the spike protein S1 subunit (including a neutralizing, ACE2-blocking clone that protects in vivo ), and others recognizing non-RBD epitopes that bound the heptad repeat 1 region of the S2 domain. Germline-revertant forms of some public clonotypes bound efficiently to spike protein, suggesting these common germline-encoded antibodies are preconfigured for avid recognition. Identification of large numbers of public clonotypes provides insight into the molecular basis of efficacy of SARS-CoV-2 vaccines and sheds light on the immune pressures driving the selection of common viral escape mutants.
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48
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To Include or Occlude: Rational Engineering of HCV Vaccines for Humoral Immunity. Viruses 2021; 13:v13050805. [PMID: 33946211 PMCID: PMC8146105 DOI: 10.3390/v13050805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
Direct-acting antiviral agents have proven highly effective at treating existing hepatitis C infections but despite their availability most countries will not reach the World Health Organization targets for elimination of HCV by 2030. A prophylactic vaccine remains a high priority. Whilst early vaccines focused largely on generating T cell immunity, attention is now aimed at vaccines that generate humoral immunity, either alone or in combination with T cell-based vaccines. High-resolution structures of hepatitis C viral glycoproteins and their interaction with monoclonal antibodies isolated from both cleared and chronically infected people, together with advances in vaccine technologies, provide new avenues for vaccine development.
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49
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Seaton KE, Deal A, Han X, Li SS, Clayton A, Heptinstall J, Duerr A, Allen MA, Shen X, Sawant S, Yates NL, Spearman P, Churchyard G, Goepfert PA, Maenza J, Gray G, Pantaleo G, Polakowski L, Robinson HL, Grant S, Randhawa AK, Huang Y, Morgan C, Grunenberg N, Karuna S, Gilbert PB, McElrath MJ, Huang Y, Tomaras GD. Meta-analysis of HIV-1 vaccine elicited mucosal antibodies in humans. NPJ Vaccines 2021; 6:56. [PMID: 33859204 PMCID: PMC8050318 DOI: 10.1038/s41541-021-00305-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
We studied mucosal immune responses in six HIV-1 vaccine trials investigating different envelope (Env)-containing immunogens. Regimens were classified into four categories: DNA/vector, DNA/vector plus protein, protein alone, and vector alone. We measured HIV-1-specific IgG and IgA in secretions from cervical (n = 111) and rectal swabs (n = 154), saliva (n = 141), and seminal plasma (n = 124) and compared to corresponding blood levels. Protein-containing regimens had up to 100% response rates and the highest Env-specific IgG response rates. DNA/vector groups elicited mucosal Env-specific IgG response rates of up to 67% that varied across specimen types. Little to no mucosal IgA responses were observed. Overall, gp41- and gp140-specific antibodies dominated gp120 mucosal responses. In one trial, prior vaccination with a protein-containing immunogen maintained durability of cervical and rectal IgG for up to 17 years. Mucosal IgG responses were boosted after revaccination. These findings highlight a role for protein immunization in eliciting HIV-1-specific mucosal antibodies and the ability of HIV-1 vaccines to elicit durable HIV-1-specific mucosal IgG.
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Affiliation(s)
- Kelly E Seaton
- Duke Human Vaccine Institute, Durham, NC, USA.
- Department of Surgery, Duke University, Durham, NC, USA.
- Department of Immunology, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
| | - Aaron Deal
- Duke Human Vaccine Institute, Durham, NC, USA
| | - Xue Han
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shuying S Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ashley Clayton
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jack Heptinstall
- Duke Human Vaccine Institute, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
| | - Ann Duerr
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Sheetal Sawant
- Duke Human Vaccine Institute, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
| | - Nicole L Yates
- Duke Human Vaccine Institute, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
| | - Paul Spearman
- Division of Infectious Diseases, Cincinnati Children's Hospital, Cincinnatti, OH, USA
| | - Gavin Churchyard
- Aurum Institute, Johannesburg, South Africa
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Janine Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Glenda Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- South African Medical Research Council, Cape Town, South Africa
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, and Swiss Vaccine Research Institute, Lausanne University Hospital, Lausanne, Switzerland
| | | | | | - Shannon Grant
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - April K Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Cecilia Morgan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nicole Grunenberg
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shelly Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Durham, NC, USA.
- Department of Surgery, Duke University, Durham, NC, USA.
- Department of Immunology, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
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Fries CN, Curvino EJ, Chen JL, Permar SR, Fouda GG, Collier JH. Advances in nanomaterial vaccine strategies to address infectious diseases impacting global health. NATURE NANOTECHNOLOGY 2021; 16:1-14. [PMID: 32807876 DOI: 10.1038/s41565-020-0739-9] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 06/23/2020] [Indexed: 05/18/2023]
Abstract
Despite the overwhelming success of vaccines in preventing infectious diseases, there remain numerous globally devastating diseases without fully protective vaccines, particularly human immunodeficiency virus (HIV), malaria and tuberculosis. Nanotechnology approaches are being developed both to design new vaccines against these diseases as well as to facilitate their global implementation. The reasons why a given pathogen may present difficulties for vaccine design are unique and tied to the co-evolutionary history of the pathogen and humans, but there are common challenges that nanotechnology is beginning to help address. In each case, a successful vaccine will need to raise immune responses that differ from the immune responses raised by normal infection. Nanomaterials, with their defined compositions, commonly modular construction, and length scales allowing the engagement of key immune pathways, collectively facilitate the iterative design process necessary to identify such protective immune responses and achieve them reliably. Nanomaterials also provide strategies for engineering the trafficking and delivery of vaccine components to key immune cells and lymphoid tissues, and they can be highly multivalent, improving their engagement with the immune system. This Review will discuss these aspects along with recent nanomaterial advances towards vaccines against infectious disease, with a particular emphasis on HIV/AIDS, malaria and tuberculosis.
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Affiliation(s)
- Chelsea N Fries
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Jui-Lin Chen
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sallie R Permar
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Genevieve G Fouda
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
| | - Joel H Collier
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA.
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