1
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Shin OS, Monticelli SR, Hjorth CK, Hornet V, Doyle M, Abelson D, Kuehne AI, Wang A, Bakken RR, Mishra AK, Middlecamp M, Champney E, Stuart L, Maurer DP, Li J, Berrigan J, Barajas J, Balinandi S, Lutwama JJ, Lobel L, Zeitlin L, Walker LM, Dye JM, Chandran K, Herbert AS, Pauli NT, McLellan JS. Crimean-Congo hemorrhagic fever survivors elicit protective non-neutralizing antibodies that target 11 overlapping regions on glycoprotein GP38. Cell Rep 2024; 43:114502. [PMID: 39002130 PMCID: PMC11346345 DOI: 10.1016/j.celrep.2024.114502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/03/2024] [Accepted: 06/27/2024] [Indexed: 07/15/2024] Open
Abstract
Crimean-Congo hemorrhagic fever virus can cause lethal disease in humans yet there are no approved medical countermeasures. Viral glycoprotein GP38, exclusive to Nairoviridae, is a target of protective antibodies and is a key antigen in preclinical vaccine candidates. Here, we isolate 188 GP38-specific antibodies from human survivors of infection. Competition experiments show that these antibodies bind across 5 distinct antigenic sites, encompassing 11 overlapping regions. Additionally, we show structures of GP38 bound with 9 of these antibodies targeting different antigenic sites. Although these GP38-specific antibodies are non-neutralizing, several display protective efficacy equal to or better than murine antibody 13G8 in two highly stringent rodent models of infection. Together, these data expand our understanding regarding this important viral protein and may inform the development of broadly effective CCHFV antibody therapeutics.
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Affiliation(s)
| | - Stephanie R Monticelli
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA; Geneva Foundation, Tacoma, WA 98042, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | - Dafna Abelson
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | - Ana I Kuehne
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Russell R Bakken
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Akaash K Mishra
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | - Lauran Stuart
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | | | | | - Jacob Berrigan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | | | - Leslie Lobel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | | | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | | | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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2
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Barbieri ES, Sosa-Holt C, Ibañez LI, Baztarrica J, Garaicoechea L, Gay CL, Caceres CJ, Aduriz M, Baumeister E, Escribano JA, Perez D, Wigdorovitz A, Parreño GV, Puntel M. Anti-hemagglutinin monomeric nanobody provides prophylactic immunity against H1 subtype influenza A viruses. PLoS One 2024; 19:e0301664. [PMID: 38985719 PMCID: PMC11236207 DOI: 10.1371/journal.pone.0301664] [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: 08/12/2022] [Accepted: 03/20/2024] [Indexed: 07/12/2024] Open
Abstract
Influenza viruses constitute a major threat to human health globally. The viral surface glycoprotein hemagglutinin (HA) is the immunodominant antigen, contains the site for binding to the cellular receptor (RBS), and it is the major target of neutralizing antibody responses post-infection. We developed llama-derived single chain antibody fragments (VHHs) specific for type A influenza virus. Four VHHs were identified and further characterized. VHH D81 bound residues in the proximity of the C-terminal region of HA1 of H1 and H5 subtypes, and showed weak neutralizing activity, whereas VHH B33 bound residues in the proximity of the N-terminal region of the HA's stem domain (HA2) of H1, H5, and H9 subtypes, and showed no neutralizing activity. Of most relevance, VHHs E13 and G41 recognized highly conserved conformational epitopes on the H1 HA's globular domain (HA1) and showed high virus neutralizing activity (ranging between 0.94 to 0.01μM), when tested against several human H1N1 isolates. Additionally, E13 displayed abrogated virus replication of a panel of H1N1 strains spanning over 80 years of antigenic drift and isolated from human, avian, and swine origin. Interestingly, E13 conferred protection in vivo at a dose as low as 0.05 mg/kg. Mice treated with E13 intranasally resulted in undetectable virus challenge loads in the lungs at day 4 post-challenge. The transfer of sterilizing pan-H1 immunity, by a dose in the range of micrograms given intranasally, is of major significance for a monomeric VHH and supports the further development of E13 as an immunotherapeutic agent for the mitigation of influenza infections.
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Affiliation(s)
- Elena Susana Barbieri
- Virology Institute IncuINTA (IVIT-CONICET), National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- National Council for Scientific and Technical Research (CONICET), Buenos Aires City, Buenos Aires, Argentina
| | - Carla Sosa-Holt
- Virology Institute IncuINTA (IVIT-CONICET), National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- National Council for Scientific and Technical Research (CONICET), Buenos Aires City, Buenos Aires, Argentina
| | - Lorena Itati Ibañez
- National Council for Scientific and Technical Research (CONICET), Buenos Aires City, Buenos Aires, Argentina
- Institute of Science and Technology, Buenos Aires City, Buenos Aires, Argentina
| | - Josefina Baztarrica
- Virology Institute IncuINTA (IVIT-CONICET), National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
| | - Lorena Garaicoechea
- Virology Institute IncuINTA (IVIT-CONICET), National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- National Council for Scientific and Technical Research (CONICET), Buenos Aires City, Buenos Aires, Argentina
| | - Claire Lindsey Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Carlos Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Matias Aduriz
- Virology Institute IncuINTA (IVIT-CONICET), National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- National Council for Scientific and Technical Research (CONICET), Buenos Aires City, Buenos Aires, Argentina
| | - Elsa Baumeister
- National Institute of Infectious Diseases, Malbran Institute, Buenos Aires City, Buenos Aires, Argentina
| | | | - Daniel Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Andrés Wigdorovitz
- Virology Institute IncuINTA (IVIT-CONICET), National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- National Council for Scientific and Technical Research (CONICET), Buenos Aires City, Buenos Aires, Argentina
| | - Gladys Viviana Parreño
- Virology Institute IncuINTA (IVIT-CONICET), National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- National Council for Scientific and Technical Research (CONICET), Buenos Aires City, Buenos Aires, Argentina
| | - Mariana Puntel
- Virology Institute IncuINTA (IVIT-CONICET), National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- National Council for Scientific and Technical Research (CONICET), Buenos Aires City, Buenos Aires, Argentina
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3
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Shin OS, Monticelli SR, Hjorth CK, Hornet V, Doyle M, Abelson D, Kuehne AI, Wang A, Bakken RR, Mishra A, Middlecamp M, Champney E, Stuart L, Maurer DP, Li J, Berrigan J, Barajas J, Balinandi S, Lutwama JJ, Lobel L, Zeitlin L, Walker LM, Dye JM, Chandran K, Herbert AS, Pauli NT, McLellan JS. Crimean-Congo Hemorrhagic Fever Survivors Elicit Protective Non-Neutralizing Antibodies that Target 11 Overlapping Regions on Viral Glycoprotein GP38. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.583110. [PMID: 38496658 PMCID: PMC10942344 DOI: 10.1101/2024.03.02.583110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Crimean-Congo hemorrhagic fever virus can cause lethal disease in humans yet there are no approved medical countermeasures. Viral glycoprotein GP38, unique to Nairoviridae, is a target of protective antibodies, but extensive mapping of the human antibody response to GP38 has not been previously performed. Here, we isolated 188 GP38-specific antibodies from human survivors of infection. Competition experiments showed that these antibodies bind across five distinct antigenic sites, encompassing eleven overlapping regions. Additionally, we reveal structures of GP38 bound with nine of these antibodies targeting different antigenic sites. Although GP38-specific antibodies were non-neutralizing, several antibodies were found to have protection equal to or better than murine antibody 13G8 in two highly stringent rodent models of infection. Together, these data expand our understanding regarding this important viral protein and inform the development of broadly effective CCHFV antibody therapeutics.
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Affiliation(s)
| | - Stephanie R. Monticelli
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
- Geneva Foundation, Tacoma, WA 98042, USA
| | - Christy K. Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | - Dafna Abelson
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | - Ana I. Kuehne
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Russell R. Bakken
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Akaash Mishra
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | - Lauran Stuart
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | | | | | - Jacob Berrigan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | | | - Leslie Lobel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | | | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrew S. Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | | | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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4
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Collins AM, Ohlin M, Corcoran M, Heather JM, Ralph D, Law M, Martínez-Barnetche J, Ye J, Richardson E, Gibson WS, Rodriguez OL, Peres A, Yaari G, Watson CT, Lees WD. AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes. Front Immunol 2024; 14:1330153. [PMID: 38406579 PMCID: PMC10884231 DOI: 10.3389/fimmu.2023.1330153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/27/2023] [Indexed: 02/27/2024] Open
Abstract
Introduction Analysis of an individual's immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene reference sets. When sets only contain alleles supported by strong evidence, AIRR sequencing (AIRR-seq) data analysis is more accurate and studies of the evolution of IG genes, their allelic variants and the expressed immune repertoire is therefore facilitated. Methods The Adaptive Immune Receptor Repertoire Community (AIRR-C) IG Reference Sets have been developed by including only human IG heavy and light chain alleles that have been confirmed by evidence from multiple high-quality sources. To further improve AIRR-seq analysis, some alleles have been extended to deal with short 3' or 5' truncations that can lead them to be overlooked by alignment utilities. To avoid other challenges for analysis programs, exact paralogs (e.g. IGHV1-69*01 and IGHV1-69D*01) are only represented once in each set, though alternative sequence names are noted in accompanying metadata. Results and discussion The Reference Sets include less than half the previously recognised IG alleles (e.g. just 198 IGHV sequences), and also include a number of novel alleles: 8 IGHV alleles, 2 IGKV alleles and 5 IGLV alleles. Despite their smaller sizes, erroneous calls were eliminated, and excellent coverage was achieved when a set of repertoires comprising over 4 million V(D)J rearrangements from 99 individuals were analyzed using the Sets. The version-tracked AIRR-C IG Reference Sets are freely available at the OGRDB website (https://ogrdb.airr-community.org/germline_sets/Human) and will be regularly updated to include newly observed and previously reported sequences that can be confirmed by new high-quality data.
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Affiliation(s)
- Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mats Ohlin
- Department of Immunotechnology, and SciLifeLab, Lund University, Lund, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - James M. Heather
- Mass General Cancer Center, Massachusetts General Hospital, Charlestown, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Jesus Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Jian Ye
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Eve Richardson
- La Jolla Institute for Immunology, San Diego, CA, United States
| | - William S. Gibson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Ayelet Peres
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - William D. Lees
- Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
- Human-Centered Computing and Information Science, Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
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5
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Monson N, Smith C, Greenberg H, Plumb P, Guzman A, Tse K, Chen D, Zhang W, Morgan M, Speed H, Powell C, Batra S, Cowell L, Christley S, Vernino S, Blackburn K, Greenberg B. VH2+ Antigen-Experienced B Cells in the Cerebrospinal Fluid Are Expanded and Enriched in Pediatric Anti-NMDA Receptor Encephalitis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1332-1339. [PMID: 37712756 PMCID: PMC10593502 DOI: 10.4049/jimmunol.2300156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
Pediatric and adult autoimmune encephalitis (AE) are often associated with Abs to the NR1 subunit of the N-methyl-d-aspartate (NMDA) receptor (NMDAR). Very little is known regarding the cerebrospinal fluid humoral immune profile and Ab genetics associated with pediatric anti-NMDAR-AE. Using a combination of cellular, molecular, and immunogenetics tools, we collected cerebrospinal fluid from pediatric subjects and generated 1) flow cytometry data to calculate the frequency of B cell subtypes in the cerebrospinal fluid of pediatric subjects with anti-NMDAR-AE and controls, 2) a panel of recombinant human Abs from a pediatric case of anti-NMDAR-AE that was refractory to treatment, and 3) a detailed analysis of the Ab genes that bound the NR1 subunit of the NMDAR. Ag-experienced B cells including memory cells, plasmablasts, and Ab-secreting cells were expanded in the pediatric anti-NMDAR-AE cohort, but not in the controls. These Ag-experienced B cells in the cerebrospinal fluid of a pediatric case of NMDAR-AE that was refractory to treatment had expanded use of variable H chain family 2 (VH2) genes with high somatic hypermutation that all bound to the NR1 subunit of the NMDAR. A CDR3 motif was identified in this refractory case that likely drove early stage activation and expansion of naive B cells to Ab-secreting cells, facilitating autoimmunity associated with pediatric anti-NMDAR-AE through the production of Abs that bind NR1. These features of humoral immune responses in the cerebrospinal fluid of pediatric anti-NMDAR-AE patients may be relevant for clinical diagnosis and treatment.
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Affiliation(s)
- Nancy Monson
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX
| | - Chad Smith
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Hannah Greenberg
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Patricia Plumb
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Alyssa Guzman
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Key Tse
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Ding Chen
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Wei Zhang
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Miles Morgan
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Haley Speed
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Craig Powell
- Department of Neurobiology, Civitan International Research Center, University of Alabama Marnix E. Heersink School of Medicine, Birmingham, AL
| | - Sushobhna Batra
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Lindsay Cowell
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX
| | - Scott Christley
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX
| | - Steve Vernino
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Kyle Blackburn
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
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6
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Xu Z, Peng Q, Liu W, Demongeot J, Wei D. Antibody Dynamics Simulation-A Mathematical Exploration of Clonal Deletion and Somatic Hypermutation. Biomedicines 2023; 11:2048. [PMID: 37509687 PMCID: PMC10377040 DOI: 10.3390/biomedicines11072048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
We have employed mathematical modeling techniques to construct a comprehensive framework for elucidating the intricate response mechanisms of the immune system, facilitating a deeper understanding of B-cell clonal deletion and somatic hypermutation. Our improved model introduces innovative mechanisms that shed light on positive and negative selection processes during T-cell and B-cell development. Notably, clonal deletion is attributed to the attenuated immune stimulation exerted by self-antigens with high binding affinities, rendering them less effective in eliciting subsequent B-cell maturation and differentiation. Secondly, our refined model places particular emphasis on the crucial role played by somatic hypermutation in modulating the immune system's functionality. Through extensive investigation, we have determined that somatic hypermutation not only expedites the production of highly specific antibodies pivotal in combating microbial infections but also serves as a regulatory mechanism to dampen autoimmunity and enhance self-tolerance within the organism. Lastly, our model advances the understanding of the implications of antibody in vivo evolution in the overall process of organismal aging. With the progression of time, the age-associated amplification of autoimmune activity becomes apparent. While somatic hypermutation effectively delays this process, mitigating the levels of autoimmune response, it falls short of reversing this trajectory entirely. In conclusion, our advanced mathematical model offers a comprehensive and scholarly approach to comprehend the intricacies of the immune system. By encompassing novel mechanisms for selection, emphasizing the functional role of somatic hypermutation, and illuminating the consequences of in vivo antibody evolution, our model expands the current understanding of immune responses and their implications in aging.
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Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou 253023, China
| | - Qingzhi Peng
- Department of Life Science, Dezhou University, Dezhou 253023, China
| | - Weidong Liu
- Department of Physical Education, Dezhou University, Dezhou 253023, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France
| | - Dongqing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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7
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Martin Beem J, Venkatayogi S, Haynes BF, Wiehe K. ARMADiLLO: a web server for analyzing antibody mutation probabilities. Nucleic Acids Res 2023; 51:W51-W56. [PMID: 37260077 PMCID: PMC10320107 DOI: 10.1093/nar/gkad398] [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: 03/24/2023] [Revised: 04/25/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Antibodies are generated by B cells that evolve receptor specificity to pathogens through rounds of mutation and selection in a process called affinity maturation. Somatic hypermutation is mediated by an enzyme with DNA sequence context-dependent targeting and substitution resulting in variable probabilities of amino acid substitutions during affinity maturation. We have previously developed a program called Antigen Receptor Mutation Analyzer for the Detection of Low Likelihood Occurrences (ARMADiLLO) that performs simulations of the somatic hypermutation process to estimate the probabilities of observed antibody mutations. Here we describe the ARMADiLLO web server (https://armadillo.dhvi.duke.edu), an easy-to-use web interface that analyzes input antibody sequences and displays the probability estimates for all possible amino acid changes over the full length of an antibody sequence. The probability of antibody mutations can be used by immunologists studying B cell ontogenies and by vaccine designers that are pursuing strategies to elicit broadly neutralizing antibodies which are enriched with developmentally rate-limiting improbable mutations. The ARMADiLLO web server also contains precomputed results reporting the probability of amino acid substitutions in all human V gene segments and in a collection of HIV broadly neutralizing antibodies.
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Affiliation(s)
- Joshua S Martin Beem
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC27710, USA
- Department of Immunology, Duke University Medical Center; Durham, NC27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC27710, USA
- Department of Medicine, Duke University Medical Center; Durham, NC27710, USA
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8
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Abdulla ZA, Al-Bashir SM, Alzoubi H, Al-Salih NS, Aldamen AA, Abdulazeez AZ. The Role of Immunity in the Pathogenesis of SARS-CoV-2 Infection and in the Protection Generated by COVID-19 Vaccines in Different Age Groups. Pathogens 2023; 12:329. [PMID: 36839601 PMCID: PMC9967364 DOI: 10.3390/pathogens12020329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
This study aims to review the available data regarding the central role of immunity in combating SARS-CoV-2 infection and in the generation of protection by vaccination against COVID-19 in different age groups. Physiologically, the immune response and the components involved in it are variable, both functionally and quantitatively, in neonates, infants, children, adolescents, and adults. These immunological differences are mirrored during COVID-19 infection and in the post-vaccination period. The outcome of SARS-CoV-2 infection is greatly dependent on the reaction orchestrated by the immune system. This is clearly obvious in relation to the clinical status of COVID-19 infection, which can be symptomless, mild, moderate, or severe. Even the complications of the disease show a proportional pattern in relation to the immune response. On the contrary, the commonly used anti-COVID-19 vaccines generate protective humoral and cellular immunity. The magnitude of this immunity and the components involved in it are discussed in detail. Furthermore, many of the adverse effects of these vaccines can be explained on the basis of immune reactions against the different components of the vaccines. Regarding the appropriate choice of vaccine for different age groups, many factors have to be considered. This is a cornerstone, particularly in the following age groups: 1 day to 5 years, 6 to 11 years, and 12 to 17 years. Many factors are involved in deciding the route, doses, and schedule of vaccination for children. Another important issue in this dilemma is the hesitancy of families in making the decision about whether to vaccinate their children. Added to these difficulties is the choice by health authorities and governments concerning whether to make children's vaccination compulsory. In this respect, although rare and limited, adverse effects of vaccines in children have been detected, some of which, unfortunately, have been serious or even fatal. However, to achieve comprehensive control over COVID-19 in communities, both children and adults have to be vaccinated, as the former group represents a reservoir for viral transmission. The understanding of the various immunological mechanisms involved in SARS-CoV-2 infection and in the preparation and application of its vaccines has given the sciences a great opportunity to further deepen and expand immunological knowledge. This will hopefully be reflected positively on other diseases through gaining an immunological background that may aid in diagnosis and therapy. Humanity is still in continuous conflict with SARS-CoV-2 infection and will be for a while, but the future is expected to be in favor of the prevention and control of this disease.
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Affiliation(s)
| | - Sharaf M. Al-Bashir
- Department of Clinical Sciences, Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan
| | - Hiba Alzoubi
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan
| | - Noor S. Al-Salih
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan
| | - Ala A. Aldamen
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan
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9
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Mallaby J, Mwangi W, Ng J, Stewart A, Dorey-Robinson D, Kipling D, Hershberg U, Fraternali F, Nair V, Dunn-Walters D. Diversification of immunoglobulin genes by gene conversion in the domestic chicken ( Gallus gallus domesticus). DISCOVERY IMMUNOLOGY 2023; 2:kyad002. [PMID: 38567069 PMCID: PMC10917233 DOI: 10.1093/discim/kyad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 12/29/2022] [Accepted: 01/18/2023] [Indexed: 04/04/2024]
Abstract
Sustainable modern poultry production depends on effective protection against infectious diseases and a diverse range of antibodies is key for an effective immune response. In the domestic chicken, somatic gene conversion is the dominant process in which the antibody immunoglobulin genes are diversified. Affinity maturation by somatic hypermutation (SHM) also occurs, but the relative contribution of gene conversion versus somatic hypermutation to immunoglobulin (Ig) gene diversity is poorly understood. In this study, we use high throughput long-read sequencing to study immunoglobulin diversity in multiple immune-associated tissues in Rhode Island Red chickens. To better understand the impact of genetic diversification in the chicken, a novel gene conversion identification software was developed (BrepConvert). In this study, BrepConvert enabled the identification of over 1 million gene conversion events. Mapping the occurrence of putative somatic gene conversion (SGC) events throughout the variable gene region revealed repetitive and highly restricted patterns of genetic insertions in both the antibody heavy and light chains. These patterns coincided with the locations of genetic variability in available pseudogenes and align with antigen binding sites, predominately the complementary determining regions (CDRs). We found biased usage of pseudogenes during gene conversion, as well as immunoglobulin heavy chain diversity gene (IGHD) preferences during V(D)J gene rearrangement, suggesting that antibody diversification in chickens is more focused than the genetic potential for diversity would suggest.
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Affiliation(s)
- Jessica Mallaby
- Department of Bioscience and Medicine, University of Surrey, Guildford, UK
- Pirbright Institute, Woking, UK
| | | | - Joseph Ng
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, UK
| | - Alexander Stewart
- Department of Bioscience and Medicine, University of Surrey, Guildford, UK
| | | | - David Kipling
- Department of Bioscience and Medicine, University of Surrey, Guildford, UK
| | - Uri Hershberg
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, UK
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10
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Safra M, Tamari Z, Polak P, Shiber S, Matan M, Karameh H, Helviz Y, Levy-Barda A, Yahalom V, Peretz A, Ben-Chetrit E, Brenner B, Tuller T, Gal-Tanamy M, Yaari G. Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity. Front Immunol 2023; 14:1031914. [PMID: 37153628 PMCID: PMC10154551 DOI: 10.3389/fimmu.2023.1031914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/22/2023] [Indexed: 05/10/2023] Open
Abstract
Introduction The success of the human body in fighting SARS-CoV2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance. Methods We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls. Results In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients. Discussion These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.
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Affiliation(s)
- Modi Safra
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Zvi Tamari
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Pazit Polak
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Shachaf Shiber
- Emergency Department, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Matan
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poriya, Israel
| | - Hani Karameh
- Jesselson Integrated Heart Center, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Yigal Helviz
- Intensive Care Unit, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Adva Levy-Barda
- Biobank, Department of Pathology, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
| | - Vered Yahalom
- Blood Services and Apheresis Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poriya, Israel
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Eli Ben-Chetrit
- Infectious Diseases Unit, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Baruch Brenner
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Oncology, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering and The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | | | - Gur Yaari
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
- *Correspondence: Gur Yaari,
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11
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Mallaby J, Ng J, Stewart A, Sinclair E, Dunn-Walters D, Hershberg U. Chickens, more than humans, focus the diversity of their immunoglobulin genes on the complementarity-determining region but utilise amino acids, indicative of a more cross-reactive antibody repertoire. Front Immunol 2022; 13:837246. [PMID: 36569888 PMCID: PMC9772431 DOI: 10.3389/fimmu.2022.837246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanisms of B-cell diversification differ greatly between aves and mammals, but both produce B cells and antibodies capable of supporting an effective immune response. To see how differences in the generation of diversity might affect overall repertoire diversity, we have compared the diversity characteristics of immunoglobulin genes from domestic chickens to those from humans. Both use V(D)J gene rearrangement and somatic hypermutation, but only chickens use somatic gene conversion. A range of diversity analysis tools were used to investigate multiple aspects of amino acid diversity at both the germline and repertoire levels. The effect of differing amino acid usages on antibody characteristics was assessed. At both the germline and repertoire levels, chickens exhibited lower amino acid diversity in comparison to the human immunoglobulin genes, especially outside of the complementarity-determining region (CDR). Chickens were also found to possess much larger and more hydrophilic CDR3s with a higher predicted protein binding potential, suggesting that the antigen-binding site in chicken antibodies is more flexible and more polyreactive than that seen in human antibodies.
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Affiliation(s)
- Jessica Mallaby
- Department of Bioscience and Medicine, University of Surrey, Guildford, United Kingdom
| | - Joseph Ng
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Alex Stewart
- Department of Bioscience and Medicine, University of Surrey, Guildford, United Kingdom
| | - Emma Sinclair
- Department of Bioscience and Medicine, University of Surrey, Guildford, United Kingdom
| | - Deborah Dunn-Walters
- Department of Bioscience and Medicine, University of Surrey, Guildford, United Kingdom
| | - Uri Hershberg
- Department of Human Biology, University of Haifa, Haifa, Israel
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12
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Banach BB, Tripathi P, Da Silva Pereira L, Gorman J, Nguyen TD, Dillon M, Fahad AS, Kiyuka PK, Madan B, Wolfe JR, Bonilla B, Flynn B, Francica JR, Hurlburt NK, Kisalu NK, Liu T, Ou L, Rawi R, Schön A, Shen CH, Teng IT, Zhang B, Pancera M, Idris AH, Seder RA, Kwong PD, DeKosky BJ. Highly protective antimalarial antibodies via precision library generation and yeast display screening. J Exp Med 2022; 219:e20220323. [PMID: 35736810 PMCID: PMC9242090 DOI: 10.1084/jem.20220323] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/03/2023] Open
Abstract
The monoclonal antibody CIS43 targets the Plasmodium falciparum circumsporozoite protein (PfCSP) and prevents malaria infection in humans for up to 9 mo following a single intravenous administration. To enhance the potency and clinical utility of CIS43, we used iterative site-saturation mutagenesis and DNA shuffling to screen precise gene-variant yeast display libraries for improved PfCSP antigen recognition. We identified several mutations that improved recognition, predominately in framework regions, and combined these to produce a panel of antibody variants. The most improved antibody, CIS43_Var10, had three mutations and showed approximately sixfold enhanced protective potency in vivo compared to CIS43. Co-crystal and cryo-electron microscopy structures of CIS43_Var10 with the peptide epitope or with PfCSP, respectively, revealed functional roles for each of these mutations. The unbiased site-directed mutagenesis and screening pipeline described here represent a powerful approach to enhance protective potency and to enable broader clinical use of antimalarial antibodies.
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Affiliation(s)
- Bailey B. Banach
- Bioengineering Graduate Program, The University of Kansas, Lawrence, KS
| | - Prabhanshu Tripathi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Lais Da Silva Pereira
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Thuy Duong Nguyen
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
| | - Marlon Dillon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Ahmed S. Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
| | - Patience K. Kiyuka
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
| | - Jacy R. Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
| | - Brian Bonilla
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Barbara Flynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Joseph R. Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Nicholas K. Hurlburt
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA
| | - Neville K. Kisalu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA
| | - Azza H. Idris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Robert A. Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Brandon J. DeKosky
- Bioengineering Graduate Program, The University of Kansas, Lawrence, KS
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
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13
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Dale GA, Wilkins DJ, Rowley J, Scharer CD, Tipton CM, Hom J, Boss JM, Corces V, Sanz I, Jacob J. Somatic Diversification of Rearranged Antibody Gene Segments by Intra- and Interchromosomal Templated Mutagenesis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2141-2153. [PMID: 35418472 PMCID: PMC9047068 DOI: 10.4049/jimmunol.2100434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The ability of the humoral immune system to generate Abs capable of specifically binding a myriad of Ags is critically dependent on the somatic hypermutation program. This program induces both templated mutations (i.e., gene conversion) and untemplated mutations. In humans, somatic hypermutation is widely believed to result in untemplated point mutations. In this study, we demonstrate detection of large-scale templated events that occur in human memory B cells and circulating plasmablasts. We find that such mutations are templated intrachromosomally from IGHV genes and interchromosomally from IGHV pseudogenes as well as other homologous regions unrelated to IGHV genes. These same donor regions are used in multiple individuals, and they predominantly originate from chromosomes 14, 15, and 16. In addition, we find that exogenous sequences placed at the IgH locus, such as LAIR1, undergo templated mutagenesis and that homology appears to be the major determinant for donor choice. Furthermore, we find that donor tracts originate from areas in proximity with open chromatin, which are transcriptionally active, and are found in spatial proximity with the IgH locus during the germinal center reaction. These donor sequences are inserted into the Ig gene segment in association with overlapping activation-induced cytidine deaminase hotspots. Taken together, these studies suggest that diversity generated during the germinal center response is driven by untemplated point mutations as well as templated mutagenesis using local and distant regions of the genome.
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Affiliation(s)
- Gordon A Dale
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA
| | - Daniel J Wilkins
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA
| | - Jordan Rowley
- Department of Biology, Emory University, Atlanta, GA
| | | | - Christopher M Tipton
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA
| | - Jennifer Hom
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA
| | - Jeremy M Boss
- Emory University School of Medicine, Emory University, Atlanta, GA; and
| | - Victor Corces
- Department of Biology, Emory University, Atlanta, GA
| | - Ignacio Sanz
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA
| | - Joshy Jacob
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA;
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14
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Pappalardo F, Russo G, Corsini E, Paini A, Worth A. Translatability and transferability of in silico models: Context of use switching to predict the effects of environmental chemicals on the immune system. Comput Struct Biotechnol J 2022; 20:1764-1777. [PMID: 35495116 PMCID: PMC9035946 DOI: 10.1016/j.csbj.2022.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/08/2023] Open
Abstract
Immunotoxicity hazard identification of chemicals aims to evaluate the potential for unintended effects of chemical exposure on the immune system. Perfluorinated alkylate substances (PFAS), such as perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA), are persistent, globally disseminated environmental contaminants known to be immunotoxic. Elevated PFAS exposure is associated with lower antibody responses to vaccinations in children and in adults. In addition, some studies have reported a correlation between PFAS levels in the body and lower resistance to disease, in other words an increased risk of infections or cancers. In this context, modelling and simulation platforms could be used to simulate the human immune system with the aim to evaluate the adverse effects that immunotoxicants may have. Here, we show the conditions under which a mathematical model developed for one purpose and application (e.g., in the pharmaceutical domain) can be successfully translated and transferred to another (e.g., in the chemicals domain) without undergoing significant adaptation. In particular, we demonstrate that the Universal Immune System Simulator was able to simulate the effects of PFAS on the immune system, introducing entities and new interactions that are biologically involved in the phenomenon. This also revealed a potentially exploitable pathway for assessing immunotoxicity through a computational model.
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Affiliation(s)
- Francesco Pappalardo
- Department of Health and Drug Sciences, Università degli Studi di Catania, Italy
| | - Giulia Russo
- Department of Health and Drug Sciences, Università degli Studi di Catania, Italy
| | - Emanuela Corsini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Italy
| | - Alicia Paini
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrew Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
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15
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany. .,Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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16
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Williams WB, Wiehe K, Saunders KO, Haynes BF. Strategies for induction of HIV-1 envelope-reactive broadly neutralizing antibodies. J Int AIDS Soc 2021; 24 Suppl 7:e25831. [PMID: 34806332 PMCID: PMC8606870 DOI: 10.1002/jia2.25831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/23/2021] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION A primary focus of HIV-1 vaccine development is the activation of B cell receptors for naïve or precursor broadly neutralizing antibodies (bnAbs), followed by expansion and maturation of bnAb B cell lineage intermediates leading to highly affinity-matured bnAbs. HIV-1 envelope (Env) encodes epitopes for bnAbs of different specificities. Design of immunogens to induce bnAb precursors of different specificities and mature them into bnAb status is a goal for HIV-1 vaccine development. We review vaccine strategies for bnAb lineages development and highlight the immunological barriers that these strategies must overcome to generate bnAbs. METHODS We provide perspectives based on published research articles and reviews. DISCUSSION The recent Antibody Mediated Protection (AMP) trial that tested the protective efficacy of one HIV-1 Env bnAb specificity demonstrated that relatively high levels of long-lasting serum titers of multiple specificities of bnAbs will be required for protection from HIV-1 transmission. Current vaccine efforts for induction of bnAb lineages are focused on immunogens designed to expand naïve HIV-1 bnAb precursor B cells following the recent success of vaccine-induction of bnAb precursor B cells in macaques and humans. BnAb precursor B cells serve as templates for priming-immunogen design. However, design of boosting immunogens for bnAb maturation requires knowledge of the optimal immunogen design and immunological environment for bnAb B cell lineage affinity maturation. BnAb lineages acquire rare genetic changes as mutations during B cell maturation. Moreover, the immunological environment that supports bnAb development during HIV-1 infection is perturbed with an altered B cell repertoire and dysfunctional immunoregulatory controls, suggesting that in normal settings, bnAb development will be disfavoured. Thus, strategies for vaccine induction of bnAbs must circumvent immunological barriers for bnAb development that normally constrain bnAb B cell affinity maturation. CONCLUSIONS A fully protective HIV-1 vaccine needs to induce durable high titers of bnAbs that can be generated by a sequential set of Env immunogens for expansion and maturation of bnAb B cell lineages in a permitted immunological environment. Moreover, multiple specificities of bnAbs will be required to be sufficiently broad to prevent the escape of HIV-1 strains during transmission.
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Affiliation(s)
- Wilton B. Williams
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin Wiehe
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin O. Saunders
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Barton F. Haynes
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
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17
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Petersen BM, Ulmer SA, Rhodes ER, Gutierrez-Gonzalez MF, Dekosky BJ, Sprenger KG, Whitehead TA. Regulatory Approved Monoclonal Antibodies Contain Framework Mutations Predicted From Human Antibody Repertoires. Front Immunol 2021; 12:728694. [PMID: 34646268 PMCID: PMC8503325 DOI: 10.3389/fimmu.2021.728694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/03/2021] [Indexed: 11/13/2022] Open
Abstract
Monoclonal antibodies (mAbs) are an important class of therapeutics used to treat cancer, inflammation, and infectious diseases. Identifying highly developable mAb sequences in silico could greatly reduce the time and cost required for therapeutic mAb development. Here, we present position-specific scoring matrices (PSSMs) for antibody framework mutations developed using baseline human antibody repertoire sequences. Our analysis shows that human antibody repertoire-based PSSMs are consistent across individuals and demonstrate high correlations between related germlines. We show that mutations in existing therapeutic antibodies can be accurately predicted solely from baseline human antibody sequence data. We find that mAbs developed using humanized mice had more human-like FR mutations than mAbs originally developed by hybridoma technology. A quantitative assessment of entire framework regions of therapeutic antibodies revealed that there may be potential for improving the properties of existing therapeutic antibodies by incorporating additional mutations of high frequency in baseline human antibody repertoires. In addition, high frequency mutations in baseline human antibody repertoires were predicted in silico to reduce immunogenicity in therapeutic mAbs due to the removal of T cell epitopes. Several therapeutic mAbs were identified to have common, universally high-scoring framework mutations, and molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Our results suggest that baseline human antibody repertoires may be useful as predictive tools to guide mAb development in the future.
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Affiliation(s)
- Brian M Petersen
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | - Sophia A Ulmer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | - Emily R Rhodes
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | | | - Brandon J Dekosky
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States.,Department of Chemical Engineering, University of Kansas, Lawrence, KS, United States
| | - Kayla G Sprenger
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
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18
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Liu Y, Wu Y, Liu B, Zhang Y, San D, Chen Y, Zhou Y, Yu L, Zeng H, Zhou Y, Zhou F, Yang H, Yin L, Huang Y. Biomarkers and Immune Repertoire Metrics Identified by Peripheral Blood Transcriptomic Sequencing Reveal the Pathogenesis of COVID-19. Front Immunol 2021; 12:677025. [PMID: 34504487 PMCID: PMC8421539 DOI: 10.3389/fimmu.2021.677025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/30/2021] [Indexed: 01/10/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global crisis; however, our current understanding of the host immune response to SARS-CoV-2 infection remains limited. Herein, we performed RNA sequencing using peripheral blood from acute and convalescent patients and interrogated the dynamic changes of adaptive immune response to SARS-CoV-2 infection over time. Our results revealed numerous alterations in these cohorts in terms of gene expression profiles and the features of immune repertoire. Moreover, a machine learning method was developed and resulted in the identification of five independent biomarkers and a collection of biomarkers that could accurately differentiate and predict the development of COVID-19. Interestingly, the increased expression of one of these biomarkers, UCHL1, a molecule related to nervous system damage, was associated with the clustering of severe symptoms. Importantly, analyses on immune repertoire metrics revealed the distinct kinetics of T-cell and B-cell responses to SARS-CoV-2 infection, with B-cell response plateaued in the acute phase and declined thereafter, whereas T-cell response can be maintained for up to 6 months post-infection onset and T-cell clonality was positively correlated with the serum level of anti-SARS-CoV-2 IgG. Together, the significantly altered genes or biomarkers, as well as the abnormally high levels of B-cell response in acute infection, may contribute to the pathogenesis of COVID-19 through mediating inflammation and immune responses, whereas prolonged T-cell response in the convalescents might help these patients in preventing reinfection. Thus, our findings could provide insight into the underlying molecular mechanism of host immune response to COVID-19 and facilitate the development of novel therapeutic strategies and effective vaccines.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yankang Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bing Liu
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Youpeng Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan San
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Long Yu
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haihong Zeng
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Zhou
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fuxiang Zhou
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Heng Yang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lei Yin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yafei Huang
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Tang C, MacCarthy T. Characterization of DNA G-Quadruplex Structures in Human Immunoglobulin Heavy Variable (IGHV) Genes. Front Immunol 2021; 12:671944. [PMID: 34040612 PMCID: PMC8141862 DOI: 10.3389/fimmu.2021.671944] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
Activation-induced deaminase (AID) is a key enzyme involved in antibody diversification by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) of the Immunoglobulin (Ig) loci. AID preferentially targets WRC (W=A/T, R=A/G) hotspot motifs and avoids SYC (S=C/G, Y=C/T) coldspots. G-quadruplex (G4) structures are four-stranded DNA secondary structures with key functions in transcription, translation and replication. In vitro studies have shown G4s to form and bind AID in Ig switch (S) regions. Alterations in the gene encoding AID can further disrupt AID-G4 binding and reduce CSR in vivo. However, it is still unclear whether G4s form in the variable (V) region, or how they may affect SHM. To assess the possibility of G4 formation in human V regions, we analyzed germline human Ig heavy chain V (IGHV) sequences, using a pre-trained deep learning model that predicts G4 potential. This revealed that many genes from the IGHV3 and IGHV4 families are predicted to have high G4 potential in the top and bottom strand, respectively. Different IGHV alleles also showed variability in G4 potential. Using a high-resolution (G4-seq) dataset of biochemically confirmed potential G4s in IGHV genes, we validated our computational predictions. G4-seq also revealed variation between S and V regions in the distribution of potential G4s, with the V region having overall reduced G4 abundance compared to the S region. The density of AGCT motifs, where two AGC hotspots overlap on both strands, was roughly 2.6-fold greater in the V region than the Constant (C) region, which does not mutate despite having predicted G4s at similar levels. However, AGCT motifs in both V and C regions were less abundant than in S regions. In silico mutagenesis experiments showed that G4 potentials were generally robust to mutation, although large deviations from germline states were found, mostly in framework regions. G4 potential is also associated with higher mutability of certain WRC hotspots on the same strand. In addition, CCC coldspots opposite a predicted G4 were shown to be targeted significantly more for mutation. Our overall assessment reveals plausible evidence of functional G4s forming in the Ig V region.
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Affiliation(s)
- Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States
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20
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Large-scale analysis of 2,152 Ig-seq datasets reveals key features of B cell biology and the antibody repertoire. Cell Rep 2021; 35:109110. [PMID: 33979623 DOI: 10.1016/j.celrep.2021.109110] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/09/2021] [Accepted: 04/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibody repertoire sequencing enables researchers to acquire millions of B cell receptors and investigate these molecules at the single-nucleotide level. This power and resolution in studying humoral responses have led to its wide applications. However, most of these studies were conducted with a limited number of samples. Given the extraordinary diversity, assessment of these key features with a large sample set is demanded. Thus, we collect and systematically analyze 2,152 high-quality heavy-chain antibody repertoires. Our study reveals that 52 core variable genes universally contribute to more than 99% of each individual's repertoire; a distal interspersed preferences characterize V gene recombination; the number of public clones between two repertoires follows a linear model, and the positive selection dominates at RGYW motif in somatic hypermutations. Thus, this population-level analysis resolves some critical features of the antibody repertoire and may have significant value to the large cadre of scientists.
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21
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Krantsevich A, Tang C, MacCarthy T. Correlations in Somatic Hypermutation Between Sites in IGHV Genes Can Be Explained by Interactions Between AID and/or Polη Hotspots. Front Immunol 2021; 11:618409. [PMID: 33603748 PMCID: PMC7884765 DOI: 10.3389/fimmu.2020.618409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/18/2020] [Indexed: 12/27/2022] Open
Abstract
The somatic hypermutation (SHM) of Immunoglobulin (Ig) genes is a key process during antibody affinity maturation in B cells. The mutagenic enzyme activation induced deaminase (AID) is required for SHM and has a preference for WRC hotspots in DNA. Error-prone repair mechanisms acting downstream of AID introduce further mutations, including DNA polymerase eta (Polη), part of the non-canonical mismatch repair pathway (ncMMR), which preferentially generates mutations at WA hotspots. Previously proposed mechanistic models lead to a variety of predictions concerning interactions between hotspots, for example, how mutations in one hotspot will affect another hotspot. Using a large, high-quality, Ig repertoire sequencing dataset, we evaluated pairwise correlations between mutations site-by-site using an unbiased measure similar to mutual information which we termed “mutational association” (MA). Interactions are dominated by relatively strong correlations between nearby sites (short-range MAs), which can be almost entirely explained by interactions between overlapping hotspots for AID and/or Polη. We also found relatively weak dependencies between almost all sites throughout each gene (longer-range MAs), although these arise mostly as a statistical consequence of high pairwise mutation frequencies. The dominant short-range interactions are also highest within the most highly mutating IGHV sub-regions, such as the complementarity determining regions (CDRs), where there is a high hotspot density. Our results suggest that the hotspot preferences for AID and Polη have themselves evolved to allow for greater interactions between AID and/or Polη induced mutations.
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Affiliation(s)
- Artem Krantsevich
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States
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22
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Doepker LE, Danon S, Harkins E, Ralph DK, Yaffe Z, Garrett ME, Dhar A, Wagner C, Stumpf MM, Arenz D, Williams JA, Jaoko W, Mandaliya K, Lee KK, Matsen FA, Overbaugh JM. Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies. eLife 2021; 10:e63444. [PMID: 33427196 PMCID: PMC7884072 DOI: 10.7554/elife.63444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/08/2021] [Indexed: 11/27/2022] Open
Abstract
A prerequisite for the design of an HIV vaccine that elicits protective antibodies is understanding the developmental pathways that result in desirable antibody features. The development of antibodies that mediate antibody-dependent cellular cytotoxicity (ADCC) is particularly relevant because such antibodies have been associated with HIV protection in humans. We reconstructed the developmental pathways of six human HIV-specific ADCC antibodies using longitudinal antibody sequencing data. Most of the inferred naive antibodies did not mediate detectable ADCC. Gain of antigen binding and ADCC function typically required mutations in complementarity determining regions of one or both chains. Enhancement of ADCC potency often required additional mutations in framework regions. Antigen binding affinity and ADCC activity were correlated, but affinity alone was not sufficient to predict ADCC potency. Thus, elicitation of broadly active ADCC antibodies may require mutations that enable high-affinity antigen recognition along with mutations that optimize factors contributing to functional ADCC activity.
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Affiliation(s)
- Laura E Doepker
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Sonja Danon
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Elias Harkins
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Duncan K Ralph
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Zak Yaffe
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Medical Scientist Training Program, University of Washington School of MedicineSeattleUnited States
| | - Meghan E Garrett
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Amrit Dhar
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Statistics, University of WashingtonSeattleUnited States
| | - Cassia Wagner
- Medical Scientist Training Program, University of Washington School of MedicineSeattleUnited States
| | - Megan M Stumpf
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Dana Arenz
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - James A Williams
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Walter Jaoko
- Department of Medicinal Microbiology, University of NairobiNairobiKenya
| | - Kishor Mandaliya
- Coast Provincial General Hospital, Women’s Health ProjectMombasaKenya
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Julie M Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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23
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Spisak N, Walczak AM, Mora T. Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data. Nucleic Acids Res 2020; 48:10702-10712. [PMID: 33035336 PMCID: PMC7641750 DOI: 10.1093/nar/gkaa825] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/07/2020] [Accepted: 09/18/2020] [Indexed: 01/23/2023] Open
Abstract
Somatic hypermutations of immunoglobulin (Ig) genes occurring during affinity maturation drive B-cell receptors’ ability to evolve strong binding to their antigenic targets. The landscape of these mutations is highly heterogeneous, with certain regions of the Ig gene being preferentially targeted. However, a rigorous quantification of this bias has been difficult because of phylogenetic correlations between sequences and the interference of selective forces. Here, we present an approach that corrects for these issues, and use it to learn a model of hypermutation preferences from a recently published large IgH repertoire dataset. The obtained model predicts mutation profiles accurately and in a reproducible way, including in the previously uncharacterized Complementarity Determining Region 3, revealing that both the sequence context of the mutation and its absolute position along the gene are important. In addition, we show that hypermutations occurring concomittantly along B-cell lineages tend to co-localize, suggesting a possible mechanism for accelerating affinity maturation.
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Affiliation(s)
- Natanael Spisak
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, 24 rue Lhomond, 75005 Paris, France
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24
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Zhou JQ, Kleinstein SH. Position-Dependent Differential Targeting of Somatic Hypermutation. THE JOURNAL OF IMMUNOLOGY 2020; 205:3468-3479. [PMID: 33188076 DOI: 10.4049/jimmunol.2000496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/04/2020] [Indexed: 01/28/2023]
Abstract
Somatic hypermutation (SHM) generates much of the Ab diversity necessary for affinity maturation and effective humoral immunity. The activation-induced cytidine deaminase-induced DNA lesions and error-prone repair that underlie SHM are known to exhibit intrinsic biases when targeting the Ig sequences. Computational models for SHM targeting often model the targeting probability of a nucleotide in a motif-based fashion, assuming that the same DNA motif is equally likely to be targeted regardless of its position along the Ig sequence. The validity of this assumption, however, has not been rigorously studied in vivo. In this study, by analyzing a large collection of 956,157 human Ig sequences while controlling for the confounding influence of selection, we show that the likelihood of a DNA 5-mer motif being targeted by SHM is not the same at different positions in the same Ig sequence. We found position-dependent differential SHM targeting for about three quarters of the 38 and 269 unique motifs from more than half of the 292 and 1912 motif-allele pairs analyzed using productive and nonproductive Ig sequences, respectively. The direction of the differential SHM targeting was largely conserved across individuals with no allele-specific effect within an IgH variable gene family, but was not consistent with general decay of SHM targeting with increasing distance from the transcription start site. However, SHM targeting did correlate positively with the mutability of the wider sequence neighborhood surrounding the motif. These findings provide insights and future directions for computational efforts toward modeling SHM.
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Affiliation(s)
- Julian Q Zhou
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511; and
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511; and .,Department of Pathology and Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511
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25
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Isolation of anti-VEGF monoclonal antibodies with neutralizing effects from an Astragalus-induced immune antibody library. Int Immunopharmacol 2020; 88:107007. [PMID: 33182041 DOI: 10.1016/j.intimp.2020.107007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022]
Abstract
The Astragalus membranaceus polysaccharides (APS) can improve immunity and enhance treatment reactions. This study analyzed the effects of effective antivascular endothelial growth factor (anti-VEGF) antibody production in mice treated with APS. After APS treatment, the serum of mice produced the antibody reactions that can cross-validate VEGF. The isolated single-chain fragment variable (scFv) antibodies could neutralize VEGF and inhibit in vivo tumor growth. Of the scFvs, scFv 4E can significantly compete the interaction of bevacizumab with VEGF. In cell experiments, scFv 4E effectively inhibited human umbilical vein endothelial cells induced by VEGF in vitro. In a matrix gel-assisted angiogenesis model, scFv 4E significantly inhibited angiogenesis reactions. In addition, in a xenograft model established in the colorectal cancer cell strain HCT116, scFv 4E treatment inhibited tumor growth by up to 52.7%. Finally, molecule docking was performed to simulate the complex interactions of scFv 4E and VEGF, the main driving forces of which involve the hydrophobic interactions and hydrogen bonds of Tyr108 and Tyr 109 of the complementarity-determining region H3 loop with VEGF. The results help in establishing antibody library with high diversity for selecting antibodies with specificity. In addition, this study indirectly expounded the correlations of APS enhancing immunity regulation in vivo.
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26
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Swiatczak B. Genomic Stress Responses Drive Lymphocyte Evolvability: An Ancient and Ubiquitous Mechanism. Bioessays 2020; 42:e2000032. [PMID: 32767393 DOI: 10.1002/bies.202000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/03/2020] [Indexed: 12/15/2022]
Abstract
Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general.
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Affiliation(s)
- Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, 96 Jinzhai Rd., Hefei, 230026, China
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27
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Marks C, Deane CM. How repertoire data are changing antibody science. J Biol Chem 2020; 295:9823-9837. [PMID: 32409582 DOI: 10.1074/jbc.rev120.010181] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Antibodies are vital proteins of the immune system that recognize potentially harmful molecules and initiate their removal. Mammals can efficiently create vast numbers of antibodies with different sequences capable of binding to any antigen with high affinity and specificity. Because they can be developed to bind to many disease agents, antibodies can be used as therapeutics. In an organism, after antigen exposure, antibodies specific to that antigen are enriched through clonal selection, expansion, and somatic hypermutation. The antibodies present in an organism therefore report on its immune status, describe its innate ability to deal with harmful substances, and reveal how it has previously responded. Next-generation sequencing technologies are being increasingly used to query the antibody, or B-cell receptor (BCR), sequence repertoire, and the amount of BCR data in public repositories is growing. The Observed Antibody Space database, for example, currently contains over a billion sequences from 68 different studies. Repertoires are available that represent both the naive state (i.e. antigen-inexperienced) and that after immunization. This wealth of data has created opportunities to learn more about our immune system. In this review, we discuss the many ways in which BCR repertoire data have been or could be exploited. We highlight its utility for providing insights into how the naive immune repertoire is generated and how it responds to antigens. We also consider how structural information can be used to enhance these data and may lead to more accurate depictions of the sequence space and to applications in the discovery of new therapeutics.
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Affiliation(s)
- Claire Marks
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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28
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Abstract
The origins of the various elements in the human antibody repertoire have been and still are subject to considerable uncertainty. Uncertainty in respect of whether the various elements have always served a specific defense function or whether they were co-opted from other organismal roles to form a crude naïve repertoire that then became more complex as combinatorial mechanisms were added. Estimates of the current size of the human antibody naïve repertoire are also widely debated with numbers anywhere from 10 million members, based on experimentally derived numbers, to in excess of one thousand trillion members or more, based on the different sequences derived from theoretical combinatorial calculations. There are questions that are relevant at both ends of this number spectrum. At the lower bound it could be questioned whether this is an insufficient repertoire size to counter all the potential antigen-bearing pathogens. At the upper bound the question is rather simpler: How can any individual interrogate such an astronomical number of antibody-bearing B cells in a timeframe that is meaningful? This review evaluates the evolutionary aspects of the adaptive immune system, the calculations that lead to the large repertoire estimates, some of the experimental evidence pointing to a more restricted repertoire whose variation appears to derive from convergent 'structure and specificity features', and includes a theoretical model that seems to support it. Finally, a solution that may reconcile the size difference anomaly, which is still a hot subject of debate, is suggested.
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29
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Kreer C, Gruell H, Mora T, Walczak AM, Klein F. Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies. Vaccines (Basel) 2020; 8:vaccines8010013. [PMID: 31906351 PMCID: PMC7157687 DOI: 10.3390/vaccines8010013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/22/2022] Open
Abstract
The human antibody repertoire is generated by the recombination of different gene segments as well as by processes of somatic mutation. Together these mechanisms result in a tremendous diversity of antibodies that are able to combat various pathogens including viruses and bacteria, or malignant cells. In this review, we summarize the opportunities and challenges that are associated with the analyses of the B cell receptor repertoire and the antigen-specific B cell response. We will discuss how recent advances have increased our understanding of the antibody response and how repertoire analyses can be exploited to inform on vaccine strategies, particularly against HIV-1.
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Affiliation(s)
- Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure (PSL University), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France; (T.M.); (A.M.W.)
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure (PSL University), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France; (T.M.); (A.M.W.)
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Correspondence:
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30
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Saunders KO, Wiehe K, Tian M, Acharya P, Bradley T, Alam SM, Go EP, Scearce R, Sutherland L, Henderson R, Hsu AL, Borgnia MJ, Chen H, Lu X, Wu NR, Watts B, Jiang C, Easterhoff D, Cheng HL, McGovern K, Waddicor P, Chapdelaine-Williams A, Eaton A, Zhang J, Rountree W, Verkoczy L, Tomai M, Lewis MG, Desaire HR, Edwards RJ, Cain DW, Bonsignori M, Montefiori D, Alt FW, Haynes BF. Targeted selection of HIV-specific antibody mutations by engineering B cell maturation. Science 2019; 366:eaay7199. [PMID: 31806786 PMCID: PMC7168753 DOI: 10.1126/science.aay7199] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/05/2019] [Indexed: 12/16/2022]
Abstract
INTRODUCTION A major goal of HIV-1 vaccine development is the design of immunogens that induce broadly neutralizing antibodies (bnAbs). However, vaccination of humans has not resulted in the induction of affinity-matured and potent HIV-1 bnAbs. To devise effective vaccine strategies, we previously determined the maturation pathway of select HIV-1 bnAbs from acute infection through neutralizing antibody development. During their evolution, bnAbs acquire an abundance of improbable amino acid substitutions as a result of nucleotide mutations at variable region sequences rarely targeted by activation-induced cytidine deaminase, the enzyme responsible for antibody mutation. A subset of improbable mutations is essential for broad neutralization activity, and their acquisition represents a key roadblock to bnAb development. RATIONALE Current bnAb lineage-based vaccine strategies can initiate bnAb lineage development in animal models but have not specifically elicited the improbable mutations required for neutralization breadth. Induction of bnAbs requires vaccine strategies that specifically engage bnAb precursors and subsequently select for improbable mutations required for broadly neutralizing activity. We hypothesized that vaccination with immunogens that bind with moderate to high affinity to bnAb B cell precursors, and with higher affinity to precursors that have acquired improbable mutations, could initiate bnAb B cell lineages and select for key improbable mutations required for bnAb development. RESULTS We elicited serum neutralizing HIV-1 antibodies in human bnAb precursor knock-in mice and wild-type macaques vaccinated with immunogens designed to select for improbable mutations. We designed two HIV-1 envelope immunogens that bound precursor B cells of either a CD4 binding site or V3-glycan bnAb lineage. In vitro, these immunogens bound more strongly to bnAb precursors once the precursor acquired the desired improbable mutations. Vaccination of macaques with the CD4 binding site–targeting immunogen induced CD4 binding site serum neutralizing antibodies. Antibody sequences elicited in human bnAb precursor knock-in mice encoded functional improbable mutations critical for bnAb development. In bnAb precursor knock-in mice, we isolated a vaccine-elicited monoclonal antibody bearing functional improbable mutations that was capable of neutralizing multiple HIV-1 global isolates. Structures of a bnAb precursor, a bnAb, and the vaccine-elicited antibody revealed the precise roles that acquired improbable mutations played in recognizing the HIV-1 envelope. Thus, our immunogens elicited antibody responses in macaques and knock-in mice that exhibited the mutational patterns, structural characteristics, or neutralization profiles of nascent broadly neutralizing antibodies. CONCLUSION Our study represents a proof of concept for targeted selection of improbable mutations to guide antibody affinity maturation. Moreover, this study demonstrates a rational strategy for sequential immunogen design to circumvent the difficult roadblocks in HIV-1 bnAb induction by vaccination. We show that immunogens should exhibit differences in affinity across antibody maturation stages where improbable mutations are necessary for the desired antibody function. This strategy of selection of specific antibody nucleotides by immunogen design can be applied to B cell lineages targeting other pathogens where guided affinity maturation is needed for a protective antibody response.
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Affiliation(s)
- Kevin O Saunders
- Human Vaccine Institute and 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
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Priyamvada Acharya
- Human Vaccine Institute and Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Todd Bradley
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - S Munir Alam
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eden P Go
- Department of Chemistry, University of Kansas, Lawrence, KS 66049, USA
| | - Richard Scearce
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura Sutherland
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rory Henderson
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Haiyan Chen
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nelson R Wu
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Brian Watts
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chuancang Jiang
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David Easterhoff
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hwei-Ling Cheng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kelly McGovern
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peyton Waddicor
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aimee Chapdelaine-Williams
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Eaton
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jinsong Zhang
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wes Rountree
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laurent Verkoczy
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark Tomai
- Corporate Research Materials Lab, 3M Company, St. Paul, MN 55144, USA
| | | | - Heather R Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66049, USA
| | - Robert J Edwards
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Derek W Cain
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David Montefiori
- Human Vaccine Institute and Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Barton F Haynes
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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Abstract
Neutralizing antibodies against human immunodeficiency virus subtype 1 (HIV-1) bind to its envelope glycoprotein (Env). Half of the molecular mass of Env is carbohydrate making it one of the most heavily glycosylated proteins known in nature. HIV-1 Env glycans are derived from the host and present a formidable challenge for host anti-glycan antibody induction. Anti-glycan antibody induction is challenging because anti-HIV-1 glycan antibodies should recognize Env antigen while not acquiring autoreactivity. Thus, the glycan network on HIV-1 Env is referred to as the glycan shield. Despite the challenges presented by immune recognition of host-derived glycans, neutralizing antibodies capable of binding the glycans on HIV-1 Env can be generated by the host immune system in the setting of HIV-1 infection. In particular, a cluster of high mannose glycans, including an N-linked glycan at position 332, form the high mannose patch and are targeted by a variety of broadly neutralizing antibodies. These high mannose patch-directed HIV-1 antibodies can be categorized into distinct categories based on their antibody paratope structure, neutralization activity, and glycan and peptide reactivity. Below we will compare and contrast each of these classes of HIV-1 glycan-dependent antibodies and describe vaccine design efforts to elicit each of these antibody types.
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32
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Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen IV FA, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM. Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming. Front Immunol 2019; 10:435. [PMID: 30936866 PMCID: PMC6431624 DOI: 10.3389/fimmu.2019.00435] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulins or antibodies are the main effector molecules of the B-cell lineage and are encoded by hundreds of variable (V), diversity (D), and joining (J) germline genes, which recombine to generate enormous IG diversity. Recently, high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) of recombined V-(D)-J genes has offered unprecedented insights into the dynamics of IG repertoires in health and disease. Faithful biological interpretation of AIRR-seq studies depends upon the annotation of raw AIRR-seq data, using reference germline gene databases to identify the germline genes within each rearrangement. Existing reference databases are incomplete, as shown by recent AIRR-seq studies that have inferred the existence of many previously unreported polymorphisms. Completing the documentation of genetic variation in germline gene databases is therefore of crucial importance. Lymphocyte receptor genes and alleles are currently assigned by the Immunoglobulins, T cell Receptors and Major Histocompatibility Nomenclature Subcommittee of the International Union of Immunological Societies (IUIS) and managed in IMGT®, the international ImMunoGeneTics information system® (IMGT). In 2017, the IMGT Group reached agreement with a group of AIRR-seq researchers on the principles of a streamlined process for identifying and naming inferred allelic sequences, for their incorporation into IMGT®. These researchers represented the AIRR Community, a network of over 300 researchers whose objective is to promote all aspects of immunoglobulin and T-cell receptor repertoire studies, including the standardization of experimental and computational aspects of AIRR-seq data generation and analysis. The Inferred Allele Review Committee (IARC) was established by the AIRR Community to devise policies, criteria, and procedures to perform this function. Formalized evaluations of novel inferred sequences have now begun and submissions are invited via a new dedicated portal (https://ogrdb.airr-community.org). Here, we summarize recommendations developed by the IARC-focusing, to begin with, on human IGHV genes-with the goal of facilitating the acceptance of inferred allelic variants of germline IGHV genes. We believe that this initiative will improve the quality of AIRR-seq studies by facilitating the description of human IG germline gene variation, and that in time, it will expand to the documentation of TR and IG genes in many vertebrate species.
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Affiliation(s)
- Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Cathrine Scheepers
- Center for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - William D. Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Christian E. Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Davide Bagnara
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | | | | | | | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Chaim A. Schramm
- Vaccine Research Center, National Institutes of Health, Washington, DC, United States
| | - Nishanth Marthandan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Jamie Scott
- Department of Molecular Biology and Biochemistry, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Victor Greiff
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | | | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jacob S. Sherkow
- Innovation Center for Law and Technology, New York Law School, New York, NY, United States
| | - Sofia Kossida
- IMGT, The International ImMunoGenetics information system (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), CNRS, Institut de Génétique Humaine, Université de Montpellier, Montpellier, France
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGenetics information system (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), CNRS, Institut de Génétique Humaine, Université de Montpellier, Montpellier, France
| | - Menno C. van Zelm
- Department of Immunology and Pathology, Central Clinical School, The Alfred Hospital, Monash University, Melbourne, VIC, 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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33
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V H1-69 antiviral broadly neutralizing antibodies: genetics, structures, and relevance to rational vaccine design. Curr Opin Virol 2019; 34:149-159. [PMID: 30884330 DOI: 10.1016/j.coviro.2019.02.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) are potential therapeutic molecules and valuable tools for studying conserved viral targets for vaccine and drug design. Interestingly, antibody responses to conserved epitopes can be highly convergent at the molecular level. Human antibodies targeting a number of viral antigens have often been found to utilize a restricted set of immunoglobulin germline genes in different individuals. Here we review recent knowledge on VH1-69-encoded antibodies in antiviral responses to influenza virus, HCV, and HIV-1. These antibodies share common genetic and structural features, and often develop neutralizing activity against a broad spectrum of viral strains. Understanding the genetic and structural characteristics of such antibodies and the target epitopes should help advance novel strategies to elicit bnAbs through vaccination.
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