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Fall AKDJ, Dechavanne C, Sabbagh A, Guitard E, Milet J, Garcia A, Dugoujon JM, Courtin D, Migot-Nabias F. Susceptibility to Plasmodium falciparum Malaria: Influence of Combined Polymorphisms of IgG3 Gm Allotypes and Fc Gamma Receptors IIA, IIIA, and IIIB. Front Immunol 2020; 11:608016. [PMID: 33424858 PMCID: PMC7786284 DOI: 10.3389/fimmu.2020.608016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/13/2020] [Indexed: 02/04/2023] Open
Abstract
The binding of immunoglobulin (Ig) to Fc gamma receptors (FcgR) at the immune cell surface is an important step to initiate immunological defense against malaria. However, polymorphisms in receptors and/or constant regions of the IgG heavy chains may modulate this binding. Here, we investigated whether polymorphisms located in FcgR and constant regions of the heavy chain of IgG are associated with susceptibility to P. falciparum malaria. For this purpose, a clinical and parasitological follow-up on malaria was conducted among 656 infants in southern Benin. G3m allotypes (from total IgG3) were determined by a serological method of hemagglutination inhibition. FcgRIIA 131R/H and FcgRIIIA 176F/V genotypes were determined using the TaqMan method and FcgRIIIB NA1/NA2 genotypes were assessed by polymerase chain reaction using allele-specific primers. Association analyses between the number of malaria infections during the follow-up and polymorphisms in IgG G3m allotypes and FcgR were studied independently by zero inflated binomial negative regression. The influence of combinations of G3m allotypes and FcgRIIA/FcgRIIIA/FcgRIIIB polymorphisms on the number of P. falciparum infections, and their potential interaction with environmental exposure to malaria was assessed by using the generalized multifactor dimensionality reduction (GMDR) method. Results showed that individual carriage of G3m24 single allotype and of G3m5,6,10,11,13,14,24 phenotype was independently associated with a high risk of malaria infection. A risk effect for G3m6 was observed only under high environmental exposure. FcgRIIIA 176VV single genotype and combined carriage of FcgRIIA 131RH/FcgRIIIA 176VV/FcgRIIIB NA1NA2, FcgRIIA 131HH/FcgRIIIA 176FF/FcgRIIIB NA1NA1, FcgRIIA 131HH/FcgRIIIA 176VV/FcgRIIIB NA2NA2 and FcgRIIA 131HH/FcgRIIIA 176VV/FcgRIIIB NA1NA2 genotypes were related to a high number of malaria infections. The risk was accentuated for FcgRIIIA 176VV when considering the influence of environmental exposure to malaria. Finally, the GMDR analysis including environmental exposure showed strengthened associations with a malaria risk when FcgRIIA/FcgRIIIA/FcgRIIIB genotypes were combined to G3m5,6,11,24 and G3m5,6,10,11,13,15,24 phenotypes or G3m10 and G3m13 single allotypes. Our results highlight the relevance of studying IgG heavy chain and FcgR polymorphisms, independently as well as in combination, in relation to the individual susceptibility to P. falciparum infection. The intensity of individual exposure to mosquito bites was demonstrated to impact the relationships found.
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Affiliation(s)
| | - Celia Dechavanne
- Université de Paris, Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Paris, France
| | - Audrey Sabbagh
- Université de Paris, Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Paris, France
| | - Evelyne Guitard
- CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, Toulouse, France
| | - Jacqueline Milet
- Université de Paris, Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Paris, France
| | - André Garcia
- Université de Paris, Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Paris, France
| | - Jean-Michel Dugoujon
- CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, Toulouse, France
| | - David Courtin
- Université de Paris, Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Paris, France
| | - Florence Migot-Nabias
- Université de Paris, Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Paris, France
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202
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Scott JK, Breden F. The adaptive immune receptor repertoire community as a model for FAIR stewardship of big immunology data. CURRENT OPINION IN SYSTEMS BIOLOGY 2020; 24:71-77. [PMID: 33073065 PMCID: PMC7547575 DOI: 10.1016/j.coisb.2020.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Systems biology involves network-oriented, computational approaches to modeling biological systems through analysis of big biological data. To contribute maximally to scientific progress, big biological data should be FAIR: findable, accessible, interoperable, and reusable. Here, we describe high-throughput sequencing data that characterize the vast diversity of B- and T-cell clones comprising the adaptive immune receptor repertoire (AIRR-seq data) and its contribution to our understanding of COVID-19 (coronavirus disease 19). We describe the accomplishments of the AIRR community, a grass-roots network of interdisciplinary laboratory scientists, bioinformaticians, and policy wonks, in creating and publishing standards, software and repositories for AIRR-seq data based on the FAIR principles.
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Affiliation(s)
- Jamie K Scott
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
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203
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Barnes CO, Jette CA, Abernathy ME, Dam KMA, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West AP, Bjorkman PJ. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 2020; 588:682-687. [PMID: 33045718 PMCID: PMC8092461 DOI: 10.1038/s41586-020-2852-1] [Citation(s) in RCA: 1102] [Impact Index Per Article: 275.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein1-5 show promise therapeutically and are being evaluated clinically6-8. Here, to identify the structural correlates of SARS-CoV-2 neutralization, we solved eight new structures of distinct COVID-19 human neutralizing antibodies5 in complex with the SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed us to classify the antibodies into categories: (1) neutralizing antibodies encoded by the VH3-53 gene segment with short CDRH3 loops that block ACE2 and bind only to 'up' RBDs; (2) ACE2-blocking neutralizing antibodies that bind both up and 'down' RBDs and can contact adjacent RBDs; (3) neutralizing antibodies that bind outside the ACE2 site and recognize both up and down RBDs; and (4) previously described antibodies that do not block ACE2 and bind only to up RBDs9. Class 2 contained four neutralizing antibodies with epitopes that bridged RBDs, including a VH3-53 antibody that used a long CDRH3 with a hydrophobic tip to bridge between adjacent down RBDs, thereby locking the spike into a closed conformation. Epitope and paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 to escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Angiotensin-Converting Enzyme 2/ultrastructure
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Neutralizing/ultrastructure
- Binding Sites/genetics
- Binding Sites/immunology
- COVID-19/immunology
- Cell Line
- Cryoelectron Microscopy
- Humans
- Models, Molecular
- Mutation
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- Receptors, Coronavirus/ultrastructure
- SARS-CoV-2/chemistry
- SARS-CoV-2/immunology
- SARS-CoV-2/metabolism
- SARS-CoV-2/ultrastructure
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/ultrastructure
- COVID-19 Drug Treatment
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Affiliation(s)
- Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Claudia A Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan E Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shannon R Esswein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrey G Malyutin
- Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Naima G Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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204
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The respiratory syncytial virus fusion protein-specific B cell receptor repertoire reshaped by post-fusion subunit vaccination. Vaccine 2020; 38:7916-7927. [PMID: 33131932 DOI: 10.1016/j.vaccine.2020.10.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 01/21/2023]
Abstract
Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory illness in children of less than 5 years of age which usually results in hospitalization or even in death. Vaccine development is hampered in consequence of a failed vaccine trial with fatalities in the 1960s. Even though research has been more focused on the RSV fusion protein in its pre-fusion conformation, maternal vaccination with post-fusion protein (post F) was considered as a promising vaccine strategy for passive immunization of babies, because post F preserves very potent neutralizing epitopes. We extensively analyzed post F-binding B cell receptor (BCR) repertoires of three vaccinees who received a post F-subunit vaccine in the context of a first-in-human, Phase 1, randomized, observer-blind, placebo-controlled clinical trial (ClinicalTrials.gov Identifier: NCT02298179). In order to compare the vaccine-induced BCR repertoires with BCR repertoires induced by natural infection, we also analyzed pre F- and post F-binding BCRs isolated from a healthy blood donor with relatively high F-binding memory B cell (MBC) frequencies. Analysis of the vaccine-induced repertoires revealed that preferentially VH4-encoded BCRs were expanded in response to vaccination. Estimation of antigen-driven selection further demonstrated that expanded BCRs accumulated positively selected replacement mutations which substantiated the hypothesis that post F-vaccination induces diversification of VH4-encoded BCRs in germinal centers. Comparison of the vaccine-induced BCR repertoires with clonally related pre and post F-binding BCRs of the healthy blood donor suggested that the vaccine expanded pre/post F cross-reactive MBCs. Interestingly, several vaccine-induced BCRs shared stereotypic VDJ gene junctions with known neutralizing Abs. Once expressed for functional characterization, the selected monoclonal Abs demonstrated the predicted neutralization activities in plaque reduction neutralization assays indicating that the post F-vaccine induced expansion of neutralizing BCRs.
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205
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Schneikart G, Tavarini S, Sammicheli C, Torricelli G, Guidotti S, D'Oro U, Finco O, Bardelli M. Dataset of antibody variable region sequence features inferred from a respiratory syncytial virus fusion protein-specific B cell receptor repertoire induced by natural infection of a healthy adult. Data Brief 2020; 33:106499. [PMID: 33225034 PMCID: PMC7666335 DOI: 10.1016/j.dib.2020.106499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/30/2020] [Indexed: 11/17/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the primary cause for acute lower respiratory syndrome in children younger than 5 years. Research on B cell repertoires and antibodies binding the RSV fusion protein (RSV F) is of major interest in the development of potential vaccine candidates and therapies. B cell receptors (BCRs) which have higher affinities for a specific antigen are preferentially selected for B cell clonal expansion in germinal center reactions. Consequently, antigen-specific BCR repertoires share common features, as for instance preferential variable gene usage, variable region mutation levels or lengths of the heavy chain complementarity-determining region 3. Since RSV repeatedly infects every person throughout life, memory B cells (MBC) expressing RSV F-binding BCRs circulate in the blood of healthy adults. This dataset of BCR variable region sequence features was derived from single cell-sorted RSV F-directed MBCs of a healthy adult blood donor [1]. The dataset was produced with publicly available data analysis software programs and scripts, which facilitates integration or comparison with antibody sequence repertoire data of different individuals derived with the same or comparable data analysis approaches and tools.
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Affiliation(s)
- Gerald Schneikart
- GSK, Via Fiorentina 1, 53100 Siena, Italy
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | | | | | | | | | - Ugo D'Oro
- GSK, Via Fiorentina 1, 53100 Siena, Italy
| | | | - Monia Bardelli
- GSK, Via Fiorentina 1, 53100 Siena, Italy
- Corresponding author.
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206
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Suzuki T, Hayman L, Kilbey A, Edwards J, Coffelt SB. Gut γδ T cells as guardians, disruptors, and instigators of cancer. Immunol Rev 2020; 298:198-217. [PMID: 32840001 DOI: 10.1111/imr.12916] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 08/17/2023]
Abstract
Colorectal cancer is the third most common cancer worldwide with nearly 2 million cases per year. Immune cells and inflammation are a critical component of colorectal cancer progression, and they are used as reliable prognostic indicators of patient outcome. With the growing appreciation for immunology in colorectal cancer, interest is growing on the role γδ T cells have to play, as they represent one of the most prominent immune cell populations in gut tissue. This group of cells consists of both resident populations-γδ intraepithelial lymphocytes (γδ IELs)-and transient populations that each has unique functions. The homeostatic role of these γδ T cell subsets is to maintain barrier integrity and prevent microorganisms from breaching the mucosal layer, which is accomplished through crosstalk with enterocytes and other immune cells. Recent years have seen a surge in discoveries regarding the regulation of γδ IELs in the intestine and the colon with particular new insights into the butyrophilin family. In this review, we discuss the development, specialities, and functions of γδ T cell subsets during cancer progression. We discuss how these cells may be used to predict patient outcome, as well as how to exploit their behavior for cancer immunotherapy.
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Affiliation(s)
- Toshiyasu Suzuki
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Liam Hayman
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Anna Kilbey
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Joanne Edwards
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Seth B Coffelt
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
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207
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Kotouza MT, Gemenetzi K, Galigalidou C, Vlachonikola E, Pechlivanis N, Agathangelidis A, Sandaltzopoulos R, Mitkas PA, Stamatopoulos K, Chatzidimitriou A, Psomopoulos FE. TRIP - T cell receptor/immunoglobulin profiler. BMC Bioinformatics 2020; 21:422. [PMID: 32993478 PMCID: PMC7525938 DOI: 10.1186/s12859-020-03669-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
Abstract
Background Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era of high-throughput immunoprofiling by next generation sequencing (NGS). The T cell Receptor/Immunoglobulin Profiler (TRIP) tool offers the opportunity for an in-depth analysis based on the processing of the output files of the IMGT/HighV-Quest tool, a standard in NGS immunoprofiling, through a number of interoperable modules. These provide detailed information about antigen receptor gene rearrangements, including variable (V), diversity (D) and joining (J) gene usage, CDR3 amino acid and nucleotide composition and clonality of both T cell receptors (TR) and B cell receptor immunoglobulins (BcR IG), and characteristics of the somatic hypermutation within the BcR IG genes. TRIP is a web application implemented in R shiny. Results Two sets of experiments have been performed in order to evaluate the efficiency and performance of the TRIP tool. The first used a number of synthetic datasets, ranging from 250k to 1M sequences, and established the linear response time of the tool (about 6 h for 1M sequences processed through the entire BcR IG data pipeline). The reproducibility of the tool was tested comparing the results produced by the main TRIP workflow with the results from a previous pipeline used on the Galaxy platform. As expected, no significant differences were noted between the two tools; although the preselection process seems to be stricter within the TRIP pipeline, about 0.1% more rearrangements were filtered out, with no impact on the final results. Conclusions TRIP is a software framework that provides analytical services on antigen receptor gene sequence data. It is accurate and contains functions for data wrangling, cleaning, analysis and visualization, enabling the user to build a pipeline tailored to their needs. TRIP is publicly available at https://bio.tools/TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler.
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Affiliation(s)
- Maria Th Kotouza
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Katerina Gemenetzi
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Pericles A Mitkas
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Fotis E Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece. .,Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
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208
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Norman RA, Ambrosetti F, Bonvin AMJJ, Colwell LJ, Kelm S, Kumar S, Krawczyk K. Computational approaches to therapeutic antibody design: established methods and emerging trends. Brief Bioinform 2020; 21:1549-1567. [PMID: 31626279 PMCID: PMC7947987 DOI: 10.1093/bib/bbz095] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/07/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.
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209
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Giannico F, Massari S, Caputi Jambrenghi A, Soriano A, Pala A, Linguiti G, Ciccarese S, Antonacci R. The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species. BMC Genomics 2020; 21:623. [PMID: 32912163 PMCID: PMC7488459 DOI: 10.1186/s12864-020-07022-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Goats (Capra hircus), one of the first domesticated species, are economically important for milk and meat production, and their broad geographical distribution reflects their successful adaptation to diverse environmental conditions. Despite the relevance of this species, the genetic research on the goat traits is limited compared to other domestic species. Thanks to the latest goat reference genomic sequence (ARS1), which is considered to be one of the most continuous assemblies in livestock, we deduced the genomic structure of the T cell receptor beta (TRB) and gamma (TRG) loci in this ruminant species. RESULTS Our analyses revealed that although the organization of the goat TRB locus is broadly similar to that of the other artiodactyl species, with three in-tandem D-J-C clusters located at the 3' end, a complex and extensive series of duplications have occurred in the V genes at the 5' end, leading to a marked expansion in the number of the TRBV genes. This phenomenon appears to be a feature of the ruminant lineage since similar gene expansions have also occurred in sheep and cattle. Likewise, the general organization of the goat TRG genes is typical of ruminant species studied so far, with two paralogous TRG loci, TRG1 and TRG2, located in two distinct and distant positions on the same chromosome as result of a split in the ancestral locus. Each TRG locus consists of reiterated V-J-J-C cassettes, with the goat TRG2 containing an additional cassette relative to the corresponding sheep and cattle loci. CONCLUSIONS Taken together, these findings demonstrate that strong evolutionary pressures in the ruminant lineage have selected for the development of enlarged sets of TRB and TRG genes that contribute to a diverse T cell receptor repertoire. However, differences observed among the goat, sheep and cattle TRB and TRG genes indicate that distinct evolutionary histories, with independent expansions and/or contractions, have also affected each ruminant species.
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Affiliation(s)
- Francesco Giannico
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Soriano
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Angela Pala
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Giovanna Linguiti
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | | | - Rachele Antonacci
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy.
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210
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Lau A, Avery DT, Jackson K, Lenthall H, Volpi S, Brigden H, Russell AJ, Bier J, Reed JH, Smart JM, Cole T, Choo S, Gray PE, Berglund LJ, Hsu P, Wong M, O'Sullivan M, Boztug K, Meyts I, Uzel G, Notarangelo LD, Brink R, Goodnow CC, Tangye SG, Deenick EK. Activated PI3Kδ breaches multiple B cell tolerance checkpoints and causes autoantibody production. J Exp Med 2020; 217:132760. [PMID: 31841125 PMCID: PMC7041712 DOI: 10.1084/jem.20191336] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/29/2019] [Accepted: 11/07/2019] [Indexed: 12/17/2022] Open
Abstract
In patients, gain-of-function (GOF) mutations in PIK3CD break tolerance, causing highly penetrant secretion of autoreactive IgM. Mouse models reveal that Pik3cd GOF subverts the response to self-antigen, preventing the induction of anergy and instead stimulating plasmablast and GC formation. Antibody-mediated autoimmune diseases are a major health burden. However, our understanding of how self-reactive B cells escape self-tolerance checkpoints to secrete pathogenic autoantibodies remains incomplete. Here, we demonstrate that patients with monogenic immune dysregulation caused by gain-of-function mutations in PIK3CD, encoding the p110δ catalytic subunit of phosphoinositide 3-kinase (PI3K), have highly penetrant secretion of autoreactive IgM antibodies. In mice with the corresponding heterozygous Pik3cd activating mutation, self-reactive B cells exhibit a cell-autonomous subversion of their response to self-antigen: instead of becoming tolerized and repressed from secreting autoantibody, Pik3cd gain-of-function B cells are activated by self-antigen to form plasmablasts that secrete high titers of germline-encoded IgM autoantibody and hypermutating germinal center B cells. However, within the germinal center, peripheral tolerance was still enforced, and there was selection against B cells with high affinity for self-antigen. These data show that the strength of PI3K signaling is a key regulator of pregerminal center B cell self-tolerance and thus represents a druggable pathway to treat antibody-mediated autoimmunity.
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Affiliation(s)
- Anthony Lau
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Danielle T Avery
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Katherine Jackson
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Helen Lenthall
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Stefano Volpi
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini and Dipartimento di Neuroscienze, riabilitazione, oftalmologia, genetica e scienze materno-infantili (DINOGMI), Università degli Studi di Genova, Genova, Italy
| | - Henry Brigden
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Amanda J Russell
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Julia Bier
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Joanne H Reed
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Joanne M Smart
- Department of Allergy and Immunology, Royal Children's Hospital Melbourne, Victoria, Australia
| | - Theresa Cole
- Department of Allergy and Immunology, Royal Children's Hospital Melbourne, Victoria, Australia
| | - Sharon Choo
- Department of Allergy and Immunology, Royal Children's Hospital Melbourne, Victoria, Australia
| | - Paul E Gray
- School of Women's and Children's Health, UNSW Sydney, Sydney, Australia.,Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia
| | - Lucinda J Berglund
- Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia.,Immunopathology Department, Westmead Hospital, Westmead, New South Wales, Australia.,Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Peter Hsu
- Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia.,Children's Hospital at Westmead, New South Wales, Australia
| | - Melanie Wong
- Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia.,Children's Hospital at Westmead, New South Wales, Australia
| | - Michael O'Sullivan
- Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia.,Department of Immunology and Allergy, Princess Margaret Hospital, Subiaco, Western Australia, Australia
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Isabelle Meyts
- Department of Immunology and Microbiology, Inborn Errors of Immunity, Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Robert Brink
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia.,Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia
| | - Christopher C Goodnow
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia.,UNSW Cellular Genomics Futures Institute, UNSW Sydney, Sydney, Australia
| | - Stuart G Tangye
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia.,Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia
| | - Elissa K Deenick
- Immunity and Inflammatory Diseases, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,Clinical Immunogenomics Research Consortium of Australasia, Sydney, Australia.,Faculty of Medicine, UNSW Sydney, Sydney, Australia
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211
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Abstract
Our understanding of the human genome has continuously expanded since its draft publication in 2001. Over the years, novel assays have allowed us to progressively overlay layers of knowledge above the raw sequence of A's, T's, G's, and C's. The reference human genome sequence is now a complex knowledge base maintained under the shared stewardship of multiple specialist communities. Its complexity stems from the fact that it is simultaneously a template for transcription, a record of evolution, a vehicle for genetics, and a functional molecule. In short, the human genome serves as a frame of reference at the intersection of a diversity of scientific fields. In recent years, the progressive fall in sequencing costs has given increasing importance to the quality of the human reference genome, as hundreds of thousands of individuals are being sequenced yearly, often for clinical applications. Also, novel sequencing-based assays shed light on novel functions of the genome, especially with respect to gene expression regulation. Keeping the human genome annotation up to date and accurate is therefore an ongoing partnership between reference annotation projects and the greater community worldwide.
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Affiliation(s)
- Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom; , ,
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom; , ,
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom; , ,
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212
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Lefranc MP, Lefranc G. Immunoglobulins or Antibodies: IMGT ® Bridging Genes, Structures and Functions. Biomedicines 2020; 8:E319. [PMID: 32878258 PMCID: PMC7555362 DOI: 10.3390/biomedicines8090319] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as 'genes' as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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213
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Barnes CO, Jette CA, Abernathy ME, Dam KMA, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West AP, Bjorkman PJ. Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.30.273920. [PMID: 32869026 PMCID: PMC7457611 DOI: 10.1101/2020.08.30.273920] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic presents an urgent health crisis. Human neutralizing antibodies (hNAbs) that target the host ACE2 receptor-binding domain (RBD) of the SARS-CoV-2 spike1-5 show therapeutic promise and are being evaluated clincally6-8. To determine structural correlates of SARS-CoV-2 neutralization, we solved 8 new structures of distinct COVID-19 hNAbs5 in complex with SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed classification into categories: (1) VH3-53 hNAbs with short CDRH3s that block ACE2 and bind only to "up" RBDs, (2) ACE2-blocking hNAbs that bind both "up" and "down" RBDs and can contact adjacent RBDs, (3) hNAbs that bind outside the ACE2 site and recognize "up" and "down" RBDs, and (4) Previously-described antibodies that do not block ACE2 and bind only "up" RBDs9. Class 2 comprised four hNAbs whose epitopes bridged RBDs, including a VH3-53 hNAb that used a long CDRH3 with a hydrophobic tip to bridge between adjacent "down" RBDs, thereby locking spike into a closed conformation. Epitope/paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally-occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects, suggesting combinations for clinical use, and providing insight into immune responses against SARS-CoV-2.
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Affiliation(s)
- Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan E. Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shannon R. Esswein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B. Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrey G. Malyutin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Naima G. Sharaf
- Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Present address: Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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214
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Barnes CO, West AP, Huey-Tubman KE, Hoffmann MAG, Sharaf NG, Hoffman PR, Koranda N, Gristick HB, Gaebler C, Muecksch F, Lorenzi JCC, Finkin S, Hägglöf T, Hurley A, Millard KG, Weisblum Y, Schmidt F, Hatziioannou T, Bieniasz PD, Caskey M, Robbiani DF, Nussenzweig MC, Bjorkman PJ. Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell 2020; 182:828-842.e16. [PMID: 32645326 PMCID: PMC7311918 DOI: 10.1016/j.cell.2020.06.025] [Citation(s) in RCA: 599] [Impact Index Per Article: 149.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/27/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022]
Abstract
Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1A and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryo-electron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.
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MESH Headings
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- Betacoronavirus/chemistry
- Betacoronavirus/immunology
- COVID-19
- Coronavirus Infections/blood
- Coronavirus Infections/immunology
- Coronavirus Infections/therapy
- Cross Reactions
- Cryoelectron Microscopy
- Epitope Mapping
- Epitopes
- Humans
- Immunization, Passive
- Immunoglobulin Fab Fragments/blood
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/isolation & purification
- Immunoglobulin Fab Fragments/ultrastructure
- Immunoglobulin G/blood
- Immunoglobulin G/chemistry
- Immunoglobulin G/isolation & purification
- Immunoglobulin G/ultrastructure
- Middle East Respiratory Syndrome Coronavirus/chemistry
- Middle East Respiratory Syndrome Coronavirus/immunology
- Models, Molecular
- Pandemics
- Pneumonia, Viral/blood
- Pneumonia, Viral/immunology
- Severe acute respiratory syndrome-related coronavirus/chemistry
- Severe acute respiratory syndrome-related coronavirus/immunology
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- COVID-19 Serotherapy
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Affiliation(s)
- Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Magnus A G Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Naima G Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Thomas Hägglöf
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Arlene Hurley
- Hospital Program Direction, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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215
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Beshnova D, Ye J, Onabolu O, Moon B, Zheng W, Fu YX, Brugarolas J, Lea J, Li B. De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection. Sci Transl Med 2020; 12:eaaz3738. [PMID: 32817363 PMCID: PMC7887928 DOI: 10.1126/scitranslmed.aaz3738] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/05/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023]
Abstract
The adaptive immune system recognizes tumor antigens at an early stage to eradicate cancer cells. This process is accompanied by systemic proliferation of the tumor antigen-specific T lymphocytes. While detection of asymptomatic early-stage cancers is challenging due to small tumor size and limited somatic alterations, tracking peripheral T cell repertoire changes may provide an attractive solution to cancer diagnosis. Here, we developed a deep learning method called DeepCAT to enable de novo prediction of cancer-associated T cell receptors (TCRs). We validated DeepCAT using cancer-specific or non-cancer TCRs obtained from multiple major histocompatibility complex I (MHC-I) multimer-sorting experiments and demonstrated its prediction power for TCRs specific to cancer antigens. We blindly applied DeepCAT to distinguish over 250 patients with cancer from over 600 healthy individuals using blood TCR sequences and observed high prediction accuracy, with area under the curve (AUC) ≥ 0.95 for multiple early-stage cancers. This work sets the stage for using the peripheral blood TCR repertoire for noninvasive cancer detection.
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Affiliation(s)
- Daria Beshnova
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Oreoluwa Onabolu
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin Moon
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenxin Zheng
- Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jayanthi Lea
- Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA.
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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216
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Warrender AK, Kelton W. Beyond Allotypes: The Influence of Allelic Diversity in Antibody Constant Domains. Front Immunol 2020; 11:2016. [PMID: 32973808 PMCID: PMC7461860 DOI: 10.3389/fimmu.2020.02016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/24/2020] [Indexed: 01/25/2023] Open
Abstract
Polymorphic diversity in antibody constant domains has long been defined by allotypic motifs that cross react with the sera of other individuals. Improvements in sequencing technologies have led to the discovery of a large number of new allelic sequences that underlie this diversity. Many of the point mutations lie outside traditional allotypic motifs suggesting they do not elicit immunogenic responses. As antibodies play an important role in immune defense and biotechnology, understanding how this newly resolved diversity influences the function of antibodies is important. This review investigates the current known diversity of antibody alleles at a protein level for each antibody isotype as well as the kappa and lambda light chains. We focus on evidence emerging for how these mutations perturb antibody interactions with antigens and Fc receptors that are critical for function, as well as the influence this might have on the use of antibodies as therapeutics and reagents.
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Affiliation(s)
| | - William Kelton
- Te Huataki Waiora School of Health, The University of Waikato, Hamilton, New Zealand
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217
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A minority of T cells recognizing tumor-associated antigens presented in self-HLA can provoke antitumor reactivity. Blood 2020; 136:455-467. [DOI: 10.1182/blood.2019004443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/14/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
Tumor-associated antigens (TAAs) are monomorphic self-antigens that are proposed as targets for immunotherapeutic approaches to treat malignancies. We investigated whether T cells with sufficient avidity to recognize naturally overexpressed self-antigens in the context of self-HLA can be found in the T-cell repertoire of healthy donors. Minor histocompatibility antigen (MiHA)-specific T cells were used as a model, as the influence of thymic selection on the T-cell repertoire directed against MiHA can be studied in both self (MiHApos donors) and non-self (MiHAneg donors) backgrounds. T-cell clones directed against the HLA*02:01-restricted MiHA HA-1H were isolated from HA-1Hneg/HLA-A*02:01pos and HA-1Hpos/HLA-A*02:01pos donors. Of the 16 unique HA-1H–specific T-cell clones, five T-cell clones derived from HA-1Hneg/HLA-A*02:01pos donors and one T-cell clone derived from an HA-1Hpos/HLA-A*02:01pos donor showed reactivity against HA-1Hpos target cells. In addition, in total, 663 T-cell clones (containing at least 91 unique clones expressing different T-cell receptors) directed against HLA*02:01-restricted peptides of TAA WT1-RMF, RHAMM-ILS, proteinase-3-VLQ, PRAME-VLD, and NY-eso-1-SLL were isolated from HLA-A*02:01pos donors. Only 3 PRAME-VLD–specific and one NY-eso-1-SLL–specific T-cell clone provoked interferon-γ production and/or cytolysis upon stimulation with HLA-A*02:01pos malignant cell lines (but not primary malignant samples) naturally overexpressing the TAA. These results show that self-HLA–restricted T cells specific for self-antigens such as MiHA in MiHApos donors and TAAs are present in peripheral blood of healthy individuals. However, clinical efficacy would require highly effective in vivo priming by peptide vaccination in the presence of proper adjuvants or in vitro expansion of the low numbers of self-antigen–specific T cells of sufficient avidity to recognize endogenously processed antigen.
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218
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Meunier S, de Bourayne M, Hamze M, Azam A, Correia E, Menier C, Maillère B. Specificity of the T Cell Response to Protein Biopharmaceuticals. Front Immunol 2020; 11:1550. [PMID: 32793213 PMCID: PMC7387651 DOI: 10.3389/fimmu.2020.01550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022] Open
Abstract
The anti-drug antibody (ADA) response is an undesired humoral response raised against protein biopharmaceuticals (BPs) which can dramatically disturb their therapeutic properties. One particularity of the ADA response resides in the nature of the immunogens, which are usually human(ized) proteins and are therefore expected to be tolerated. CD4 T cells initiate, maintain and regulate the ADA response and are therefore key players of this immune response. Over the last decade, advances have been made in characterizing the T cell responses developed by patients treated with BPs. Epitope specificity and phenotypes of BP-specific T cells have been reported and highlight the effector and regulatory roles of T cells in the ADA response. BP-specific T cell responses are assessed in healthy subjects to anticipate the immunogenicity of BP prior to their testing in clinical trials. Immunogenicity prediction, also called preclinical immunogenicity assessment, aims at identifying immunogenic BPs and immunogenic BP sequences before any BP injection in humans. All of the approaches that have been developed to date rely on the detection of BP-specific T cells in donors who have never been exposed to BPs. The number of BP-specific T cells circulating in the blood of these donors is therefore limited. T cell assays using cells collected from healthy donors might reveal the weak tolerance induced by BPs, whose endogenous form is expressed at a low level. These BPs have a complete human sequence, but the level of their endogenous form appears insufficient to promote the negative selection of autoreactive T cell clones. Multiple T cell epitopes have also been identified in therapeutic antibodies and some other BPs. The pattern of identified T cell epitopes differs across the antibodies, notwithstanding their humanized, human or chimeric nature. However, in all antibodies, the non-germline amino acid sequences mainly found in the CDRs appear to be the main driver of immunogenicity, provided they can be presented by HLA class II molecules. Considering the fact that the BP field is expanding to include new formats and gene and cell therapies, we face new challenges in understanding and mastering the immunogenicity of new biological products.
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Affiliation(s)
- Sylvain Meunier
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Marie de Bourayne
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Moustafa Hamze
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Aurélien Azam
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Evelyne Correia
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Catherine Menier
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Bernard Maillère
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
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219
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Soto C, Finn JA, Willis JR, Day SB, Sinkovits RS, Jones T, Schmitz S, Meiler J, Branchizio A, Crowe JE. PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST. BMC Bioinformatics 2020; 21:314. [PMID: 32677886 PMCID: PMC7364545 DOI: 10.1186/s12859-020-03649-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/09/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Recent advances in DNA sequencing technologies have enabled significant leaps in capacity to generate large volumes of DNA sequence data, which has spurred a rapid growth in the use of bioinformatics as a means of interrogating antibody variable gene repertoires. Common tools used for annotation of antibody sequences are often limited in functionality, modularity and usability. RESULTS We have developed PyIR, a Python wrapper and library for IgBLAST, which offers a minimal setup CLI and API, FASTQ support, file chunking for large sequence files, JSON and Python dictionary output, and built-in sequence filtering. CONCLUSIONS PyIR offers improved processing speed over multithreaded IgBLAST (version 1.14) when spawning more than 16 processes on a single computer system. Its customizable filtering and data encapsulation allow it to be adapted to a wide range of computing environments. The API allows for IgBLAST to be used in customized bioinformatics workflows.
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Affiliation(s)
- Cinque Soto
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jessica A Finn
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Jordan R Willis
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Samuel B Day
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Robert S Sinkovits
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Taylor Jones
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37212, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37212, USA
| | - Andre Branchizio
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA.
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220
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Stutz C, Blein S. A single mutation increases heavy-chain heterodimer assembly of bispecific antibodies by inducing structural disorder in one homodimer species. J Biol Chem 2020; 295:9392-9408. [PMID: 32404368 PMCID: PMC7363136 DOI: 10.1074/jbc.ra119.012335] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/08/2020] [Indexed: 12/31/2022] Open
Abstract
We previously reported efficient heavy-chain assembly of heterodimeric bispecific antibodies by exchanging the interdomain protein interface of the human IgG1 CH3 dimer with the protein interface of the constant α and β domains of the human T-cell receptor, a technology known as bispecific engagement by antibodies based on the T-cell receptor (BEAT). Efficient heterodimerization in mammalian cell transient transfections was observed, but levels were influenced by the nature of the binding arms, particularly in the Fab-scFv-Fc format. In this study, we report a single amino acid change that significantly and consistently improved the heterodimerization rate of this format (≥95%) by inducing partial disorder in one homodimer species without affecting the heterodimer. Correct folding and assembly of the heterodimer were confirmed by the high-resolution (1.88-1.98 Å) crystal structure presented here. Thermal stability and 1-anilinonaphthalene-8-sulfonic acid-binding experiments, comparing original BEAT, mutated BEAT, and "knobs-into-holes" interfaces, suggested a cooperative assembly process of heavy chains in heterodimers. The observed gain in stability of the interfaces could be classified in the following rank order: mutated BEAT > original BEAT > knobs-into-holes. We therefore propose that the superior cooperativity found in BEAT interfaces is the key driver of their greater performance. Furthermore, we show how the mutated BEAT interface can be exploited for the routine preparation of drug candidates, with minimal risk of homodimer contamination using a single Protein A chromatography step.
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Affiliation(s)
- Cian Stutz
- Department of Antibody Engineering, Ichnos Sciences S.A., Biopôle Lausanne-Epalinges, Epalinges, Switzerland
| | - Stanislas Blein
- Department of Antibody Engineering, Ichnos Sciences S.A., Biopôle Lausanne-Epalinges, Epalinges, Switzerland
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221
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Souter MNT, Loh L, Li S, Meehan BS, Gherardin NA, Godfrey DI, Rossjohn J, Fairlie DP, Kedzierska K, Pellicci DG, Chen Z, Kjer-Nielsen L, Corbett AJ, McCluskey J, Eckle SBG. Characterization of Human Mucosal-associated Invariant T (MAIT) Cells. ACTA ACUST UNITED AC 2020; 127:e90. [PMID: 31763790 DOI: 10.1002/cpim.90] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are a subset of unconventional T cells restricted by the major histocompatibility complex (MHC) class I-like molecule MHC-related protein 1 (MR1). MAIT cells are found throughout the body, especially in human blood and liver. Unlike conventional T cells, which are stimulated by peptide antigens presented by MHC molecules, MAIT cells recognize metabolite antigens derived from an intermediate in the microbial biosynthesis of riboflavin. MAIT cells mediate protective immunity to infections by riboflavin-producing microbes via the production of cytokines and cytotoxicity. The discovery of stimulating MAIT cell antigens allowed for the development of an analytical tool, the MR1 tetramer, that binds specifically to the MAIT T cell receptor (TCR) and is becoming the gold standard for identification of MAIT cells by flow cytometry. This article describes protocols to characterize the phenotype of human MAIT cells in blood and tissues by flow cytometry using fluorescently labeled human MR1 tetramers alongside antibodies specific for MAIT cell markers. © 2019 by John Wiley & Sons, Inc. The main protocols include: Basic Protocol 1: Determining the frequency and steady-state surface phenotype of human MAIT cells Basic Protocol 2: Determining the activation phenotype of human MAIT cells in blood Basic Protocol 3: Characterizing MAIT cell TCRs using TCR-positive reporter cell lines Alternate protocols are provided for determining the absolute number, transcription factor phenotype, and TCR usage of human MAIT cells; and determining activation phenotype by staining for intracellular markers, measuring secreted cytokines, and measuring fluorescent dye dilution due to proliferation. Additional methods are provided for determining the capacity of MAIT cells to produce cytokine independently of antigen using plate-bound or bead-immobilized CD3/CD28 stimulation; and determining the MR1-Ag dependence of MAIT cell activation using MR1-blocking antibody or competitive inhibition. For TCR-positive reporter cell lines, methods are also provided for evaluating the MAIT TCR-mediated MR1-Ag response, determining the capacity of the reporter lines to produce cytokine independently of antigen, determining the MR1-Ag dependence of the reporter lines, and evaluating the MR1-Ag response of the reporter lines using IL-2 secretion. Support Protocols describe the preparation of PBMCs from human blood, the preparation of single-cell suspensions from tissue, the isolation of MAIT cells by FACS and MACS, cloning MAIT TCRα and β chain genes and MR1 genes for transduction, generating stably and transiently transfected cells lines, generating a stable MR1 knockout antigen-presenting cell line, and generating monocyte-derived dendritic cells.
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Affiliation(s)
- Michael N T Souter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Liyen Loh
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Bronwyn S Meehan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Wales, United Kingdom
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Parkville, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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222
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Foglierini M, Pappas L, Lanzavecchia A, Corti D, Perez L. AncesTree: An interactive immunoglobulin lineage tree visualizer. PLoS Comput Biol 2020; 16:e1007731. [PMID: 32649725 PMCID: PMC7375605 DOI: 10.1371/journal.pcbi.1007731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 07/22/2020] [Accepted: 06/14/2020] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing of human immunoglobulin genes allows analysis of antibody repertoires and the reconstruction of clonal lineage evolution. The study of antibodies (Abs) affinity maturation is of specific interest to understand the generation of Abs with high affinity or broadly neutralizing activities. Moreover, phylogenic analysis enables the identification of the key somatic mutations required to achieve optimal antigen binding. The Immcantation framework provides a start-to-finish set of analytical methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) data. Furthermore, Immcantation's Change-O package has developed IgPhyML, an algorithm designed to build specifically immunoglobulin (Ig) phylogenic trees. Meanwhile Phylip, an algorithm that has been originally developed for applications in ecology and macroevolution, can also be used for the phylogenic reconstruction of antibodies maturation pathway. To complement Ig lineages made by IgPhyML or Dnaml (Phylip), we developed AncesTree, a graphic user interface (GUI) that aims to give researchers the opportunity to interactively explore antibodies clonal evolution. AncesTree displays interactive immunoglobulins phylogenic tree, Ig related mutations and sequence alignments using additional information coming from specialized antibody tools. The GUI is a Java standalone application allowing interaction with Ig tree that can run under Windows, Linux and Mac OS.
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Affiliation(s)
- Mathilde Foglierini
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Leontios Pappas
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Laurent Perez
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
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223
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Tu Z, Huang X, Fu J, Hu N, Zheng W, Li Y, Zhang Y. Landscape of variable domain of heavy-chain-only antibody repertoire from alpaca. Immunology 2020; 161:53-65. [PMID: 32506493 DOI: 10.1111/imm.13224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/05/2023] Open
Abstract
Heavy-chain-only antibodies (HCAbs), which are devoid of light chains, have been found naturally occurring in various species including camelids and cartilaginous fish. Because of their high thermostability, refoldability and capacity for cell permeation, the variable regions of the heavy chain of HCAbs (VHHs) have been widely used in diagnosis, bio-imaging, food safety and therapeutics. Most immunogenetic and functional studies of HCAbs are based on case studies or a limited number of low-throughput sequencing data. A complete picture derived from more abundant high-throughput sequencing (HTS) data can help us gain deeper insights. We cloned and sequenced the full-length coding region of VHHs in Alpaca (Vicugna pacos) via HTS in this study. A new pipeline was developed to conduct an in-depth analysis of the HCAb repertoires. Various critical features, including the length distribution of complementarity-determining region 3 (CDR3), V(D)J usage, VJ pairing, germline-specific mutation rate and germline-specific scoring profiles (GSSPs), were systematically characterized. The quantitative data show that V(D)J usage and VHH recombination are highly biased. Interestingly, we found that the average CDR3 length of classical VHHs is longer than that of non-classical ones, whereas the mutation rates are similar in both kinds of VHHs. Finally, GSSPs were built to quantitatively describe and compare sequences that originate from each VJ pair. Overall, this study presents a comprehensive landscape of the HCAb repertoire, which can provide useful guidance for the modeling of somatic hypermutation and the design of novel functional VHHs or VHH repertoires via evolutionary profiles.
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Affiliation(s)
- Zhui Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jinheng Fu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, China
| | - Na Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China.,Maternal and Child Medical Research Institute, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yanping Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China.,Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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224
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Mandric I, Rotman J, Yang HT, Strauli N, Montoya DJ, Van Der Wey W, Ronas JR, Statz B, Yao D, Petrova V, Zelikovsky A, Spreafico R, Shifman S, Zaitlen N, Rossetti M, Ansel KM, Eskin E, Mangul S. Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nat Commun 2020; 11:3126. [PMID: 32561710 PMCID: PMC7305308 DOI: 10.1038/s41467-020-16857-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 05/24/2020] [Indexed: 11/09/2022] Open
Abstract
Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid and accurate profiling of the Ig repertoire, including the complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. Using ImReP and GTEx v6 data, we generate a collection of 3.6 million Ig sequences, termed the atlas of immunoglobulin repertoires (TAIR), across a broad range of tissue types that often do not have reported Ig repertoires information. Moreover, the flow of Ig clonotypes and inter-tissue repertoire similarities across immune-related tissues are also evaluated. In summary, TAIR is one of the largest collections of CDR3 sequences and tissue types, and should serve as an important resource for studying immunological diseases. Information on immune receptor repertoire provides important insights on disease progression and therapy development, but can be expensive and time-consuming to obtain. Here the authors report ImReP, a computational method that can extract detailed immune repertoire information from existing tissue-specific RNA sequencing data.
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Affiliation(s)
- Igor Mandric
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Jeremy Rotman
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.,Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA
| | - Harry Taegyun Yang
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.,Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095-1570, USA
| | - Nicolas Strauli
- Biomedical Sciences Graduate Program, University of California, San Francisco, 1675 Owens Street, Suite 310, San Francisco, CA, 94143-0523, USA
| | - Dennis J Montoya
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - William Van Der Wey
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Jiem R Ronas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 609 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Benjamin Statz
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Douglas Yao
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.,Program in Bioinformatics and Integrative Genomics, Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, MA, 02115, USA
| | - Velislava Petrova
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, 33 Gilmer Street SE, Atlanta, GA, 30303, USA.,The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Noah Zaitlen
- Department of Medicine, University of California, San Francisco, 533 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Maura Rossetti
- Immunogenetics Center, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 1000 Veteran Avenue, Los Angeles, CA, 90095-1652, USA
| | - K Mark Ansel
- Sandler Asthma Basic Research Center, Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143-0414, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA, 90095, USA.,Department of Computational Medicine, David Geffen School of Medicine at UCLA, 73-235 CHS, Los Angeles, CA, 90095, USA
| | - Serghei Mangul
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA. .,Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA. .,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
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225
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Wong J, Tai CM, Hurt AC, Tan HX, Kent SJ, Wheatley AK. Sequencing B cell receptors from ferrets (Mustela putorius furo). PLoS One 2020; 15:e0233794. [PMID: 32470013 PMCID: PMC7259655 DOI: 10.1371/journal.pone.0233794] [Citation(s) in RCA: 4] [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: 02/26/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
The domestic ferret (Mustela putorius furo) provides a critical animal model to study human respiratory diseases. However immunological insights are restricted due to a lack of ferret-specific reagents and limited genetic information about ferret B and T cell receptors. Here, variable, diversity and joining genes within the ferret kappa, lambda and heavy chain immunoglobulin loci were annotated using available genomic information. A multiplex PCR approach was derived that facilitated the recovery of paired heavy and light chain immunoglobulin sequences from single sorted ferret B cells, allowing validation of predicted germline gene sequences and the identification of putative novel germlines. Eukaryotic expression vectors were developed that enabled the generation of recombinant ferret monoclonal antibodies. This work advances the ferret as an informative immunological model for viral diseases by allowing the in-depth interrogation of antibody-based immunity.
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Affiliation(s)
- Julius Wong
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Celeste M. Tai
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Aeron C. Hurt
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- ARC Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AKW); (SJK)
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- ARC Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AKW); (SJK)
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226
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Barnes CO, West AP, Huey-Tubman KE, Hoffmann MA, Sharaf NG, Hoffman PR, Koranda N, Gristick HB, Gaebler C, Muecksch F, Cetrulo Lorenzi JC, Finkin S, Hagglof T, Hurley A, Millard KG, Weisblum Y, Schmidt F, Hatziioannou T, Bieniasz PD, Caskey M, Robbiani DF, Nussenzweig MC, Bjorkman PJ. Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.28.121533. [PMID: 32577645 PMCID: PMC7302198 DOI: 10.1101/2020.05.28.121533] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their degree of focus on RBD epitopes, recognition of SARS-CoV, MERS-CoV, and mild coronaviruses, and how avidity effects contributed to increased binding/neutralization of IgGs over Fabs. Electron microscopy reconstructions of polyclonal plasma Fab-spike complexes showed recognition of both S1A and RBD epitopes. A 3.4Å cryo-EM structure of a neutralizing monoclonal Fab-S complex revealed an epitope that blocks ACE2 receptor-binding on "up" RBDs. Modeling suggested that IgGs targeting these sites have different potentials for inter-spike crosslinking on viruses and would not be greatly affected by identified SARS-CoV-2 spike mutations. These studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.
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Affiliation(s)
- Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Magnus A.G. Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Naima G. Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pauline R. Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B. Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thomas Hagglof
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Arlene Hurley
- Hospital Program Direction, The Rockefeller University, New York, NY 10065, USA
| | - Katrina G. Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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Lima WC, Gasteiger E, Marcatili P, Duek P, Bairoch A, Cosson P. The ABCD database: a repository for chemically defined antibodies. Nucleic Acids Res 2020; 48:D261-D264. [PMID: 31410491 PMCID: PMC6943046 DOI: 10.1093/nar/gkz714] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022] Open
Abstract
The ABCD (for AntiBodies Chemically Defined) database is a repository of sequenced antibodies, integrating curated information about the antibody and its antigen with cross-links to standardized databases of chemical and protein entities. It is freely available to the academic community, accessible through the ExPASy server (https://web.expasy.org/abcd/). The ABCD database aims at helping to improve reproducibility in academic research by providing a unique, unambiguous identifier associated to each antibody sequence. It also allows to determine rapidly if a sequenced antibody is available for a given antigen.
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Affiliation(s)
- Wanessa C Lima
- Geneva Antibody Facility, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Elisabeth Gasteiger
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CH-1211 Geneva, Switzerland
| | - Paolo Marcatili
- Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Paula Duek
- CALIPHO Group, Faculty of Medicine, University of Geneva and SIB Swiss Institute of Bioinformatics, CH-1211 Geneva, Switzerland
| | - Amos Bairoch
- CALIPHO Group, Faculty of Medicine, University of Geneva and SIB Swiss Institute of Bioinformatics, CH-1211 Geneva, Switzerland
| | - Pierre Cosson
- Geneva Antibody Facility, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
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228
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Gupta SK, Viswanatha DS, Patel KP. Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing. Front Cell Dev Biol 2020; 8:357. [PMID: 32509784 PMCID: PMC7248390 DOI: 10.3389/fcell.2020.00357] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/21/2020] [Indexed: 01/22/2023] Open
Abstract
Somatic hypermutation (SHM) status provides an important prognostic indicator for chronic lymphocytic leukemia (CLL), a very common type of mature B-cell leukemia. Owing to the adverse prognosis associated with an unmutated immunoglobulin heavy chain variable (IGHV) status, SHM testing is performed as a standard of care in CLL. Conventionally, SHM testing has been performed using labor intensive and primarily analog Sanger sequencing method following PCR amplification of the clonal immunoglobulin heavy chain gene rearrangements in CLL cells. In comparison, recent availability of next generation sequencing (NGS) allows more versatile detection and direct identification of clonal immunoglobulin gene rearrangements in neoplastic B-cell populations. The ability to identify specific clonal IGHV signature(s) in both baseline (diagnostic) and post-treatment settings enables unique clinical applications of NGS such as determination of SHM status, minimal residual disease (MRD) monitoring, clonal heterogeneity and B cell receptor IG stereotypy. We provide a review of current practices and recommendations for SHM determination using NGS including examples of difficult cases.
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Affiliation(s)
- Sanjeev Kumar Gupta
- Laboratory Oncology Unit, Dr. B.R.A IRCH, All India Institute of Medical Sciences, New Delhi, New Delhi, India
| | | | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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229
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Lees W, Busse CE, Corcoran M, Ohlin M, Scheepers C, Matsen FA, Yaari G, Watson CT, Collins A, Shepherd AJ. OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Res 2020; 48:D964-D970. [PMID: 31566225 PMCID: PMC6943078 DOI: 10.1093/nar/gkz822] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/05/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.
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Affiliation(s)
- William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Box 280, 171 77 Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, S-223 81 Lund, Sweden
| | - Cathrine Scheepers
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringam, Gauteng 2131, South Africa.,Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Frederick A Matsen
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | | | - Andrew Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Adrian J Shepherd
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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230
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Apgar JR, Tam ASP, Sorm R, Moesta S, King AC, Yang H, Kelleher K, Murphy D, D’Antona AM, Yan G, Zhong X, Rodriguez L, Ma W, Ferguson DE, Carven GJ, Bennett EM, Lin L. Modeling and mitigation of high-concentration antibody viscosity through structure-based computer-aided protein design. PLoS One 2020; 15:e0232713. [PMID: 32379792 PMCID: PMC7205207 DOI: 10.1371/journal.pone.0232713] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/20/2020] [Indexed: 01/07/2023] Open
Abstract
For an antibody to be a successful therapeutic many competing factors require optimization, including binding affinity, biophysical characteristics, and immunogenicity risk. Additional constraints may arise from the need to formulate antibodies at high concentrations (>150 mg/ml) to enable subcutaneous dosing with reasonable volume (ideally <1.0 mL). Unfortunately, antibodies at high concentrations may exhibit high viscosities that place impractical constraints (such as multiple injections or large needle diameters) on delivery and impede efficient manufacturing. Here we describe the optimization of an anti-PDGF-BB antibody to reduce viscosity, enabling an increase in the formulated concentration from 80 mg/ml to greater than 160 mg/ml, while maintaining the binding affinity. We performed two rounds of structure guided rational design to optimize the surface electrostatic properties. Analysis of this set demonstrated that a net-positive charge change, and disruption of negative charge patches were associated with decreased viscosity, but the effect was greatly dependent on the local surface environment. Our work here provides a comprehensive study exploring a wide sampling of charge-changes in the Fv and CDR regions along with targeting multiple negative charge patches. In total, we generated viscosity measurements for 40 unique antibody variants with full sequence information which provides a significantly larger and more complete dataset than has previously been reported.
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Affiliation(s)
- James R. Apgar
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Amy S. P. Tam
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Rhady Sorm
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Sybille Moesta
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Amy C. King
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Han Yang
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Kerry Kelleher
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Denise Murphy
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Aaron M. D’Antona
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Guoying Yan
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Xiaotian Zhong
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Linette Rodriguez
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Weijun Ma
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Darren E. Ferguson
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Gregory J. Carven
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Eric M. Bennett
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
| | - Laura Lin
- BioMedicine Design, Pfizer Inc, Cambridge, Massachusetts, United States of America
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231
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Pégorier P, Bertignac M, Chentli I, Nguefack Ngoune V, Folch G, Jabado-Michaloud J, Hadi-Saljoqi S, Giudicelli V, Duroux P, Lefranc MP, Kossida S. IMGT® Biocuration and Comparative Study of the T Cell Receptor Beta Locus of Veterinary Species Based on Homo sapiens TRB. Front Immunol 2020; 11:821. [PMID: 32431713 PMCID: PMC7216736 DOI: 10.3389/fimmu.2020.00821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics information system® is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and proteins of the IgSF and MhSF superfamilies. T cell receptors are divided into two groups, αβ and γδ TR, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRβ locus (TRB) was recently described and annotated by IMGT® biocurators for several veterinary species, i.e., cat (Felis catus), dog (Canis lupus familiaris), ferret (Mustela putorius furo), pig (Sus scrofa), rabbit (Oryctolagus cuniculus), rhesus monkey (Macaca mulatta), and sheep (Ovis aries). The aim of the present study is to compare the genes of the TRB locus among these different veterinary species based on Homo sapiens. The results reveal that there are similarities but also differences including the number of genes by subgroup which may demonstrate duplications and/or deletions during evolution.
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Affiliation(s)
- Perrine Pégorier
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Morgane Bertignac
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Imène Chentli
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Viviane Nguefack Ngoune
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Géraldine Folch
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Joumana Jabado-Michaloud
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Saida Hadi-Saljoqi
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Véronique Giudicelli
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Patrice Duroux
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
| | - Sofia Kossida
- IMGT®, The International ImMunoGeneTics Information System®, Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Montpellier, France
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232
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Collins CM, Scharer CD, Murphy TJ, Boss JM, Speck SH. Murine gammaherpesvirus infection is skewed toward Igλ+ B cells expressing a specific heavy chain V-segment. PLoS Pathog 2020; 16:e1008438. [PMID: 32353066 PMCID: PMC7217478 DOI: 10.1371/journal.ppat.1008438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/12/2020] [Accepted: 02/27/2020] [Indexed: 12/24/2022] Open
Abstract
One of the defining characteristics of the B cell receptor (BCR) is the extensive diversity in the repertoire of immunoglobulin genes that make up the BCR, resulting in broad range of specificity. Gammaherpesviruses are B lymphotropic viruses that establish life-long infection in B cells, and although the B cell receptor plays a central role in B cell biology, very little is known about the immunoglobulin repertoire of gammaherpesvirus infected cells. To begin to characterize the Ig genes expressed by murine gammaherpesvirus 68 (MHV68) infected cells, we utilized single cell sorting to sequence and clone the Ig variable regions of infected germinal center (GC) B cells and plasma cells. We show that MHV68 infection is biased towards cells that express the Igλ light chain along with a single heavy chain variable gene, IGHV10-1*01. This population arises through clonal expansion but is not viral antigen specific. Furthermore, we show that class-switching in MHV68 infected cells differs from that of uninfected cells. Fewer infected GC B cells are class-switched compared to uninfected GC B cells, while more infected plasma cells are class-switched compared to uninfected plasma cells. Additionally, although they are germinal center derived, the majority of class switched plasma cells display no somatic hypermutation regardless of infection status. Taken together, these data indicate that selection of infected B cells with a specific BCR, as well as virus mediated manipulation of class switching and somatic hypermutation, are critical aspects in establishing life-long gammaherpesvirus infection.
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Affiliation(s)
- Christopher M. Collins
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Christopher D. Scharer
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Thomas J. Murphy
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jeremy M. Boss
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Samuel H. Speck
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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233
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Li X, Van Deventer JA, Hassoun S. ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning. PLoS Comput Biol 2020; 16:e1007779. [PMID: 32339164 PMCID: PMC7205315 DOI: 10.1371/journal.pcbi.1007779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/07/2020] [Accepted: 03/08/2020] [Indexed: 11/18/2022] Open
Abstract
Antibodies are capable of potently and specifically binding individual antigens and, in some cases, disrupting their functions. The key challenge in generating antibody-based inhibitors is the lack of fundamental information relating sequences of antibodies to their unique properties as inhibitors. We develop a pipeline, Antibody Sequence Analysis Pipeline using Statistical testing and Machine Learning (ASAP-SML), to identify features that distinguish one set of antibody sequences from antibody sequences in a reference set. The pipeline extracts feature fingerprints from sequences. The fingerprints represent germline, CDR canonical structure, isoelectric point and frequent positional motifs. Machine learning and statistical significance testing techniques are applied to antibody sequences and extracted feature fingerprints to identify distinguishing feature values and combinations thereof. To demonstrate how it works, we applied the pipeline on sets of antibody sequences known to bind or inhibit the activities of matrix metalloproteinases (MMPs), a family of zinc-dependent enzymes that promote cancer progression and undesired inflammation under pathological conditions, against reference datasets that do not bind or inhibit MMPs. ASAP-SML identifies features and combinations of feature values found in the MMP-targeting sets that are distinct from those in the reference sets.
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Affiliation(s)
- Xinmeng Li
- Department of Computer Science, Tufts University, Massachusetts, United States of America
| | - James A. Van Deventer
- Department of Chemical and Biological Engineering, Tufts University, Massachusetts, United States of America
- Department of Biomedical Engineering, Tufts University, Massachusetts, United States of America
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Massachusetts, United States of America
- Department of Chemical and Biological Engineering, Tufts University, Massachusetts, United States of America
- * E-mail:
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234
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Sng XYX, Li J, Zareie P, Assmus LM, Lee JKC, Jones CM, Turner SJ, Daley SR, Quinn KM, La Gruta NL. The Impact of MHC Class I Dose on Development and Maintenance of the Polyclonal Naive CD8+ T Cell Repertoire. THE JOURNAL OF IMMUNOLOGY 2020; 204:3108-3116. [DOI: 10.4049/jimmunol.2000081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/02/2020] [Indexed: 12/14/2022]
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235
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Jia M, Liberatore RA, Guo Y, Chan KW, Pan R, Lu H, Waltari E, Mittler E, Chandran K, Finzi A, Kaufmann DE, Seaman MS, Ho DD, Shapiro L, Sheng Z, Kong XP, Bieniasz PD, Wu X. VSV-Displayed HIV-1 Envelope Identifies Broadly Neutralizing Antibodies Class-Switched to IgG and IgA. Cell Host Microbe 2020; 27:963-975.e5. [PMID: 32315598 PMCID: PMC7294236 DOI: 10.1016/j.chom.2020.03.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/27/2020] [Accepted: 03/26/2020] [Indexed: 12/25/2022]
Abstract
The HIV-1 envelope (Env) undergoes conformational changes during infection. Broadly neutralizing antibodies (bNAbs) are typically isolated by using soluble Env trimers, which do not capture all Env states. To address these limitations, we devised a vesicular stomatitis virus (VSV)-based probe to display membrane-embedded Env trimers and isolated five bNAbs from two chronically infected donors, M4008 and M1214. Donor B cell receptor (BCR) repertoires identified two bNAb lineages, M4008_N1 and M1214_N1, that class-switched to immunoglobulin G (IgG) and IgA. Variants of these bNAbs reconstituted as IgA demonstrated broadly neutralizing activity, and the IgA fraction of M1214 plasma conferred neutralization. M4008_N1 epitope mapping revealed a glycan-independent V3 epitope conferring tier 2 virus neutralization. A 4.86-Å-resolution cryogenic electron microscopy (cryo-EM) structure of M1214_N1 complexed with CH505 SOSIP revealed another elongated epitope, the V2V5 corridor, extending from V2 to V5. Overall, the VSVENV probe identified bNAb lineages with neutralizing IgG and IgA members targeting distinct sites of HIV-1 Env vulnerability. VSV-displayed HIV-1 envelope trimers identified five HIV-1 bNAbs BCR repertoires identified two bNAb lineages class-switched to both IgG and IgA The V3 crown-targeting bNAb M4008_N1 conferred tier 2 virus neutralization Cryo-EM structure of bNAb M1214_N1 with CH505 SOSIP defined a V2V5 corridor epitope
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Affiliation(s)
- Manxue Jia
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA
| | - Rachel A Liberatore
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10016, USA
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kun-Wei Chan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA
| | - Eric Waltari
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA
| | - Eva Mittler
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM and Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM and Université de Montréal, Montreal, QC H2X 0A9, Canada; Center for HIV-1/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA 92037, USA
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10016, USA
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA.
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236
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Sadighi Akha AA, Tschumper RC, Mills JR, Isham CR, Witty EE, Viswanatha DS, Dasari S, Snyder MR, Murray DL, Katzmann JA, Jelinek DF, Willrich MAV. A rare case of selective Igκ chain deficiency: Biologic and clinical implications. J Allergy Clin Immunol 2020; 146:1208-1210.e6. [PMID: 32278584 DOI: 10.1016/j.jaci.2020.02.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 10/24/2022]
Affiliation(s)
- Amir A Sadighi Akha
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn.
| | | | - John R Mills
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - Crescent R Isham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - Elizabeth E Witty
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - David S Viswanatha
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - Surendra Dasari
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - Melissa R Snyder
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - David L Murray
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - Jerry A Katzmann
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | | | - Maria A V Willrich
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn.
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237
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Hammer SE, Leopold M, Prawits LM, Mair KH, Schwartz JC, Hammond JA, Ravens S, Gerner W, Saalmüller A. Development of a RACE-based RNA-Seq approach to characterize the T-cell receptor repertoire of porcine γδ T cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 105:103575. [PMID: 31846687 DOI: 10.1016/j.dci.2019.103575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Recent data suggest that porcine γδ T cells exhibit a similar degree of functional plasticity as human and murine γδ T cells. Due to the high frequency of TCR-γδ+ cells in blood and secondary lymphatic organs, the pig is an attractive model to study these cells, especially their combined features of the innate and the adaptive immune system. Using a 5' RACE-like approach, we translated a human/murine NGS library preparation strategy to capture full-length V-(D)-J TRG and TRD clonotypes in swine. After oligo(dT) primed conversion of input RNA, the cDNA population was enriched for full-length V(D)J TCR transcripts with porcine-specific primers including Illumina adaptor sequences as overhangs for Illumina MiSeq analysis. After quality control and processing by FastQC and ea-utils, porcine TRG and TRD sequences were mapped against the human IMGT reference directory. Porcine blood-derived CD2+ and CD2‾ TCR-γδ+ cells exhibited two distinct clonotypes Vγ11JγP1 (74.6%) and Vγ10JγP1 (57.7%), respectively. Despite the high TCR-δ diversity among CD2+ cells (39 clonotypes), both subsets shared the same abundant Vδ1DδxJδ4 clonotype at approximately identically frequencies (CD2+: 31.2%; CD2‾: 37.0%). The flexible nature of this approach will facilitate the assessment of organ-specific phenotypes of γδ T cell subsets alongside with their respective TCR diversity at single cell resolution.
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Affiliation(s)
- Sabine E Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria.
| | - Melanie Leopold
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Lisa-Maria Prawits
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Kerstin H Mair
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria; CD Laboratory for an Optimized Prediction of Vaccination Success in Pigs, Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | | | | | - Sarina Ravens
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Wilhelm Gerner
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria; CD Laboratory for an Optimized Prediction of Vaccination Success in Pigs, Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Armin Saalmüller
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
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238
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Ford M, Haghshenas E, Watson CT, Sahinalp SC. Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes Using Long Reads. iScience 2020; 23:100883. [PMID: 32109676 PMCID: PMC7044747 DOI: 10.1016/j.isci.2020.100883] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/08/2019] [Accepted: 01/29/2020] [Indexed: 11/22/2022] Open
Abstract
One of the remaining challenges to describing an individual's genetic variation lies in the highly heterogeneous and complex genomic regions that impede the use of classical reference-guided mapping and assembly approaches. Once such region is the Immunoglobulin heavy chain locus (IGH), which is critical for the development of antibodies and the adaptive immune system. We describe ImmunoTyper, the first PacBio-based genotyping and copy number calling tool specifically designed for IGH V genes (IGHV). We demonstrate that ImmunoTyper's multi-stage clustering and combinatorial optimization approach represents the most comprehensive IGHV genotyping approach published to date, through validation using gold-standard IGH reference sequence. This preliminary work establishes the feasibility of fine-grained genotype and copy number analysis using error-prone long reads in complex multi-gene loci and opens the door for in-depth investigation into IGHV heterogeneity using accessible and increasingly common whole-genome sequence.
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Affiliation(s)
- Michael Ford
- School of Computing Science, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Ehsan Haghshenas
- School of Computing Science, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville 40292, USA
| | - S Cenk Sahinalp
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD 20892, USA.
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239
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Ming L, Wang Z, Yi L, Batmunkh M, Liu T, Siren D, He J, Juramt N, Jambl T, Li Y, Jirimutu. Chromosome-level assembly of wild Bactrian camel genome reveals organization of immune gene loci. Mol Ecol Resour 2020; 20. [PMID: 32012460 DOI: 10.1111/1755-0998.13141] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 01/22/2023]
Abstract
Camelids are characterized by their unique adaptive immune system that exhibits the generation of homodimeric heavy-chain immunoglobulins, somatic hypermutation of T-cell receptors, and low genetic diversity of major histocompatibility complex (MHC) genes. However, short-read assemblies are typically highly fragmented in these gene loci owing to their repetitive and polymorphic nature. Here, we constructed a chromosome-level assembly of wild Bactrian camel genome based on high-coverage long-read sequencing and chromatin interaction mapping. The assembly with a contig N50 of 5.37 Mb and a scaffold N50 of 76.03 Mb, represents the most contiguous camelid genome to date. The genomic organization of immunoglobulin heavy-chain locus was similar between the wild Bactrian camel and alpaca, and genes encoding for conventional and heavy-chain antibodies were intermixed. The organizations of two immunoglobulin light-chain loci and four T cell receptor loci were also fully deciphered using the new assembly. Additionally, the complete classical MHC region was resolved into a single contig. The high-quality assembly presented here provides an essential reference for future investigations examining the camelid immune system.
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Affiliation(s)
- Liang Ming
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China.,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Zhen Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Yi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Mijiddorj Batmunkh
- Mongolian Wild Camel Protection Area, Ministry of Nature and Environment, Ulaanbaatar, Mongolia
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, China
| | - Dalai Siren
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China.,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Jing He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | | | - Tuyatsetseg Jambl
- College of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaater, Mongolia
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Jirimutu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China.,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
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240
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Salmonella Typhimurium biofilm disruption by a human antibody that binds a pan-amyloid epitope on curli. Nat Commun 2020; 11:1007. [PMID: 32081907 PMCID: PMC7035420 DOI: 10.1038/s41467-020-14685-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Bacterial biofilms, especially those associated with implanted medical devices, are difficult to eradicate. Curli amyloid fibers are important components of the biofilms formed by the Enterobacteriaceae family. Here, we show that a human monoclonal antibody with pan-amyloid-binding activity (mAb 3H3) can disrupt biofilms formed by Salmonella enterica serovar Typhimurium in vitro and in vivo. The antibody disrupts the biofilm structure, enhancing biofilm eradication by antibiotics and immune cells. In mice, 3H3 injections allow antibiotic-mediated clearance of catheter-associated S. Typhimurium biofilms. Thus, monoclonal antibodies that bind a pan-amyloid epitope have potential to prevent or eradicate bacterial biofilms. Curli amyloid fibers are important components of bacterial biofilms formed by E. coli and Salmonella. Here, Tursi et al. show that a human monoclonal antibody with pan-amyloid binding activity can disrupt biofilms formed by Salmonella Typhimurium in vitro and in vivo.
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241
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Enterovirus 71 Infection Shapes Host T Cell Receptor Repertoire and Presumably Expands VP1-Specific TCRβ CDR3 Cluster. Pathogens 2020; 9:pathogens9020121. [PMID: 32075096 PMCID: PMC7169398 DOI: 10.3390/pathogens9020121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 11/17/2022] Open
Abstract
Enterovirus 71 (EV71) has become an important public health problem in the Asia-Pacific region in the past decades. EV71 infection might cause neurological and psychiatric complications and even death. Although an EV71 vaccine has been currently approved, there is no effective therapy for treating EV71-infected patients. Virus infections have been reported to shape host T cell receptor (TCR) repertoire. Therefore, understanding of host TCR repertoire in EV71 infection could better the knowledge in viral pathogenesis and further benefit the anti-viral therapy development. In this study, we used a mouse-adapted EV71 (mEV71) model to observe changes of host TCR repertoire in an EV71-infected central nervous system. Neonate mice were infected with mEV71 and mouse brainstem TCRβ repertoires were explored. Here, we reported that mEV71 infection impacted host brainstem TCRβ repertoire, where mEV71 infection skewed TCRβ diversity, changed VJ combination usages, and further expanded specific TCRβ CDR3 clones. Using bioinformatics analysis and ligand-binding prediction, we speculated the expanded TCRβ CDR3 clone harboring CASSLGANSDYTF sequence was capable of binding cleaved EV71 VP1 peptides in concert with major histocompatibility complex (MHC) molecules. We observed that mEV71 infection shaped host TCRβ repertoire and presumably expanded VP1-specific TCRβ CDR3 in mEV71-infected mouse brainstem that integrated EV71 pathogenesis in central nervous system.
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242
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Singh G, Zarschler K, Hunoldt S, Martínez IIS, Ruehl CL, Matterna M, Bergmann R, Máthé D, Hegedüs N, Bachmann M, Comba P, Stephan H. Versatile Bispidine-Based Bifunctional Chelators for 64 Cu II -Labelling of Biomolecules. Chemistry 2020; 26:1989-2001. [PMID: 31755596 PMCID: PMC7028042 DOI: 10.1002/chem.201904654] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Indexed: 12/11/2022]
Abstract
Bifunctional chelators as parts of modular metal-based radiopharmaceuticals are responsible for stable complexation of the radiometal ion and for covalent linkage between the complex and the targeting vector. To avoid loss of complex stability, the bioconjugation strategy should not interfere with the radiometal chelation by occupying coordinating groups. The C9 position of the very stable CuII chelator 3,7-diazabicyclo[3.3.1]nonane (bispidine) is virtually predestined to introduce functional groups for facile bioconjugation as this functionalisation does not disturb the metal binding centre. We describe the preparation and characterisation of a set of novel bispidine derivatives equipped with suitable functional groups for diverse bioconjugation reactions, including common amine coupling strategies (bispidine-isothiocyanate) and the Cu-free strain-promoted alkyne-azide cycloaddition. We demonstrate their functionality and versatility in an exemplary way by conjugation to an antibody-based biomolecule and validate the obtained conjugate in vitro and in vivo.
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Affiliation(s)
- Garima Singh
- Helmholtz-Zentrum Dresden-RossendorfInstitute of Radiopharmaceutical Cancer ResearchBautzner Landstrasse 40001328DresdenGermany
| | - Kristof Zarschler
- Helmholtz-Zentrum Dresden-RossendorfInstitute of Radiopharmaceutical Cancer ResearchBautzner Landstrasse 40001328DresdenGermany
| | - Sebastian Hunoldt
- Helmholtz-Zentrum Dresden-RossendorfInstitute of Radiopharmaceutical Cancer ResearchBautzner Landstrasse 40001328DresdenGermany
| | - Irma Ivette Santana Martínez
- Helmholtz-Zentrum Dresden-RossendorfInstitute of Radiopharmaceutical Cancer ResearchBautzner Landstrasse 40001328DresdenGermany
| | - Carmen L. Ruehl
- Anorganisch-Chemisches Institut INF 270Universität Heidelberg69120HeidelbergGermany
| | - Madlen Matterna
- Helmholtz-Zentrum Dresden-RossendorfInstitute of Radiopharmaceutical Cancer ResearchBautzner Landstrasse 40001328DresdenGermany
| | - Ralf Bergmann
- Helmholtz-Zentrum Dresden-RossendorfInstitute of Radiopharmaceutical Cancer ResearchBautzner Landstrasse 40001328DresdenGermany
| | - Domokos Máthé
- Department of Biophysics and Radiation BiologySemmelweis University1094BudapestHungary
- CROmed Translational Research Centers Ltd.1047BudapestHungary
| | - Nikolett Hegedüs
- Department of Biophysics and Radiation BiologySemmelweis University1094BudapestHungary
| | - Michael Bachmann
- Helmholtz-Zentrum Dresden-RossendorfInstitute of Radiopharmaceutical Cancer ResearchBautzner Landstrasse 40001328DresdenGermany
| | - Peter Comba
- Anorganisch-Chemisches Institut INF 270Universität Heidelberg69120HeidelbergGermany
| | - Holger Stephan
- Helmholtz-Zentrum Dresden-RossendorfInstitute of Radiopharmaceutical Cancer ResearchBautzner Landstrasse 40001328DresdenGermany
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243
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Sarkizova S, Klaeger S, Le PM, Li LW, Oliveira G, Keshishian H, Hartigan CR, Zhang W, Braun DA, Ligon KL, Bachireddy P, Zervantonakis IK, Rosenbluth JM, Ouspenskaia T, Law T, Justesen S, Stevens J, Lane WJ, Eisenhaure T, Lan Zhang G, Clauser KR, Hacohen N, Carr SA, Wu CJ, Keskin DB. A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat Biotechnol 2020; 38:199-209. [PMID: 31844290 PMCID: PMC7008090 DOI: 10.1038/s41587-019-0322-9] [Citation(s) in RCA: 274] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022]
Abstract
Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.
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Affiliation(s)
- Siranush Sarkizova
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Phuong M Le
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Letitia W Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David A Braun
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Neuropathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Pavan Bachireddy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Travis Law
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jonathan Stevens
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - William J Lane
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Guang Lan Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Cancer Immunology, Massachusetts General Hospital, Boston, MA, USA.
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Derin B Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA.
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244
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Sellmann C, Pekar L, Bauer C, Ciesielski E, Krah S, Becker S, Toleikis L, Kügler J, Frenzel A, Valldorf B, Hust M, Zielonka S. A One-Step Process for the Construction of Phage Display scFv and VHH Libraries. Mol Biotechnol 2020; 62:228-239. [DOI: 10.1007/s12033-020-00236-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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245
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Roskin KM, Jackson KJL, Lee JY, Hoh RA, Joshi SA, Hwang KK, Bonsignori M, Pedroza-Pacheco I, Liao HX, Moody MA, Fire AZ, Borrow P, Haynes BF, Boyd SD. Aberrant B cell repertoire selection associated with HIV neutralizing antibody breadth. Nat Immunol 2020; 21:199-209. [PMID: 31959979 PMCID: PMC7223457 DOI: 10.1038/s41590-019-0581-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/12/2019] [Indexed: 11/09/2022]
Abstract
A goal of HIV vaccine development is to elicit antibodies with neutralizing breadth. Broadly neutralizing antibodies (bNAbs) to HIV often have unusual sequences with long heavy-chain complementarity-determining region loops, high somatic mutation rates and polyreactivity. A subset of HIV-infected individuals develops such antibodies, but it is unclear whether this reflects systematic differences in their antibody repertoires or is a consequence of rare stochastic events involving individual clones. We sequenced antibody heavy-chain repertoires in a large cohort of HIV-infected individuals with bNAb responses or no neutralization breadth and uninfected controls, identifying consistent features of bNAb repertoires, encompassing thousands of B cell clones per individual, with correlated T cell phenotypes. These repertoire features were not observed during chronic cytomegalovirus infection in an independent cohort. Our data indicate that the development of numerous B cell lineages with antibody features associated with autoreactivity may be a key aspect in the development of HIV neutralizing antibody breadth.
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Affiliation(s)
- Krishna M Roskin
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Katherine J L Jackson
- Department of Immunology, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Shilpa A Joshi
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kwan-Ki Hwang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - 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 School of Medicine, Durham, NC, USA. .,Duke Global Health Institute, Duke University School of Medicine, Durham, NC, USA.
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA, USA.
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246
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Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel KA, Karchin R. High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer Immunol Res 2019; 8:396-408. [PMID: 31871119 DOI: 10.1158/2326-6066.cir-19-0464] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 02/04/2023]
Abstract
Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins can be used to predict patient response to cancer immunotherapy. Current neoantigen predictors focus on in silico estimation of MHC binding affinity and are limited by low predictive value for actual peptide presentation, inadequate support for rare MHC alleles, and poor scalability to high-throughput data sets. To address these limitations, we developed MHCnuggets, a deep neural network method that predicts peptide-MHC binding. MHCnuggets can predict binding for common or rare alleles of MHC class I or II with a single neural network architecture. Using a long short-term memory network (LSTM), MHCnuggets accepts peptides of variable length and is faster than other methods. When compared with methods that integrate binding affinity and MHC-bound peptide (HLAp) data from mass spectrometry, MHCnuggets yields a 4-fold increase in positive predictive value on independent HLAp data. We applied MHCnuggets to 26 cancer types in The Cancer Genome Atlas, processing 26.3 million allele-peptide comparisons in under 2.3 hours, yielding 101,326 unique predicted immunogenic missense mutations (IMM). Predicted IMM hotspots occurred in 38 genes, including 24 driver genes. Predicted IMM load was significantly associated with increased immune cell infiltration (P < 2 × 10-16), including CD8+ T cells. Only 0.16% of predicted IMMs were observed in more than 2 patients, with 61.7% of these derived from driver mutations. Thus, we describe a method for neoantigen prediction and its performance characteristics and demonstrate its utility in data sets representing multiple human cancers.
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Affiliation(s)
- Xiaoshan M Shao
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Rohit Bhattacharya
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Justin Huang
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - I K Ashok Sivakumar
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland.,Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
| | - Collin Tokheim
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Lily Zheng
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dylan Hirsch
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Benjamin Kaminow
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ashton Omdahl
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Maria Bonsack
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Angelika B Riemer
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Victor E Velculescu
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kymberleigh A Pagel
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Rachel Karchin
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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247
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Busse CE, Jackson KJL, Watson CT, Collins AM. A Proposed New Nomenclature for the Immunoglobulin Genes of Mus musculus. Front Immunol 2019; 10:2961. [PMID: 31921202 PMCID: PMC6930147 DOI: 10.3389/fimmu.2019.02961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/03/2019] [Indexed: 01/26/2023] Open
Abstract
Mammalian immunoglobulin (IG) genes are found in complex loci that contain hundreds of highly similar pseudogenes, functional genes and repetitive elements, which has made their investigation particularly challenging. High-throughput sequencing has provided new avenues for the investigation of these loci, and has recently been applied to study the IG genes of important inbred mouse strains, revealing unexpected differences between their IG loci. This demonstrated that the structural differences are of such magnitude that they call into question the merits of the current mouse IG gene nomenclatures. Three nomenclatures for the mouse IG heavy chain locus (Igh) are presently in use, and they are all positional nomenclatures using the C57BL/6 genome reference sequence as their template. The continued use of these nomenclatures requires that genes of other inbred strains be confidently identified as allelic variants of C57BL/6 genes, but this is clearly impossible. The unusual breeding histories of inbred mouse strains mean that, regardless of the genetics of wild mice, no single ancestral origin for the IG loci exists for laboratory mice. Here we present a general discussion of the challenges this presents for any IG nomenclature. Furthermore, we describe principles that could be followed in the formulation of a solution to these challenges. Finally, we propose a non-positional nomenclature that accords with the guidelines of the International Mouse Nomenclature Committee, and outline strategies that can be adopted to meet the nomenclature challenges if three systems are to give way to a new one.
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Affiliation(s)
- Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Katherine J L Jackson
- Immunology Division, The Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Zhang H, Liu L, Zhang J, Chen J, Ye J, Shukla S, Qiao J, Zhan X, Chen H, Wu CJ, Fu YX, Li B. Investigation of Antigen-Specific T-Cell Receptor Clusters in Human Cancers. Clin Cancer Res 2019; 26:1359-1371. [PMID: 31831563 DOI: 10.1158/1078-0432.ccr-19-3249] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/26/2019] [Accepted: 12/05/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Cancer antigen-specific T cells are key components in antitumor immune response, yet their identification in the tumor microenvironment remains challenging, as most cancer antigens are unknown. Recent advance in immunology suggests that similar T-cell receptor (TCR) sequences can be clustered to infer shared antigen specificity. This study aims to identify antigen-specific TCRs from the tumor genomics sequencing data. EXPERIMENTAL DESIGN We used the TRUST (Tcr Repertoire Utilities for Solid Tissue) algorithm to assemble the TCR hypervariable CDR3 regions from 9,700 bulk tumor RNA-sequencing (RNA-seq) samples, and developed a computational method, iSMART, to group similar TCRs into antigen-specific clusters. Integrative analysis on the TCR clusters with multi-omics datasets was performed to profile cancer-associated T cells and to uncover novel cancer antigens. RESULTS Clustered TCRs are associated with signatures of T-cell activation after antigen encounter. We further elucidated the phenotypes of clustered T cells using single-cell RNA-seq data, which revealed a novel subset of tissue-resident memory T-cell population with elevated metabolic status. An exciting application of the TCR clusters is to identify novel cancer antigens, exemplified by our identification of a candidate cancer/testis gene, HSFX1, through integrated analysis of HLA alleles and genomics data. The target was further validated using vaccination of humanized HLA-A*02:01 mice and ELISpot assay. Finally, we showed that clustered tumor-infiltrating TCRs can differentiate patients with early-stage cancer from healthy donors, using blood TCR repertoire sequencing data, suggesting potential applications in noninvasive cancer detection. CONCLUSIONS Our analysis on the antigen-specific TCR clusters provides a unique resource for alternative antigen discovery and biomarker identification for cancer immunotherapies.
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Affiliation(s)
- Hongyi Zhang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas
| | - Longchao Liu
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Jian Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jiahui Chen
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas
| | - Sachet Shukla
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jian Qiao
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Xiaowei Zhan
- Department of Clinical Science, UT Southwestern Medical Center, Dallas, Texas
| | - Hao Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Catherine J Wu
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas.
| | - Bo Li
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas. .,Department of Immunology, UT Southwestern Medical Center, Dallas, Texas
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249
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Shteynberg DD, Deutsch EW, Campbell DS, Hoopmann MR, Kusebauch U, Lee D, Mendoza L, Midha MK, Sun Z, Whetton AD, Moritz RL. PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. J Proteome Res 2019; 18:4262-4272. [PMID: 31290668 PMCID: PMC6898736 DOI: 10.1021/acs.jproteome.9b00205] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide sequence ions, and in addition, possible sequence ions carrying post-translational modifications (PTMs), but most do not provide confidence metrics for the exact localization of those PTMs when several possible sites are available. Localization is absolutely required for downstream molecular cell biology analysis of PTM function in vitro and in vivo. Therefore, we developed PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization confidence to enable appropriate further characterization of biologic events. Localization of any type of mass modification (e.g., phosphorylation) is supported. PTMProphet applies Bayesian mixture models to compute probabilities for each site/peptide spectrum match where a PTM has been identified. These probabilities can be combined to compute a global false localization rate at any threshold to guide downstream analysis. We describe the PTMProphet tool, its underlying algorithms, and demonstrate its performance on ground-truth synthetic peptide reference data sets, one previously published small data set, one new larger data set, and also on a previously published phosphoenriched data set where the correct sites of modification are unknown. Data have been deposited to ProteomeXchange with identifier PXD013210.
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Affiliation(s)
| | | | | | | | | | - Dave Lee
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Luis Mendoza
- Institute for Systems Biology, Seattle, WA, 98008, USA
| | | | - Zhi Sun
- Institute for Systems Biology, Seattle, WA, 98008, USA
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester, M13 9PL, UK
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250
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Steichen JM, Lin YC, Havenar-Daughton C, Pecetta S, Ozorowski G, Willis JR, Toy L, Sok D, Liguori A, Kratochvil S, Torres JL, Kalyuzhniy O, Melzi E, Kulp DW, Raemisch S, Hu X, Bernard SM, Georgeson E, Phelps N, Adachi Y, Kubitz M, Landais E, Umotoy J, Robinson A, Briney B, Wilson IA, Burton DR, Ward AB, Crotty S, Batista FD, Schief WR. A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses. Science 2019; 366:eaax4380. [PMID: 31672916 PMCID: PMC7092357 DOI: 10.1126/science.aax4380] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/17/2019] [Indexed: 12/11/2022]
Abstract
Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens.
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Affiliation(s)
- Jon M Steichen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ying-Cing Lin
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Colin Havenar-Daughton
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Simone Pecetta
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Laura Toy
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sven Kratochvil
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Jonathan L Torres
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eleonora Melzi
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Daniel W Kulp
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Vaccine and Immune Therapy Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Sebastian Raemisch
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steffen M Bernard
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Umotoy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amanda Robinson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shane Crotty
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Facundo D Batista
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
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