1
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Corcoran MM, Karlsson Hedestam GB. Adaptive immune receptor germline gene variation. Curr Opin Immunol 2024; 87:102429. [PMID: 38805851 DOI: 10.1016/j.coi.2024.102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
Abstract
Recognition of antigens by T cell receptors (TCRs) and B cell receptors (BCRs) is a key step in lymphocyte activation. T and B cells mediate adaptive immune responses, which protect us against infections and provide immunological memory, and also, in some instances, drive pathogenic responses in autoimmune diseases. TCRs and BCRs are encoded within loci that are known to be genetically diverse. However, the extent and functional impact of this variation, both in humans and model animals used in immunological research, remain largely unknown. Experimental and genetic evidence has demonstrated that the complementarity determining regions 1 and 2 (HCDR1 and HCDR2), encoded by the variable (V) region of TCRs and BCRs, also often make critical contacts with the targeted antigen. Thus, knowledge about allelic variation in the genes encoding TCRs and BCRs is critically important for understanding adaptive immune responses in outbred populations and to define responder and non-responder phenotypes.
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Affiliation(s)
- Martin M Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
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2
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Malewana RD, Stalls V, May A, Lu X, Martinez DR, Schäfer A, Li D, Barr M, Sutherland LL, Lee E, Parks R, Beck WE, Newman A, Bock KW, Minai M, Nagata BM, DeMarco CT, Denny TN, Oguin TH, Rountree W, Wang Y, Mansouri K, Edwards RJ, Sempowski GD, Eaton A, Muramatsu H, Henderson R, Tam Y, Barbosa C, Tang J, Cain DW, Santra S, Moore IN, Andersen H, Lewis MG, Golding H, Seder R, Khurana S, Montefiori DC, Pardi N, Weissman D, Baric RS, Acharya P, Haynes BF, Saunders KO. Broadly neutralizing antibody induction by non-stabilized SARS-CoV-2 Spike mRNA vaccination in nonhuman primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572191. [PMID: 38187726 PMCID: PMC10769253 DOI: 10.1101/2023.12.18.572191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Immunization with mRNA or viral vectors encoding spike with diproline substitutions (S-2P) has provided protective immunity against severe COVID-19 disease. How immunization with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike elicits neutralizing antibodies (nAbs) against difficult-to-neutralize variants of concern (VOCs) remains an area of great interest. Here, we compare immunization of macaques with mRNA vaccines expressing ancestral spike either including or lacking diproline substitutions, and show the diproline substitutions were not required for protection against SARS-CoV-2 challenge or induction of broadly neutralizing B cell lineages. One group of nAbs elicited by the ancestral spike lacking diproline substitutions targeted the outer face of the receptor binding domain (RBD), neutralized all tested SARS-CoV-2 VOCs including Omicron XBB.1.5, but lacked cross-Sarbecovirus neutralization. Structural analysis showed that the macaque broad SARS-CoV-2 VOC nAbs bound to the same epitope as a human broad SARS-CoV-2 VOC nAb, DH1193. Vaccine-induced antibodies that targeted the RBD inner face neutralized multiple Sarbecoviruses, protected mice from bat CoV RsSHC014 challenge, but lacked Omicron variant neutralization. Thus, ancestral SARS-CoV-2 spike lacking proline substitutions encoded by nucleoside-modified mRNA can induce B cell lineages binding to distinct RBD sites that either broadly neutralize animal and human Sarbecoviruses or recent Omicron VOCs.
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Affiliation(s)
- R. Dilshan Malewana
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Aaron May
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David R. Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Immunobiology, Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dapeng Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura L. Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Esther Lee
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Whitney Edwards Beck
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin W. Bock
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Mahnaz Minai
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Bianca M. Nagata
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - C. Todd DeMarco
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas H. Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hiromi Muramatsu
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ying Tam
- Acuitas Therapeutics, LLC, Vancouver, BC, V6T 1Z3, Canada
| | | | - Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA
| | - Derek W. Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Ian N. Moore
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | | | | | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA
| | - Robert Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Norbert Pardi
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
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3
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Counts JA, Saunders KO. Guiding HIV-1 vaccine development with preclinical nonhuman primate research. Curr Opin HIV AIDS 2023; 18:315-322. [PMID: 37712825 PMCID: PMC10810179 DOI: 10.1097/coh.0000000000000819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
PURPOSE OF THE REVIEW Nonhuman primates (NHPs) are seen as the closest animal model to humans in terms of anatomy and immune system makeup. Here, we review how preclinical studies in this model system are teaching the field of HIV vaccinology the basic immunology that is needed to induce broadly neutralizing antibodies (bnAbs) with vaccination and elicit protective T cell responses. These lessons are being translated into clinical trials to advance towards protective active vaccination against HIV-1 infection. RECENT FINDINGS Preclinical vaccination studies in NHPs have shown that highly engineered HIV-1 immunogens can initiate bnAb precursors providing proof of concept for Phase I clinical trials. Additionally, NHP models of HIV-1 infection are elucidating the pathways for bnAb development while serving as systems to evaluate vaccine protection. Innovative immunization strategies have increased affinity maturation of HIV-1 antibodies in long-lived germinal centers. Preclinical studies in macaques have defined the protective level of neutralizing antibodies and have shown that T cell responses can synergize with antibody-mediated immunity to provide protection in the presence of lower neutralizing antibody titers. SUMMARY The NHP model provides vaccine regimens and desired antibody and T cell responses that serve as benchmarks for clinical trials, accelerating HIV vaccine design.
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Affiliation(s)
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Departments of Surgery, Immunology, and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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Mopuri R, Welbourn S, Charles T, Ralli-Jain P, Rosales D, Burton S, Aftab A, Karunakaran K, Pellegrini K, Kilembe W, Karita E, Gnanakaran S, Upadhyay AA, Bosinger SE, Derdeyn CA. High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope. PLoS Pathog 2023; 19:e1011717. [PMID: 37878666 PMCID: PMC10627474 DOI: 10.1371/journal.ppat.1011717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/06/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023] Open
Abstract
A protective HIV-1 vaccine has been hampered by a limited understanding of how B cells acquire neutralizing activity. Our previous vaccines expressing two different HIV-1 envelopes elicited robust antigen specific serum IgG titers in 20 rhesus macaques; yet serum from only two animals neutralized the autologous virus. Here, we used high throughput immunoglobulin receptor and single cell RNA sequencing to characterize the overall expansion, recall, and maturation of antigen specific B cells longitudinally over 90 weeks. Diversification and expansion of many B cell clonotypes occurred broadly in the absence of serum neutralization. However, in one animal that developed neutralization, two neutralizing B cell clonotypes arose from the same immunoglobulin germline and were tracked longitudinally. Early antibody variants with high identity to germline neutralized the autologous virus while later variants acquired somatic hypermutation and increased neutralization potency. The early engagement of precursors capable of neutralization with little to no SHM followed by prolonged affinity maturation allowed the two neutralizing lineages to successfully persist despite many other antigen specific B cells. The findings provide new insight into B cells responding to HIV-1 envelope during heterologous prime and boost immunization in rhesus macaques and the development of selected autologous neutralizing antibody lineages.
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Affiliation(s)
- Rohini Mopuri
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Sarah Welbourn
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Tysheena Charles
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Pooja Ralli-Jain
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - David Rosales
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Samantha Burton
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Areeb Aftab
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Kirti Karunakaran
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Kathryn Pellegrini
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | | | - Sandrasegaram Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Amit A. Upadhyay
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Cynthia A. Derdeyn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Infectious Diseases and Translational Medicine Unit, Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
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5
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Peres A, Lees WD, Rodriguez OL, Lee NY, Polak P, Hope R, Kedmi M, Collins AM, Ohlin M, Kleinstein S, Watson C, Yaari G. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Res 2023; 51:e86. [PMID: 37548401 PMCID: PMC10484671 DOI: 10.1093/nar/gkad603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023] Open
Abstract
In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).
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Affiliation(s)
- Ayelet Peres
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7JE, UK
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Noah Y Lee
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Pazit Polak
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Ronen Hope
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Meirav Kedmi
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, 5262000, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Andrew M Collins
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mats Ohlin
- Department of Immunotechnology Lund University, Lund, 221 00, Sweden
| | - Steven H Kleinstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
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Lees WD, Christley S, Peres A, Kos JT, Corrie B, Ralph D, Breden F, Cowell LG, Yaari G, Corcoran M, Karlsson Hedestam GB, Ohlin M, Collins AM, Watson CT, Busse CE. AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2023; 10:100025. [PMID: 37388275 PMCID: PMC10310305 DOI: 10.1016/j.immuno.2023.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.
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Affiliation(s)
- William D. Lees
- Institute of Structural and Molecular Biology, Birkbeck College, London, England
- Human-Centered Computing and Information Science, Institute for Systems and Computer Engineering Technology and Science, Porto, Portugal
| | - Scott Christley
- Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ayelet Peres
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, KY, USA
| | - Brian Corrie
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Lindsay G. Cowell
- Peter O’Donnell Jr. School of Public Health, Department of Immunology, School of Biomedical Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Swede
| | | | - Mats Ohlin
- Department of Immunotechnology and SciLifeLab, Lund University, Lund, Sweden
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, KY, USA
| | - Christian E. Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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7
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Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023; 44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The recombination between immunoglobulin (IG) gene segments determines an individual's naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity - from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
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Affiliation(s)
- Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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8
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Narang S, Kaduk M, Chernyshev M, Karlsson Hedestam GB, Corcoran MM. Adaptive immune receptor genotyping using the corecount program. Front Immunol 2023; 14:1125884. [PMID: 37114042 PMCID: PMC10126697 DOI: 10.3389/fimmu.2023.1125884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/27/2023] [Indexed: 04/29/2023] Open
Abstract
We present a new Rep-Seq analysis tool called corecount, for analyzing genotypic variation in immunoglobulin (IG) and T cell receptor (TCR) genes. corecount is highly efficient at identifying V alleles, including those that are infrequently used in expressed repertoires and those that contain 3' end variation that are otherwise refractory to reliable identification during germline inference from expressed libraries. Furthermore, corecount facilitates accurate D and J gene genotyping. The output is highly reproducible and facilitates the comparison of genotypes from multiple individuals, such as those from clinical cohorts. Here, we applied corecount to the genotypic analysis of IgM libraries from 16 individuals. To demonstrate the accuracy of corecount, we Sanger sequenced all the heavy chain IG alleles (65 IGHV, 27 IGHD and 7 IGHJ) from one individual from whom we also produced two independent IgM Rep-seq datasets. Genomic analysis revealed that 5 known IGHV and 2 IGHJ sequences are truncated in current reference databases. This dataset of genomically validated alleles and IgM libraries from the same individual provides a useful resource for benchmarking other bioinformatic programs that involve V, D and J assignments and germline inference, and may facilitate the development of AIRR-Seq analysis tools that can take benefit from the availability of more comprehensive reference databases.
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9
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Rodriguez OL, Silver CA, Shields K, Smith ML, Watson CT. Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta, and beta loci. CELL GENOMICS 2022; 2:100228. [PMID: 36778049 PMCID: PMC9903726 DOI: 10.1016/j.xgen.2022.100228] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/25/2022] [Accepted: 11/05/2022] [Indexed: 12/02/2022]
Abstract
T cell receptors (TCRs) recognize peptide fragments presented by the major histocompatibility complex (MHC) and are critical to T cell-mediated immunity. Recent data have indicated that genetic diversity within TCR-encoding gene regions is underexplored, limiting understanding of the impact of TCR loci polymorphisms on TCR function in disease, even though TCR repertoire signatures (1) are heritable and (2) associate with disease phenotypes. To address this, we developed a targeted long-read sequencing approach to generate highly accurate haplotype resolved assemblies of the TCR beta (TRB) and alpha/delta (TRA/D) loci, facilitating the genotyping of all variant types, including structural variants. We validate our approach using two mother-father-child trios and 5 unrelated donors representing multiple populations. This resulted in improved genotyping accuracy and the discovery of 84 undocumented V, D, J, and C alleles, demonstrating the utility of this framework for improving our understanding of TCR diversity and function in disease.
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Affiliation(s)
- Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Catherine A. Silver
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa L. Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA,Corresponding author
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Aartse A, Mortier D, Mooij P, Hofman S, van Haaren MM, Corcoran M, Karlsson Hedestam GB, Eggink D, Claireaux M, Bogers WMJM, van Gils MJ, Koopman G. Primary antibody response after influenza virus infection is first dominated by low-mutated HA-stem antibodies followed by higher-mutated HA-head antibodies. Front Immunol 2022; 13:1026951. [PMID: 36405682 PMCID: PMC9670313 DOI: 10.3389/fimmu.2022.1026951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 09/12/2023] Open
Abstract
Several studies have shown that the first encounter with influenza virus shapes the immune response to future infections or vaccinations. However, a detailed analysis of the primary antibody response is lacking as this is difficult to study in humans. It is therefore not known what the frequency and dynamics of the strain-specific hemagglutinin (HA) head- and stem-directed antibody responses are directly after primary influenza virus infection. Here, sera of twelve H1N1pdm2009 influenza virus-infected cynomolgus macaques were evaluated for HA-head and HA-stem domain antibody responses. We observed an early induction of HA-stem antibody responses, which was already decreased by day 56. In contrast, responses against the HA-head domain were low early after infection and increased at later timepoint. The HA-specific B cell repertoires in each animal showed diverse VH-gene usage with preferred VH-gene and JH-gene family usage for HA-head or HA-stem B cells but a highly diverse allelic variation within the VH-usage. HA-head B cells had shorter CDRH3s and higher VH-gene somatic hyper mutation levels relative to HA-stem B cells. In conclusion, our data suggest that HA-stem antibodies are the first to react to the infection while HA-head antibodies show a delayed response, but a greater propensity to enter the germinal center and undergo affinity maturation.
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Affiliation(s)
- Aafke Aartse
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
| | - Daniella Mortier
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Sam Hofman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marlies M. van Haaren
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet (KI), Stockholm, Sweden
| | | | - Dirk Eggink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Mathieu Claireaux
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | | | - Marit J. van Gils
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
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