1
|
Listov D, Goverde CA, Correia BE, Fleishman SJ. Opportunities and challenges in design and optimization of protein function. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00718-y. [PMID: 38565617 DOI: 10.1038/s41580-024-00718-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calculations, as well as machine learning tools, have dramatically improved protein engineering and design. In this Review, we discuss how these methods have enabled the design of increasingly complex structures and therapeutically relevant activities. Additionally, protein optimization methods have improved the stability and activity of complex eukaryotic proteins. Thanks to their increased reliability, computational design methods have been applied to improve therapeutics and enzymes for green chemistry and have generated vaccine antigens, antivirals and drug-delivery nano-vehicles. Moreover, the high success of design methods reflects an increased understanding of basic rules that govern the relationships among protein sequence, structure and function. However, de novo design is still limited mostly to α-helix bundles, restricting its potential to generate sophisticated enzymes and diverse protein and small-molecule binders. Designing complex protein structures is a challenging but necessary next step if we are to realize our objective of generating new-to-nature activities.
Collapse
Affiliation(s)
- Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Sarel Jacob Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
2
|
Musunuri S, Weidenbacher PAB, Kim PS. Bringing immunofocusing into focus. NPJ Vaccines 2024; 9:11. [PMID: 38195562 PMCID: PMC10776678 DOI: 10.1038/s41541-023-00792-x] [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: 05/29/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Immunofocusing is a strategy to create immunogens that redirect humoral immune responses towards a targeted epitope and away from non-desirable epitopes. Immunofocusing methods often aim to develop "universal" vaccines that provide broad protection against highly variant viruses such as influenza virus, human immunodeficiency virus (HIV-1), and most recently, severe acute respiratory syndrome coronavirus (SARS-CoV-2). We use existing examples to illustrate five main immunofocusing strategies-cross-strain boosting, mosaic display, protein dissection, epitope scaffolding, and epitope masking. We also discuss obstacles for immunofocusing like immune imprinting. A thorough understanding, advancement, and application of the methods we outline here will enable the design of high-resolution vaccines that protect against future viral outbreaks.
Collapse
Affiliation(s)
- Sriharshita Musunuri
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Payton A B Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| |
Collapse
|
3
|
Gao X, Wang X, Li S, Saif Ur Rahman M, Xu S, Liu Y. Nanovaccines for Advancing Long-Lasting Immunity against Infectious Diseases. ACS NANO 2023; 17:24514-24538. [PMID: 38055649 DOI: 10.1021/acsnano.3c07741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Infectious diseases, particularly life-threatening pathogens such as small pox and influenza, have substantial implications on public health and global economies. Vaccination is a key approach to combat existing and emerging pathogens. Immunological memory is an essential characteristic used to evaluate vaccine efficacy and durability and the basis for the long-term effects of vaccines in protecting against future infections; however, optimizing the potency, improving the quality, and enhancing the durability of immune responses remains challenging and a focus for research involving investigation of nanovaccine technologies. In this review, we describe how nanovaccines can address the challenges for conventional vaccines in stimulating adaptive immune memory responses to protect against reinfection. We discuss protein and nonprotein nanoparticles as useful antigen platforms, including those with highly ordered and repetitive antigen array presentation to enhance immunogenicity through cross-linking with multiple B cell receptors, and with a focus on antigen properties. In addition, we describe how nanoadjuvants can improve immune responses by providing enhanced access to lymph nodes, lymphnode targeting, germinal center retention, and long-lasting immune response generation. Nanotechnology has the advantage to facilitate vaccine induction of long-lasting immunity against infectious diseases, now and in the future.
Collapse
Affiliation(s)
- Xinglong Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xinlian Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Shilin Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | | | - Shanshan Xu
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, P.R. China
| | - Ying Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, P.R. China
| |
Collapse
|
4
|
Castro KM, Scheck A, Xiao S, Correia BE. Computational design of vaccine immunogens. Curr Opin Biotechnol 2022; 78:102821. [PMID: 36279815 DOI: 10.1016/j.copbio.2022.102821] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Computational protein engineering has enabled the rational design of customized proteins, which has propelled both sequence-based and structure-based immunogen engineering and delivery. By discerning antigenic determinants of viral pathogens, computational methods have been implemented to successfully engineer representative viral strains able to elicit broadly neutralizing responses or present antigenic sites of viruses for focused immune responses. Combined with improvements in customizable nanoparticle design, immunogens are multivalently displayed to enhance immune responses. These rationally designed immunogens offer unique and powerful approaches to engineer vaccines for pathogens, which have eluded traditional approaches.
Collapse
Affiliation(s)
- Karla M Castro
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Andreas Scheck
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Shuhao Xiao
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| |
Collapse
|
5
|
Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep 2022; 41:111628. [PMID: 36351401 PMCID: PMC9883670 DOI: 10.1016/j.celrep.2022.111628] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
Collapse
Affiliation(s)
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Rachel Hecht
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Anne A Roffler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elisa Marchiori
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Thomas H Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
6
|
Huang J, Miller RJ, Mousa JJ. A Pan-Pneumovirus vaccine based on immunodominant epitopes of the fusion protein. Front Immunol 2022; 13:941865. [PMID: 36003370 PMCID: PMC9393700 DOI: 10.3389/fimmu.2022.941865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are two leading causes of severe respiratory infections in children, the elderly, and immunocompromised patients. The fusion (F) protein is the major target of neutralizing antibodies. Recent developments in stabilizing the pre-fusion conformation of the F proteins, and identifying immunodominant epitopes that elicit potent neutralizing antibodies have led to the testing of numerous pre-fusion RSV F-based vaccines in clinical trials. We designed and tested the immunogenicity and protective efficacy of a chimeric fusion protein that contains immunodominant epitopes of RSV F and hMPV F (RHMS-1). RHMS-1 has several advantages over vaccination with pre-fusion RSV F or hMPV F, including a focus on recalling B cells to the most important protective epitopes and the ability to induce protection against two viruses with a single antigen. RHMS-1 was generated as a trimeric recombinant protein, and analysis by negative-stain electron microscopy demonstrated the protein resembles the pre-fusion conformation. Probing of RHMS-1 antigenicity using a panel of RSV and hMPV F-specific monoclonal antibodies (mAbs) revealed the protein retains features of both viruses, including the pre-fusion site Ø epitope of RSV F. Mice immunized with RHMS-1 generated neutralizing antibodies to both viruses and were completely protected from RSV or hMPV challenge. Overall, this study demonstrates protection against two viruses with a single antigen and supports testing of RHMS-1 in additional pre-clinical animal models.
Collapse
Affiliation(s)
- Jiachen Huang
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Rose J. Miller
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Jarrod J. Mousa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, United States
- *Correspondence: Jarrod J. Mousa,
| |
Collapse
|
7
|
Antibodies to combat viral infections: development strategies and progress. Nat Rev Drug Discov 2022; 21:676-696. [PMID: 35725925 PMCID: PMC9207876 DOI: 10.1038/s41573-022-00495-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/11/2022]
Abstract
Monoclonal antibodies (mAbs) are appealing as potential therapeutics and prophylactics for viral infections owing to characteristics such as their high specificity and their ability to enhance immune responses. Furthermore, antibody engineering can be used to strengthen effector function and prolong mAb half-life, and advances in structural biology have enabled the selection and optimization of potent neutralizing mAbs through identification of vulnerable regions in viral proteins, which can also be relevant for vaccine design. The COVID-19 pandemic has stimulated extensive efforts to develop neutralizing mAbs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with several mAbs now having received authorization for emergency use, providing not just an important component of strategies to combat COVID-19 but also a boost to efforts to harness mAbs in therapeutic and preventive settings for other infectious diseases. Here, we describe advances in antibody discovery and engineering that have led to the development of mAbs for use against infections caused by viruses including SARS-CoV-2, respiratory syncytial virus (RSV), Ebola virus (EBOV), human cytomegalovirus (HCMV) and influenza. We also discuss the rationale for moving from empirical to structure-guided strategies in vaccine development, based on identifying optimal candidate antigens and vulnerable regions within them that can be targeted by antibodies to result in a strong protective immune response. Monoclonal antibodies (mAbs) are appealing as potential therapeutics and prophylactics for viral infections. This Review describes advances in antibody discovery and engineering that have led to the development of mAbs that target viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus and Ebola virus, and also considers the implications for vaccine development.
Collapse
|
8
|
Sunita, Singh Y, Beamer G, Sun X, Shukla P. Recent developments in systems biology and genetic engineering toward design of vaccines for TB. Crit Rev Biotechnol 2022; 42:532-547. [PMID: 34641752 PMCID: PMC11208086 DOI: 10.1080/07388551.2021.1951649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Tuberculosis (TB) is one of the most prevalent diseases worldwide. The currently available Bacillus Calmette-Guérin vaccine is not sufficient in protecting against pulmonary TB. Although many vaccines have been evaluated in clinical trials, but none of them yet has proven to be more successful. Thus, new strategies are urgently needed to design more effective TB vaccines. The emergence of new technologies will undoubtedly accelerate the process of vaccine development. This review summarizes the potential and validated applications of emerging technologies, including: systems biology (genomics, proteomics, and transcriptomics), genetic engineering, and other computational tools to discover and develop novel vaccines against TB. It also discussed that the significant implementation of these approaches will play crucial roles in the development of novel vaccines to cure and control TB.
Collapse
Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Gillian Beamer
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, MA, USA
| | - Xingmin Sun
- Department of Molecular Medicine, College of Medicine (COM), University of South Florida, Tampa, FL, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| |
Collapse
|
9
|
Fragoso-Saavedra M, Ramírez-Estudillo C, Peláez-González DL, Ramos-Flores JO, Torres-Franco G, Núñez-Muñoz L, Marcelino-Pérez G, Segura-Covarrubias MG, González-González R, Ruiz-Medrano R, Xoconostle-Cázares B, Gayosso-Vázquez A, Reyes-Maya S, Ramírez-Andoney V, Alonso-Morales RA, Vega-López MA. Combined Subcutaneous-Intranasal Immunization With Epitope-Based Antigens Elicits Binding and Neutralizing Antibody Responses in Serum and Mucosae Against PRRSV-2 and SARS-CoV-2. Front Immunol 2022; 13:848054. [PMID: 35432364 PMCID: PMC9008747 DOI: 10.3389/fimmu.2022.848054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/08/2022] [Indexed: 11/23/2022] Open
Abstract
New vaccine design approaches, platforms, and immunization strategies might foster antiviral mucosal effector and memory responses to reduce asymptomatic infection and transmission in vaccinated individuals. Here, we investigated a combined parenteral and mucosal immunization scheme to induce local and serum antibody responses, employing the epitope-based antigens 3BT and NG19m. These antigens target the important emerging and re-emerging viruses PRRSV-2 and SARS-CoV-2, respectively. We assessed two versions of the 3BT protein, which contains conserved epitopes from the GP5 envelope protein of PRRSV-2: soluble and expressed by the recombinant baculovirus BacDual-3BT. On the other hand, NG19m, comprising the receptor-binding motif of the S protein of SARS-CoV-2, was evaluated as a soluble recombinant protein only. Vietnamese mini-pigs were immunized employing different inoculation routes: subcutaneous, intranasal, or a combination of both (s.c.-i.n.). Animals produced antigen-binding and neut1ralizing antibodies in serum and mucosal fluids, with varying patterns of concentration and activity, depending on the antigen and the immunization schedule. Soluble 3BT was a potent immunogen to elicit binding and neutralizing antibodies in serum, nasal mucus, and vaginal swabs. The vectored immunogen BacDual-3BT induced binding antibodies in serum and mucosae, but PRRSV-2 neutralizing activity was found in nasal mucus exclusively when administered intranasally. NG19m promoted serum and mucosal binding antibodies, which showed differing neutralizing activity. Only serum samples from subcutaneously immunized animals inhibited RBD-ACE2 interaction, while mini-pigs inoculated intranasally or via the combined s.c.-i.n. scheme produced subtle neutralizing humoral responses in the upper and lower respiratory mucosae. Our results show that intranasal immunization, alone or combined with subcutaneous delivery of epitope-based antigens, generates local and systemic binding and neutralizing antibodies. Further investigation is needed to evaluate the capability of the induced responses to prevent infection and reduce transmission.
Collapse
Affiliation(s)
- Mario Fragoso-Saavedra
- Laboratorio de Inmunobiología de las Mucosas, Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Carmen Ramírez-Estudillo
- Laboratorio de Inmunobiología de las Mucosas, Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Diana L Peláez-González
- Unidad de Producción y Experimentación de Animales de Laboratorio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Jorge O Ramos-Flores
- Unidad de Producción y Experimentación de Animales de Laboratorio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Gustavo Torres-Franco
- Unidad de Producción y Experimentación de Animales de Laboratorio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Leandro Núñez-Muñoz
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Gabriel Marcelino-Pérez
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María G Segura-Covarrubias
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Rogelio González-González
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Roberto Ruiz-Medrano
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Beatriz Xoconostle-Cázares
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Amanda Gayosso-Vázquez
- Laboratorio de Genética Molecular, Departamento de Genética y Bioestadística, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Silvia Reyes-Maya
- Laboratorio de Genética Molecular, Departamento de Genética y Bioestadística, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Vianey Ramírez-Andoney
- Laboratorio de Genética Molecular, Departamento de Genética y Bioestadística, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rogelio A Alonso-Morales
- Laboratorio de Genética Molecular, Departamento de Genética y Bioestadística, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Marco A Vega-López
- Laboratorio de Inmunobiología de las Mucosas, Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| |
Collapse
|
10
|
Scheck A, Rosset S, Defferrard M, Loukas A, Bonet J, Vandergheynst P, Correia BE. RosettaSurf—A surface-centric computational design approach. PLoS Comput Biol 2022; 18:e1009178. [PMID: 35294435 PMCID: PMC9015148 DOI: 10.1371/journal.pcbi.1009178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 04/18/2022] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
Proteins are typically represented by discrete atomic coordinates providing an accessible framework to describe different conformations. However, in some fields proteins are more accurately represented as near-continuous surfaces, as these are imprinted with geometric (shape) and chemical (electrostatics) features of the underlying protein structure. Protein surfaces are dependent on their chemical composition and, ultimately determine protein function, acting as the interface that engages in interactions with other molecules. In the past, such representations were utilized to compare protein structures on global and local scales and have shed light on functional properties of proteins. Here we describe RosettaSurf, a surface-centric computational design protocol, that focuses on the molecular surface shape and electrostatic properties as means for protein engineering, offering a unique approach for the design of proteins and their functions. The RosettaSurf protocol combines the explicit optimization of molecular surface features with a global scoring function during the sequence design process, diverging from the typical design approaches that rely solely on an energy scoring function. With this computational approach, we attempt to address a fundamental problem in protein design related to the design of functional sites in proteins, even when structurally similar templates are absent in the characterized structural repertoire. Surface-centric design exploits the premise that molecular surfaces are, to a certain extent, independent of the underlying sequence and backbone configuration, meaning that different sequences in different proteins may present similar surfaces. We benchmarked RosettaSurf on various sequence recovery datasets and showcased its design capabilities by generating epitope mimics that were biochemically validated. Overall, our results indicate that the explicit optimization of surface features may lead to new routes for the design of functional proteins. Finely orchestrated protein-protein interactions are at the heart of virtually all fundamental cellular processes. Altering these processes or encoding new functions in proteins has been a long-standing goal in computational protein design. Protein design methods commonly rely on scoring functions that seek to identify amino acid sequences that optimize structural configurations of atoms while minimizing a variety of physics-based and statistical terms. The objectives of the large majority of computational design protocols have been focused on obtaining a predefined structural conformation. However, routinely introducing a functional aspect on designer proteins has been more challenging. Our results suggest that the molecular surface features can be a useful optimization parameter to guide the design process towards functional surfaces that mimic known protein binding sites and interact with their intended targets. Specifically, we demonstrate that our design method can optimize experimental libraries through computational screening, creating a basis for highly specific protein binders, as well as design a potent immunogen that engages with site-specific antibodies. The ability to create proteins with novel functions will be transformative for biomedical applications, providing many opportunities for the design of novel immunogens, protein components for synthetic biology, and other protein-based biotechnologies.
Collapse
Affiliation(s)
- Andreas Scheck
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Stéphane Rosset
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Michaël Defferrard
- Signal Processing Laboratory (LTS2), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andreas Loukas
- Signal Processing Laboratory (LTS2), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Pierre Vandergheynst
- Signal Processing Laboratory (LTS2), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Bruno E. Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- * E-mail:
| |
Collapse
|
11
|
Abstract
Antibody immunodominance refers to the preferential and asymmetric elicitation of antibodies against specific epitopes on a complex protein antigen. Traditional vaccination approaches for rapidly evolving pathogens have had limited success in part because of this phenomenon, as elicited antibodies preferentially target highly variable regions of antigens, and thus do not confer long lasting protection. While antibodies targeting functionally conserved epitopes have the potential to be broadly protective, they often make up a minority of the overall repertoire. Here, we discuss recent protein engineering strategies used to favorably alter patterns of immunodominance, and selectively focus antibody responses toward broadly protective epitopes in the pursuit of next-generation vaccines for rapidly evolving pathogens.
Collapse
|
12
|
Tan ZC, Murphy MC, Alpay HS, Taylor SD, Meyer AS. Tensor-structured decomposition improves systems serology analysis. Mol Syst Biol 2021; 17:e10243. [PMID: 34487431 PMCID: PMC8420856 DOI: 10.15252/msb.202110243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 01/04/2023] Open
Abstract
Systems serology provides a broad view of humoral immunity by profiling both the antigen-binding and Fc properties of antibodies. These studies contain structured biophysical profiling across disease-relevant antigen targets, alongside additional measurements made for single antigens or in an antigen-generic manner. Identifying patterns in these measurements helps guide vaccine and therapeutic antibody development, improve our understanding of diseases, and discover conserved regulatory mechanisms. Here, we report that coupled matrix-tensor factorization (CMTF) can reduce these data into consistent patterns by recognizing the intrinsic structure of these data. We use measurements from two previous studies of HIV- and SARS-CoV-2-infected subjects as examples. CMTF outperforms standard methods like principal components analysis in the extent of data reduction while maintaining equivalent prediction of immune functional responses and disease status. Under CMTF, model interpretation improves through effective data reduction, separation of the Fc and antigen-binding effects, and recognition of consistent patterns across individual measurements. Data reduction also helps make prediction models more replicable. Therefore, we propose that CMTF is an effective general strategy for data exploration in systems serology.
Collapse
Affiliation(s)
- Zhixin Cyrillus Tan
- Bioinformatics Interdepartmental ProgramUniversity of California, Los AngelesLos AngelesCAUSA
| | - Madeleine C Murphy
- Computational and Systems BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Hakan S Alpay
- Department of Computer ScienceUniversity of California, Los AngelesLos AngelesCAUSA
| | - Scott D Taylor
- Department of BioengineeringUniversity of California, Los AngelesLos AngelesCAUSA
| | - Aaron S Meyer
- Bioinformatics Interdepartmental ProgramUniversity of California, Los AngelesLos AngelesCAUSA
- Department of BioengineeringUniversity of California, Los AngelesLos AngelesCAUSA
- Jonsson Comprehensive Cancer CenterUniversity of California, Los AngelesLos AngelesCAUSA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchUniversity of California, Los AngelesLos AngelesCAUSA
| |
Collapse
|
13
|
Jacque E, Chottin C, Laubreton D, Nogre M, Ferret C, de Marcos S, Baptista L, Drajac C, Mondon P, De Romeuf C, Rameix-Welti MA, Eléouët JF, Chtourou S, Riffault S, Perret G, Descamps D. Hyper-Enriched Anti-RSV Immunoglobulins Nasally Administered: A Promising Approach for Respiratory Syncytial Virus Prophylaxis. Front Immunol 2021; 12:683902. [PMID: 34163482 PMCID: PMC8215542 DOI: 10.3389/fimmu.2021.683902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 11/23/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a public health concern that causes acute lower respiratory tract infection. So far, no vaccine candidate under development has reached the market and the only licensed product to prevent RSV infection in at-risk infants and young children is a monoclonal antibody (Synagis®). Polyclonal human anti-RSV hyper-immune immunoglobulins (Igs) have also been used but were superseded by Synagis® owing to their low titer and large infused volume. Here we report a new drug class of immunoglobulins, derived from human non hyper-immune plasma that was generated by an innovative bioprocess, called Ig cracking, combining expertises in plasma-derived products and affinity chromatography. By using the RSV fusion protein (F protein) as ligand, the Ig cracking process provided a purified and concentrated product, designated hyper-enriched anti-RSV IgG, composed of at least 15-20% target-specific-antibodies from normal plasma. These anti-RSV Ig displayed a strong in vitro neutralization effect on RSV replication. Moreover, we described a novel prophylactic strategy based on local nasal administration of this unique hyper-enriched anti-RSV IgG solution using a mouse model of infection with bioluminescent RSV. Our results demonstrated that very low doses of hyper-enriched anti-RSV IgG can be administered locally to ensure rapid and efficient inhibition of virus infection. Thus, the general hyper-enriched Ig concept appeared a promising approach and might provide solutions to prevent and treat other infectious diseases.
Collapse
Affiliation(s)
| | - Claire Chottin
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Daphné Laubreton
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Cécile Ferret
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | | | - Carole Drajac
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | | | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, U1173, Montigny-Le-Bretonneux, France.,AP-HP, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | | | | | - Sabine Riffault
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | | |
Collapse
|
14
|
Pearce R, Zhang Y. Deep learning techniques have significantly impacted protein structure prediction and protein design. Curr Opin Struct Biol 2021; 68:194-207. [PMID: 33639355 PMCID: PMC8222070 DOI: 10.1016/j.sbi.2021.01.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/09/2021] [Accepted: 01/18/2021] [Indexed: 12/26/2022]
Abstract
Protein structure prediction and design can be regarded as two inverse processes governed by the same folding principle. Although progress remained stagnant over the past two decades, the recent application of deep neural networks to spatial constraint prediction and end-to-end model training has significantly improved the accuracy of protein structure prediction, largely solving the problem at the fold level for single-domain proteins. The field of protein design has also witnessed dramatic improvement, where noticeable examples have shown that information stored in neural-network models can be used to advance functional protein design. Thus, incorporation of deep learning techniques into different steps of protein folding and design approaches represents an exciting future direction and should continue to have a transformative impact on both fields.
Collapse
Affiliation(s)
- Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
15
|
Bottom-up de novo design of functional proteins with complex structural features. Nat Chem Biol 2021; 17:492-500. [PMID: 33398169 DOI: 10.1038/s41589-020-00699-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/26/2020] [Indexed: 01/28/2023]
Abstract
De novo protein design has enabled the creation of new protein structures. However, the design of functional proteins has proved challenging, in part due to the difficulty of transplanting structurally complex functional sites to available protein structures. Here, we used a bottom-up approach to build de novo proteins tailored to accommodate structurally complex functional motifs. We applied the bottom-up strategy to successfully design five folds for four distinct binding motifs, including a bifunctionalized protein with two motifs. Crystal structures confirmed the atomic-level accuracy of the computational designs. These de novo proteins were functional as components of biosensors to monitor antibody responses and as orthogonal ligands to modulate synthetic signaling receptors in engineered mammalian cells. Our work demonstrates the potential of bottom-up approaches to accommodate complex structural motifs, which will be essential to endow de novo proteins with elaborate biochemical functions, such as molecular recognition or catalysis.
Collapse
|
16
|
Mir MA, Mehraj U, Sheikh BA, Hamdani SS. Nanobodies: The "Magic Bullets" in therapeutics, drug delivery and diagnostics. Hum Antibodies 2020; 28:29-51. [PMID: 31322555 DOI: 10.3233/hab-190390] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibodies represent a well-established class of clinical diagnostics for medical applications as well as essential research and biotechnological tools. Although both polyclonal and monoclonal antibodies are indispensable reagents in basic research and diagnostics but both of them have their limitations. Hence, there is urgent need to develop strategies aimed at production of alternative scaffolds and recombinant antibodies of smaller dimensions that could be easily produced, selected and manipulated. Unlike conventional antibodies, members of Camelidae and sharks produce antibodies composed only of heavy chains with small size, high solubility, thermal stability, refolding capacity and good tissue penetration in vivo. The discovery of these naturally occurring antibodies having only heavy-chain in Camelidae family and their further development into small recombinant nanobodies represents an attractive alternative in drug delivery, diagnostics and imaging. Nanobody derivatives are soluble, stable, versatile, have unique refolding capacities, reduced aggregation tendencies and high-target binding capabilities. They can be genetically customized to target enzymes, transmembrane proteins or molecular interactions. Their ability to recognize recessed antigenic sites has been attributed to their smaller size and the ability of the extended CDR3 loop to quickly penetrate into such epitopes. With the advent of molecular engineering and phage display technology, they can be of potential use in molecular imaging, drug delivery and therapeutics for several major diseases. In this review we present the recent advances in nanobodies for modulating immune functions, for targeting cancers, viruses, toxins and microbes as well as their utility as diagnostic and biosensor tools.
Collapse
|
17
|
Abstract
The vaccine field is pursuing diverse approaches to translate the molecular insights from analyses of effective antibodies and their targeted epitopes into immunogens capable of eliciting protective immune responses. Here we review current antibody-guided strategies including conformation-based, epitope-based, and lineage-based vaccine approaches, which are yielding promising vaccine candidates now being evaluated in clinical trials. We summarize directions being employed by the field, including the use of sequencing technologies to monitor and track developing immune responses for understanding and improving antibody-based immunity. We review opportunities and challenges to transform powerful new discoveries into safe and effective vaccines, which are encapsulated by vaccine efforts against a variety of pathogens including HIV-1, influenza A virus, malaria parasites, respiratory syncytial virus, and SARS-CoV-2. Overall, this review summarizes the extensive progress that has been made to realize antibody-guided structure-based vaccines, the considerable challenges faced, and the opportunities afforded by recently developed molecular approaches to vaccine development.
Collapse
|
18
|
Remmel JL, Beauchemin KS, Mishra AK, Frei JC, Lai JR, Bailey-Kellogg C, Ackerman ME. Combinatorial Resurfacing of Dengue Envelope Protein Domain III Antigens Selectively Ablates Epitopes Associated with Serotype-Specific or Infection-Enhancing Antibody Responses. ACS COMBINATORIAL SCIENCE 2020; 22:446-456. [PMID: 32574486 DOI: 10.1021/acscombsci.0c00073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutagenesis of surface-exposed residues, or "resurfacing", is a protein engineering strategy that can be utilized to disrupt antibody recognition or modulate the capacity of a protein to elicit antibody responses. We apply resurfacing to engineer Dengue virus envelope protein domain III (DENV DIII) antigens with the goal of focusing humoral recognition on epitopes of interest by selective ablation of irrelevant and undesired epitopes. Cross-reactive but non-neutralizing antibodies have the potential to enhance Dengue virus (DENV) infection by a process called antibody-dependent enhancement, thought to be associated with severe secondary heterotypic infection. Thus, a focus on epitopes associated with broadly neutralizing antibodies is important both for understanding human antibody responses against DENV and for the development of a successful DENV vaccine. To engineer DENV DIII antigens focusing on the AG strand epitope associated with broadly neutralizing antibody responses, we generated yeast surface display libraries of DENV2 DIII where the AB loop (associated with cross-reactive but non-neutralizing antibody responses) and FG loop (associated with serotype-specific antibody responses) were mutagenized to allow for all possible amino acid substitutions. Loop variants that maintained the AG strand epitope and simultaneously disrupted the AB and FG loop epitopes exhibited high and diverse mutational loads that were amenable to loop exchange and transplantation into a DENV4 DIII background. Thus, several loop variants fulfill this antigenicity criteria regardless of serotype context. The resulting resurfaced DIII antigens may be utilized as AG strand epitope-focusing probes or immunogen candidates.
Collapse
Affiliation(s)
- Jennifer L. Remmel
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Kathryn S. Beauchemin
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Akaash K. Mishra
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Julia C. Frei
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755, United States
| |
Collapse
|
19
|
Abstract
Conventional influenza vaccines are based on predicting the circulating viruses year by year, conferring limited effectiveness since the antigenicity of vaccine strains does not always match the circulating viruses. This necessitates development of universal influenza vaccines that provide broader and lasting protection against pan-influenza viruses. The discovery of the highly conserved immunogens (epitopes) of influenza viruses provides attractive targets for universal vaccine design. Here we review the current understanding with broadly protective immunogens (epitopes) and discuss several important considerations to achieve the goal of universal influenza vaccines.
Collapse
|
20
|
Sesterhenn F, Yang C, Bonet J, Cramer JT, Wen X, Wang Y, Chiang CI, Abriata LA, Kucharska I, Castoro G, Vollers SS, Galloux M, Dheilly E, Rosset S, Corthésy P, Georgeon S, Villard M, Richard CA, Descamps D, Delgado T, Oricchio E, Rameix-Welti MA, Más V, Ervin S, Eléouët JF, Riffault S, Bates JT, Julien JP, Li Y, Jardetzky T, Krey T, Correia BE. De novo protein design enables the precise induction of RSV-neutralizing antibodies. Science 2020; 368:eaay5051. [PMID: 32409444 PMCID: PMC7391827 DOI: 10.1126/science.aay5051] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 01/30/2020] [Accepted: 04/08/2020] [Indexed: 12/27/2022]
Abstract
De novo protein design has been successful in expanding the natural protein repertoire. However, most de novo proteins lack biological function, presenting a major methodological challenge. In vaccinology, the induction of precise antibody responses remains a cornerstone for next-generation vaccines. Here, we present a protein design algorithm called TopoBuilder, with which we engineered epitope-focused immunogens displaying complex structural motifs. In both mice and nonhuman primates, cocktails of three de novo-designed immunogens induced robust neutralizing responses against the respiratory syncytial virus. Furthermore, the immunogens refocused preexisting antibody responses toward defined neutralization epitopes. Overall, our design approach opens the possibility of targeting specific epitopes for the development of vaccines and therapeutic antibodies and, more generally, will be applicable to the design of de novo proteins displaying complex functional motifs.
Collapse
Affiliation(s)
- Fabian Sesterhenn
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Che Yang
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Johannes T Cramer
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
| | - Xiaolin Wen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yimeng Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Luciano A Abriata
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Iga Kucharska
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Giacomo Castoro
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
| | - Sabrina S Vollers
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Elie Dheilly
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Stéphane Rosset
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Patricia Corthésy
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Sandrine Georgeon
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Mélanie Villard
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | | | - Delphyne Descamps
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Teresa Delgado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | | | - Vicente Más
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Sean Ervin
- Wake Forest Baptist Medical Center, Winston Salem, NC 27157, USA
| | | | - Sabine Riffault
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - John T Bates
- University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jean-Philippe Julien
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
- Department of Microbiology and Immunology & Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Theodore Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Institute of Biochemistry, Center of Structural and Cell Biology in Medicine, University of Luebeck, D-23538 Luebeck, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, 30625 Hannover, Germany
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| |
Collapse
|
21
|
Original Antigenic Sin and Respiratory Syncytial Virus Vaccines. Vaccines (Basel) 2019; 7:vaccines7030107. [PMID: 31500131 PMCID: PMC6789633 DOI: 10.3390/vaccines7030107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 02/08/2023] Open
Abstract
The original antigenic sin (OAS) theory considers the outcome of the first encounter with an antigen. It favors a memory response to the original antigen upon exposure to a similar or related antigen, and includes both positive and negative impacts of past exposure on the memory response to challenge, and, in particular, on vaccine efficacy. This phenomenon is closely linked with imprinting and the hierarchical nature of immune responses to previously encountered antigens. The focus of this commentary centers on the potential role of OAS or immunological imprinting on respiratory syncytial virus memory responses.
Collapse
|