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Franciskovic E, Thörnqvist L, Greiff L, Gasset M, Ohlin M. Linear epitopes of bony fish β-parvalbumins. Front Immunol 2024; 15:1293793. [PMID: 38504976 PMCID: PMC10948427 DOI: 10.3389/fimmu.2024.1293793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024] Open
Abstract
Introduction Fish β-parvalbumins are common targets of allergy-causing immunity. The nature of antibody responses to such allergens determines the biological outcome following exposure to fish. Specific epitopes on these allergens recognised by antibodies are incompletely characterised. Methods High-content peptide microarrays offer a solution to the identification of linear epitopes recognised by antibodies. We characterized IgG and IgG4 recognition of linear epitopes of fish β-parvalbumins defined in the WHO/IUIS allergen database as such responses hold the potential to counter an allergic reaction to these allergens. Peripheral blood samples, collected over three years, of 15 atopic but not fish-allergic subjects were investigated using a microarray platform that carried every possible 16-mer peptide of known isoforms and isoallergens of these and other allergens. Results Interindividual differences in epitope recognition patterns were observed. In contrast, reactivity patterns in a given individual were by comparison more stable during the 3 years-course of the study. Nevertheless, evidence of the induction of novel specificities over time was identified across multiple regions of the allergens. Particularly reactive epitopes were identified in the D helix of Cyp c 1 and in the C-terminus of Gad c 1 and Gad m 1.02. Residues important for the recognition of certain linear epitopes were identified. Patterns of differential recognition of isoallergens were observed in some subjects. Conclusions Altogether, comprehensive analysis of antibody recognition of linear epitopes of multiple allergens enables characterisation of the nature of the antibody responses targeting this important set of food allergens.
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Affiliation(s)
| | | | - Lennart Greiff
- Department of Otorhinolaryngology, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Maria Gasset
- Institute of Physical-Chemistry Blas Cabrera, Spanish National Research Council, Madrid, Spain
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
- SciLifeLab, Lund University, Lund, Sweden
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Almazán NM, Rahbar A, Carlsson M, Hoffman T, Kolstad L, Rönnberg B, Pantalone MR, Fuchs IL, Nauclér A, Ohlin M, Sacharczuk M, Religa P, Amér S, Molnár C, Lundkvist Å, Susrud A, Sörensen B, Söderberg-Nauclér C. Influenza-A mediated pre-existing immunity levels to SARS-CoV-2 could predict early COVID-19 outbreak dynamics. iScience 2023; 26:108441. [PMID: 38144451 PMCID: PMC10746369 DOI: 10.1016/j.isci.2023.108441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/14/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023] Open
Abstract
Susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is highly variable and could be mediated by a cross-protective pre-immunity. We identified 14 cross-reactive peptides between SARS-CoV-2 and influenza A H1N1, H3N2, and human herpesvirus (HHV)-6A/B with potential relevance. The H1N1 peptide NGVEGF was identical to a peptide in the most critical receptor binding motif in SARS-CoV-2 spike protein that interacts with the angiotensin converting enzyme 2 receptor. About 62%-73% of COVID-19-negative blood donors in Stockholm had antibodies to this peptide in the early pre-vaccination phase of the pandemic. Seasonal flu vaccination enhanced neutralizing capacity to SARS-CoV-2 and T cell immunity to this peptide. Mathematical modeling taking the estimated pre-immunity levels to flu into account could fully predict pre-Omicron SARS-CoV-2 outbreaks in Stockholm and India. This cross-immunity provides mechanistic explanations to the epidemiological observation that influenza vaccination protected people against early SARS-CoV-2 infections and implies that flu-mediated cross-protective immunity significantly dampened the first SARS-CoV-2 outbreaks.
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Affiliation(s)
- Nerea Martín Almazán
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 86 Huddinge Stockholm, Sweden
| | - Afsar Rahbar
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
| | - Marcus Carlsson
- Centre for the Mathematical Sciences, Lund University, 223 62 Lund, Sweden
| | - Tove Hoffman
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Linda Kolstad
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Bengt Rönnberg
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Mattia Russel Pantalone
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
| | - Ilona Lewensohn Fuchs
- Department of Labortory Medicine, Division of Clinical Microbiology, Karolinska Institutet, 141 86 Huddinge Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, 141 86 Huddinge Stockholm, Sweden
| | - Anna Nauclér
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology and SciLifeLab Human Antibody Therapeutics Infrastructure Unit, Lund University, 223 62 Lund, Sweden
| | - Mariusz Sacharczuk
- Faculty of Pharmacy with the Laboratory Medicine Division, Department of Pharmacodynamics, Medical University of Warsaw, Centre for Preclinical Research and Technology, Banacha 1B, 02-091 Warsaw, Poland
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Piotr Religa
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Stefan Amér
- Familjeläkarna Saltsjöbaden, 133 34 Saltsjöbaden, Sweden
| | - Christian Molnár
- Familjeläkarna Saltsjöbaden, 133 34 Saltsjöbaden, Sweden
- Department of Neurobiology, Care Sciences and Society, NVS, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | | | | | - Cecilia Söderberg-Nauclér
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Institute of Biomedicine, Unit for Infection and Immunology, MediCity Research Laboratory, University of Turku, FI-20014 Turku, Finland
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Hueting D, Schriever K, Sun R, Vlachiotis S, Zuo F, Du L, Persson H, Hofström C, Ohlin M, Walldén K, Buggert M, Hammarström L, Marcotte H, Pan-Hammarström Q, Andréll J, Syrén PO. Design, structure and plasma binding of ancestral β-CoV scaffold antigens. Nat Commun 2023; 14:6527. [PMID: 37845250 PMCID: PMC10579346 DOI: 10.1038/s41467-023-42200-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Cryo-EM analysis of the AnSAs yield high resolution structures (2.6-2.8 Å) indicating a closed pre-fusion conformation in which all three receptor-binding domains (RBDs) are facing downwards. The structures reveal an intricate hydrogen-bonding network mediated by well-resolved loops, both within and across monomers, tethering the N-terminal domain and RBD together. We show that AnSA-5 can induce and boost a broad-spectrum immune response against the wild-type RBD as well as circulating variants of concern in an immune organoid model derived from tonsils. Finally, we highlight how AnSAs are potent scaffolds by replacing the ancestral RBD with the wild-type sequence, which restores ACE2 binding and increases the interaction with convalescent plasma.
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Affiliation(s)
- David Hueting
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karen Schriever
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rui Sun
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Stelios Vlachiotis
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fanglei Zuo
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Likun Du
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Helena Persson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Camilla Hofström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Mats Ohlin
- Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Karin Walldén
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Disease, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Harold Marcotte
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juni Andréll
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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5
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Peres A, Lees WD, Rodriguez OL, Lee NY, Polak P, Hope R, Kedmi M, Collins AM, Ohlin M, Kleinstein S, Watson C, Yaari G. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Res 2023; 51:e86. [PMID: 37548401 PMCID: PMC10484671 DOI: 10.1093/nar/gkad603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023] Open
Abstract
In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).
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Affiliation(s)
- Ayelet Peres
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7JE, UK
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Noah Y Lee
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Pazit Polak
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Ronen Hope
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Meirav Kedmi
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, 5262000, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Andrew M Collins
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mats Ohlin
- Department of Immunotechnology Lund University, Lund, 221 00, Sweden
| | - Steven H Kleinstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
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Hoh RA, Thörnqvist L, Yang F, Godzwon M, King JJ, Lee JY, Greiff L, Boyd SD, Ohlin M. Clonal evolution and stereotyped sequences of human IgE lineages in aeroallergen-specific immunotherapy. J Allergy Clin Immunol 2023; 152:214-229. [PMID: 36828082 DOI: 10.1016/j.jaci.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND Allergic disease reflects specific inflammatory processes initiated by interaction between allergen and allergen-specific IgE. Specific immunotherapy (SIT) is an effective long-term treatment option, but the mechanisms by which SIT provides desensitization are not well understood. OBJECTIVE Our aim was to characterize IgE sequences expressed by allergen-specific B cells over a 3-year longitudinal study of patients with aeroallergies who were undergoing SIT. METHODS Allergen-specific IgE-expressing clones were identified by using combinatorial single-chain variable fragment libraries and tracked in PBMCs and nasal biopsy samples over a 3-year period with antibody gene repertoire sequencing. The characteristics of private IgE-expressing clones were compared with those of stereotyped or "public" IgE responses to the grass pollen allergen Phleum pratense (Phl p) 2. RESULT Members of the same allergen-specific IgE lineages were observed in nasal biopsy samples and blood, and lineages detected at baseline persisted in blood and nasal biopsy samples after 3 years of SIT, including B cells that express IgE. Evidence of progressive class switch recombination to IgG subclasses was observed after 3 years of SIT. A common stereotyped Phl p 2-specific antibody heavy chain sequence was detected in multiple donors. The amino acid residues enriched in IgE-stereotyped sequences from seropositive donors were analyzed with machine learning and k-mer motif discovery. Stereotyped IgE sequences had lower overall rates of somatic hypermutation and antigen selection than did single-chain variable fragment-derived allergen-specific sequences or IgE sequences of unknown specificity. CONCLUSION Longitudinal tracking of rare circulating and tissue-resident allergen-specific IgE+ clones demonstrates persistence of allergen-specific IgE+ clones, progressive class switch recombination to IgG subtypes, and distinct maturation of a stereotyped Phl p 2 clonotype.
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Affiliation(s)
- Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, Calif
| | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, Calif
| | | | - Jasmine J King
- Department of Pathology, Stanford University, Stanford, Calif
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, Calif
| | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden; Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, Calif; Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, Calif
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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7
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Lees WD, Christley S, Peres A, Kos JT, Corrie B, Ralph D, Breden F, Cowell LG, Yaari G, Corcoran M, Karlsson Hedestam GB, Ohlin M, Collins AM, Watson CT, Busse CE. AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets. Immunoinformatics (Amst) 2023; 10:100025. [PMID: 37388275 PMCID: PMC10310305 DOI: 10.1016/j.immuno.2023.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.
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Affiliation(s)
- William D. Lees
- Institute of Structural and Molecular Biology, Birkbeck College, London, England
- Human-Centered Computing and Information Science, Institute for Systems and Computer Engineering Technology and Science, Porto, Portugal
| | - Scott Christley
- Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ayelet Peres
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, KY, USA
| | - Brian Corrie
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Lindsay G. Cowell
- Peter O’Donnell Jr. School of Public Health, Department of Immunology, School of Biomedical Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Swede
| | | | - Mats Ohlin
- Department of Immunotechnology and SciLifeLab, Lund University, Lund, Sweden
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, KY, USA
| | - Christian E. Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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8
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Izadi A, Bahnan W, Ohlin M, Nordenfelt P. Reply to Pandey: IgG3 allotypes, modulation of antigen binding by constant domain changes, and therapeutic applications of Fc engineering. Proc Natl Acad Sci U S A 2023; 120:e2306562120. [PMID: 37216528 DOI: 10.1073/pnas.2306562120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Affiliation(s)
- Arman Izadi
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, 221 84, Lund, Sweden
| | - Wael Bahnan
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, 221 84, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, 221 00 Lund, Sweden
- SciLifeLab Drug Discovery and Development, Lund University, 221 00 Lund, Sweden
| | - Pontus Nordenfelt
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, 221 84, Lund, Sweden
- Department of Laboratory Medicine, Clinical Microbiology, Skåne University Hospital Lund, Lund University, 221 85 Lund, Sweden
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9
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Mattsson J, Ljungars A, Carlsson A, Svensson C, Nilsson B, Ohlin M, Frendéus B. Sequence enrichment profiles enable target-agnostic antibody generation for a broad range of antigens. Cell Rep Methods 2023; 3:100475. [PMID: 37323567 PMCID: PMC10261905 DOI: 10.1016/j.crmeth.2023.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/27/2023] [Accepted: 04/17/2023] [Indexed: 06/17/2023]
Abstract
Phenotypic drug discovery (PDD) enables the target-agnostic generation of therapeutic drugs with novel mechanisms of action. However, realizing its full potential for biologics discovery requires new technologies to produce antibodies to all, a priori unknown, disease-associated biomolecules. We present a methodology that helps achieve this by integrating computational modeling, differential antibody display selection, and massive parallel sequencing. The method uses the law of mass action-based computational modeling to optimize antibody display selection and, by matching computationally modeled and experimentally selected sequence enrichment profiles, predict which antibody sequences encode specificity for disease-associated biomolecules. Applied to a phage display antibody library and cell-based antibody selection, ∼105 antibody sequences encoding specificity for tumor cell surface receptors expressed at 103-106 receptors/cell were discovered. We anticipate that this approach will be broadly applicable to molecular libraries coupling genotype to phenotype and to the screening of complex antigen populations for identification of antibodies to unknown disease-associated targets.
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Affiliation(s)
- Jenny Mattsson
- BioInvent, Research, Lund, Sweden
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anne Ljungars
- BioInvent, Research, Lund, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Carolin Svensson
- BioInvent, Research, Lund, Sweden
- Section of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Björn Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Broad Institute, 415 Main Street, Cambridge, MA, USA
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
- SciLifeLab Human Antibody Therapeutics, Lund University, Lund, Sweden
| | - Björn Frendéus
- BioInvent, Research, Lund, Sweden
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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10
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Izadi A, Hailu A, Godzwon M, Wrighton S, Olofsson B, Schmidt T, Söderlund-Strand A, Elder E, Appelberg S, Valsjö M, Larsson O, Wendel-Hansen V, Ohlin M, Bahnan W, Nordenfelt P. Subclass-switched anti-spike IgG3 oligoclonal cocktails strongly enhance Fc-mediated opsonization. Proc Natl Acad Sci U S A 2023; 120:e2217590120. [PMID: 37011197 PMCID: PMC10104557 DOI: 10.1073/pnas.2217590120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Antibodies play a central role in the immune defense against SARS-CoV-2. Emerging evidence has shown that nonneutralizing antibodies are important for immune defense through Fc-mediated effector functions. Antibody subclass is known to affect downstream Fc function. However, whether the antibody subclass plays a role in anti-SARS-CoV-2 immunity remains unclear. Here, we subclass-switched eight human IgG1 anti-spike monoclonal antibodies (mAbs) to the IgG3 subclass by exchanging their constant domains. The IgG3 mAbs exhibited altered avidities to the spike protein and more potent Fc-mediated phagocytosis and complement activation than their IgG1 counterparts. Moreover, combining mAbs into oligoclonal cocktails led to enhanced Fc- and complement receptor-mediated phagocytosis, superior to even the most potent single IgG3 mAb when compared at equivalent concentrations. Finally, in an in vivo model, we show that opsonic mAbs of both subclasses can be protective against a SARS-CoV-2 infection, despite the antibodies being nonneutralizing. Our results suggest that opsonic IgG3 oligoclonal cocktails are a promising idea to explore for therapy against SARS-CoV-2, its emerging variants, and potentially other viruses.
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Affiliation(s)
- Arman Izadi
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, 221 84 Lund, Sweden
| | - Arsema Hailu
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, 221 84 Lund, Sweden
| | - Magdalena Godzwon
- Department of Immunotechnology, Faculty of Engineering, Lund University, 221 00 Lund, Sweden
| | - Sebastian Wrighton
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, 221 84 Lund, Sweden
| | - Berit Olofsson
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, 221 84 Lund, Sweden
| | - Tobias Schmidt
- Department of Clinical Sciences Lund, Division of Pediatrics, Faculty of Medicine, Lund University, 221 84 Lund, Sweden
- Wallenberg Center for Molecular Medicine, Faculty of Medicine, Lund University, 221 84 Lund, Sweden
| | - Anna Söderlund-Strand
- Department of Laboratory Medicine, Clinical Microbiology, Skåne University Hospital Lund, Lund University, 221 85 Lund, Sweden
| | - Elizabeth Elder
- Department of Microbiology, National Veterinary Institute, 751 89 Uppsala, Sweden
| | - Sofia Appelberg
- Department of Microbiology, Public Health Agency of Sweden, 171 82 Stockholm, Sweden
| | | | | | | | - Mats Ohlin
- Department of Immunotechnology, Faculty of Engineering, Lund University, 221 00 Lund, Sweden
- SciLifeLab Drug Discovery and Development, Lund University, 221 00 Lund, Sweden
| | - Wael Bahnan
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, 221 84 Lund, Sweden
| | - Pontus Nordenfelt
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, 221 84 Lund, Sweden
- Department of Laboratory Medicine, Clinical Microbiology, Skåne University Hospital Lund, Lund University, 221 85 Lund, Sweden
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11
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Jackson KJL, Kos JT, Lees W, Gibson WS, Smith ML, Peres A, Yaari G, Corcoran M, Busse CE, Ohlin M, Watson CT, Collins AM. A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice. Front Immunol 2022; 13:888555. [PMID: 35720344 PMCID: PMC9205180 DOI: 10.3389/fimmu.2022.888555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Strain variations were identified in the Ighm and Ighg2b genes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted at https://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that current MGP assemblies are unsuitable for the comprehensive documentation of germline IGHVs and more efforts will be needed to establish strain-specific reference sets.
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Affiliation(s)
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - William S. Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Melissa Laird Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Ayelet Peres
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christian E. Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
- *Correspondence: Corey T. Watson, ; Andrew M. Collins,
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
- *Correspondence: Corey T. Watson, ; Andrew M. Collins,
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12
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Thörnqvist L, Sjöberg R, Greiff L, van Hage M, Ohlin M. Linear Epitope Binding Patterns of Grass Pollen-Specific Antibodies in Allergy and in Response to Allergen-Specific Immunotherapy. Front Allergy 2022; 3:859126. [PMID: 35769580 PMCID: PMC9234942 DOI: 10.3389/falgy.2022.859126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Allergic diseases affect many individuals world-wide and are dependent on the interaction between allergens and antibodies of the IgE isotype. Allergen-specific immunotherapy (AIT) can alter the development of the disease, e.g., through induction of allergen-specific IgG that block allergen-IgE interactions. The knowledge of epitopes recognized by allergy-causing and protective antibodies are limited. Therefore, we developed an allergome-wide peptide microarray, aiming to track linear epitope binding patterns in allergic diseases and during AIT. Here, we focused on immune responses to grass pollen allergens and found that such epitopes were commonly recognized before initiation of AIT and that AIT commonly resulted in increased antibody production against additional epitopes already after 1 year of treatment. The linear epitope binding patterns were highly individual, both for subjects subjected to and for individuals not subjected to AIT. Still, antibodies against some linear epitopes were commonly developed during AIT. For example, the two rigid domains found in grass pollen group 5 allergens have previously been associated to a diversity of discontinuous epitopes. Here, we present evidence that also the flexible linker, connecting these domains, contains regions of linear epitopes against which antibodies are developed during AIT. We also describe some commonly recognized linear epitopes on Phl p 2 and suggest how antibodies against these epitopes may contribute to or prevent allergy in relation to a well-defined stereotyped/public IgE response against the same allergen. Finally, we identify epitopes that induce cross-reactive antibodies, but also antibodies that exclusively bind one of two highly similar variants of a linear epitope. Our findings highlight the complexity of antibody recognition of linear epitopes, with respect to both the studied individuals and the examined allergens. We expect that many of the findings in this study can be generalized also to discontinuous epitopes and that allergen peptide microarrays provide an important tool for enhancing the understanding of allergen-specific antibodies in allergic disease and during AIT.
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Affiliation(s)
| | - Ronald Sjöberg
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Lennart Greiff
- Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Marianne van Hage
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
- *Correspondence: Mats Ohlin
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13
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Bahnan W, Wrighton S, Sundwall M, Bläckberg A, Larsson O, Höglund U, Khakzad H, Godzwon M, Walle M, Elder E, Strand AS, Happonen L, André O, Ahnlide JK, Hellmark T, Wendel-Hansen V, Wallin RP, Malmstöm J, Malmström L, Ohlin M, Rasmussen M, Nordenfelt P. Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2. Front Immunol 2022; 12:808932. [PMID: 35095897 PMCID: PMC8796240 DOI: 10.3389/fimmu.2021.808932] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Spike-specific antibodies are central to effective COVID19 immunity. Research efforts have focused on antibodies that neutralize the ACE2-Spike interaction but not on non-neutralizing antibodies. Antibody-dependent phagocytosis is an immune mechanism enhanced by opsonization, where typically, more bound antibodies trigger a stronger phagocyte response. Here, we show that Spike-specific antibodies, dependent on concentration, can either enhance or reduce Spike-bead phagocytosis by monocytes independently of the antibody neutralization potential. Surprisingly, we find that both convalescent patient plasma and patient-derived monoclonal antibodies lead to maximum opsonization already at low levels of bound antibodies and is reduced as antibody binding to Spike protein increases. Moreover, we show that this Spike-dependent modulation of opsonization correlate with the outcome in an experimental SARS-CoV-2 infection model. These results suggest that the levels of anti-Spike antibodies could influence monocyte-mediated immune functions and propose that non-neutralizing antibodies could confer protection to SARS-CoV-2 infection by mediating phagocytosis.
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Affiliation(s)
- Wael Bahnan
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Sebastian Wrighton
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Martin Sundwall
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Anna Bläckberg
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden.,Infectious Disease Clinic, Skåne University Hospital, Lund, Sweden
| | | | | | - Hamed Khakzad
- Equipe Signalisation Calcique et Infections Microbiennes, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1282, Gif-sur-Yvette, France
| | | | - Maria Walle
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Anna Söderlund Strand
- Department of Laboratory Medicine, Clinical Microbiology, Skane University Hospital Lund, Lund University, Lund, Sweden
| | - Lotta Happonen
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Oscar André
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Johannes Kumra Ahnlide
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Thomas Hellmark
- Department of Clinical Sciences Lund, Nephrology, Skane University Hospital Lund, Lund University, Lund, Sweden
| | | | | | - Johan Malmstöm
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Lars Malmström
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden.,Institute for Computational Science, Zurich, Switzerland
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.,SciLifeLab Drug Discovery and Development, Lund University, Lund, Sweden
| | - Magnus Rasmussen
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden.,Infectious Disease Clinic, Skåne University Hospital, Lund, Sweden
| | - Pontus Nordenfelt
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
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14
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Huang Y, Thörnqvist L, Ohlin M. Computational Inference, Validation, and Analysis of 5'UTR-Leader Sequences of Alleles of Immunoglobulin Heavy Chain Variable Genes. Front Immunol 2021; 12:730105. [PMID: 34671351 PMCID: PMC8521166 DOI: 10.3389/fimmu.2021.730105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/06/2021] [Indexed: 12/05/2022] Open
Abstract
Upstream and downstream sequences of immunoglobulin genes may affect the expression of such genes. However, these sequences are rarely studied or characterized in most studies of immunoglobulin repertoires. Inference from large, rearranged immunoglobulin transcriptome data sets offers an opportunity to define the upstream regions (5'-untranslated regions and leader sequences). We have now established a new data pre-processing procedure to eliminate artifacts caused by a 5'-RACE library generation process, reanalyzed a previously studied data set defining human immunoglobulin heavy chain genes, and identified novel upstream regions, as well as previously identified upstream regions that may have been identified in error. Upstream sequences were also identified for a set of previously uncharacterized germline gene alleles. Several novel upstream region variants were validated, for instance by their segregation to a single haplotype in heterozygotic subjects. SNPs representing several sequence variants were identified from population data. Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions.
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Affiliation(s)
| | | | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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15
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Ohlin M. Poorly Expressed Alleles of Several Human Immunoglobulin Heavy Chain Variable Genes are Common in the Human Population. Front Immunol 2021; 11:603980. [PMID: 33717051 PMCID: PMC7943739 DOI: 10.3389/fimmu.2020.603980] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/08/2020] [Indexed: 12/23/2022] Open
Abstract
Extensive diversity has been identified in the human heavy chain immunoglobulin locus, including allelic variation, gene duplication, and insertion/deletion events. Several genes have been suggested to be deleted in many haplotypes. Such findings have commonly been based on inference of the germline repertoire from data sets covering antibody heavy chain encoding transcripts. The inference process operates under conditions that may limit identification of genes transcribed at low levels. The presence of rare transcripts that would indicate the existence of poorly expressed alleles in haplotypes that otherwise appear to have deleted these genes has been assessed in the present study. Alleles IGHV1-2*05, IGHV1-3*02, IGHV4-4*01, and IGHV7-4-1*01 were all identified as being expressed from multiple haplotypes, but only at low levels, haplotypes that by inference often appeared not to express these genes at all. These genes are thus not as commonly deleted as previously thought. An assessment of the 5' untranslated region (up to and including the TATA-box), the signal peptide-encoding part of the gene, and the 3'-heptamer suggests that the alleles have no or minimal sequence difference in these regions in comparison to highly expressed alleles. This suggest that they may be able to participate in immunoglobulin gene rearrangement, transcription and translation. However, all four poorly expressed alleles harbor unusual sequence variants within their coding region that may compromise the functionality of the encoded products, thereby limiting their incorporation into the immunoglobulin repertoire. Transcripts based on IGHV7-4-1*01 that had undergone somatic hypermutation and class switch had mutated the codon that encoded the unusual residue in framework region 3 (cysteine 92; located far from the antigen binding site). This finding further supports the poor compatibility of this unusual residue in a fully functional protein product. Indications of a linkage disequilibrium were identified as IGHV1-2*05 and IGHV4-4*01 co-localized to the same haplotypes. Furthermore, transcripts of two of the poorly expressed alleles (IGHV1-3*02 and IGHV4-4*01) mostly do not encode in-frame, functional products, suggesting that these alleles might be essentially non-functional. It is proposed that the functionality status of immunoglobulin genes should also include assessment of their ability to encode functional protein products.
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Affiliation(s)
- Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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16
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Collins AM, Peres A, Corcoran MM, Watson CT, Yaari G, Lees WD, Ohlin M. Commentary on Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: relevance in infectious diseases and vaccination studies in human populations. Genes Immun 2021; 22:335-338. [PMID: 34667305 PMCID: PMC8674141 DOI: 10.1038/s41435-021-00152-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Andrew M. Collins
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW Australia
| | - Ayelet Peres
- grid.22098.310000 0004 1937 0503Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel ,grid.22098.310000 0004 1937 0503Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Martin M. Corcoran
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Corey T. Watson
- grid.266623.50000 0001 2113 1622Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY USA
| | - Gur Yaari
- grid.22098.310000 0004 1937 0503Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel ,grid.22098.310000 0004 1937 0503Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - William D. Lees
- grid.509978.a0000 0004 0432 693XInstitute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Mats Ohlin
- grid.4514.40000 0001 0930 2361Department of Immunotechnology, Lund University, Lund, Sweden
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17
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Smakaj E, Babrak L, Ohlin M, Shugay M, Briney B, Tosoni D, Galli C, Grobelsek V, D'Angelo I, Olson B, Reddy S, Greiff V, Trück J, Marquez S, Lees W, Miho E. Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. Bioinformatics 2020; 36:1731-1739. [PMID: 31873728 PMCID: PMC7075533 DOI: 10.1093/bioinformatics/btz845] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/21/2019] [Accepted: 12/19/2019] [Indexed: 01/01/2023] Open
Abstract
Summary Antibody repertoires reveal insights into the biology of the adaptive immune system and empower diagnostics and therapeutics. There are currently multiple tools available for the annotation of antibody sequences. All downstream analyses such as choosing lead drug candidates depend on the correct annotation of these sequences; however, a thorough comparison of the performance of these tools has not been investigated. Here, we benchmark the performance of commonly used immunoinformatic tools, i.e. IMGT/HighV-QUEST, IgBLAST and MiXCR, in terms of reproducibility of annotation output, accuracy and speed using simulated and experimental high-throughput sequencing datasets. We analyzed changes in IMGT reference germline database in the last 10 years in order to assess the reproducibility of the annotation output. We found that only 73/183 (40%) V, D and J human genes were shared between the reference germline sets used by the tools. We found that the annotation results differed between tools. In terms of alignment accuracy, MiXCR had the highest average frequency of gene mishits, 0.02 mishit frequency and IgBLAST the lowest, 0.004 mishit frequency. Reproducibility in the output of complementarity determining three regions (CDR3 amino acids) ranged from 4.3% to 77.6% with preprocessed data. In addition, run time of the tools was assessed: MiXCR was the fastest tool for number of sequences processed per unit of time. These results indicate that immunoinformatic analyses greatly depend on the choice of bioinformatics tool. Our results support informed decision-making to immunoinformaticians based on repertoire composition and sequencing platforms. Availability and implementation All tools utilized in the paper are free for academic use. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erand Smakaj
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Lmar Babrak
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund 223, Sweden
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deniz Tosoni
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Christopher Galli
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Vendi Grobelsek
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Igor D'Angelo
- One Amgen Center Drive, Amgen, Inc., Therapeutic Discovery/Molecular Engineering, Thousand Oaks, CA 91320, USA
| | - Branden Olson
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Sai Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo 0372, Norway
| | - Johannes Trück
- Paediatric Immunology, Children's Research Center, University Children's Hospital, University of Zurich, Zurich 8032, Switzerland
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT 06511, USA
| | - William Lees
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Enkelejda Miho
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland.,aiNET GmbH, Switzerland Innovation Park Basel Area AG, Basel 4057, Switzerland
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18
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Mikus M, Zandian A, Sjöberg R, Hamsten C, Forsström B, Andersson M, Greiff L, Uhlén M, Levin M, Nilsson P, van Hage M, Ohlin M. Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy. J Allergy Clin Immunol 2020; 147:1077-1086. [PMID: 32791163 DOI: 10.1016/j.jaci.2020.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 07/22/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND The interaction of allergens and allergen-specific IgE initiates the allergic cascade after crosslinking of receptors on effector cells. Antibodies of other isotypes may modulate such a reaction. Receptor crosslinking requires binding of antibodies to multiple epitopes on the allergen. Limited information is available on the complexity of the epitope structure of most allergens. OBJECTIVES We sought to allow description of the complexity of IgE, IgG4, and IgG epitope recognition at a global, allergome-wide level during allergen-specific immunotherapy (AIT). METHODS We generated an allergome-wide microarray comprising 731 allergens in the form of more than 172,000 overlapping 16-mer peptides. Allergen recognition by IgE, IgG4, and IgG was examined in serum samples collected from subjects undergoing AIT against pollen allergy. RESULTS Extensive induction of linear peptide-specific Phl p 1- and Bet v 1-specific humoral immunity was demonstrated in subjects undergoing a 3-year-long AIT against grass and birch pollen allergy, respectively. Epitope profiles differed between subjects but were largely established already after 1 year of AIT, suggesting that dominant allergen-specific antibody clones remained as important contributors to humoral immunity following their initial establishment during the early phase of AIT. Complex, subject-specific patterns of allergen isoform and group cross-reactivities in the repertoires were observed, patterns that may indicate different levels of protection against different allergen sources. CONCLUSIONS The study highlights the complexity and subject-specific nature of allergen epitopes recognized following AIT. We envisage that epitope deconvolution will be an important aspect of future efforts to describe and analyze the outcomes of AIT in a personalized manner.
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Affiliation(s)
- Maria Mikus
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden; Unit of Experimental Asthma and Allergy Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Arash Zandian
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Ronald Sjöberg
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Carl Hamsten
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Björn Forsström
- Division of Systems Biology, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Morgan Andersson
- Department of Otorhinolaryngology, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Lennart Greiff
- Department of Otorhinolaryngology, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden; Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Mathias Uhlén
- Division of Systems Biology, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Mattias Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Marianne van Hage
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.
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19
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Lees W, Busse CE, Corcoran M, Ohlin M, Scheepers C, Matsen FA, Yaari G, Watson CT, Collins A, Shepherd AJ. OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Res 2020; 48:D964-D970. [PMID: 31566225 PMCID: PMC6943078 DOI: 10.1093/nar/gkz822] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/05/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.
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Affiliation(s)
- William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Box 280, 171 77 Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, S-223 81 Lund, Sweden
| | - Cathrine Scheepers
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringam, Gauteng 2131, South Africa.,Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Frederick A Matsen
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | | | - Andrew Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Adrian J Shepherd
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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20
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Glesner J, Kapingidza AB, Godzwon M, Offermann LR, Mueller GA, DeRose EF, Wright P, Richardson CM, Woodfolk JA, Vailes LD, Wünschmann S, London RE, Chapman MD, Ohlin M, Chruszcz M, Pomés A. A Human IgE Antibody Binding Site on Der p 2 for the Design of a Recombinant Allergen for Immunotherapy. J Immunol 2019; 203:2545-2556. [PMID: 31554696 PMCID: PMC6810898 DOI: 10.4049/jimmunol.1900580] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/15/2019] [Indexed: 01/31/2023]
Abstract
Der p 2 is one of the most important allergens from the house dust mite Dermatophagoides pteronyssinus Identification of human IgE Ab binding epitopes can be used for rational design of allergens with reduced IgE reactivity for therapy. Antigenic analysis of Der p 2 was performed by site-directed mutagenesis based on the x-ray crystal structure of the allergen in complex with a Fab from the murine IgG mAb 7A1 that binds an epitope overlapping with human IgE binding sites. Conformational changes upon Ab binding were confirmed by nuclear magnetic resonance using a 7A1-single-chain variable fragment. In addition, a human IgE Ab construct that interferes with mAb 7A1 binding was isolated from a combinatorial phage-display library constructed from a mite-allergic patient and expressed as two recombinant forms (single-chain Fab in Pichia pastoris and Fab in Escherichia coli). These two IgE Ab constructs and the mAb 7A1 failed to recognize two Der p 2 epitope double mutants designed to abolish the allergen-Ab interaction while preserving the fold necessary to bind Abs at other sites of the allergen surface. A 10-100-fold reduction in binding of IgE from allergic subjects to the mutants additionally showed that the residues mutated were involved in IgE Ab binding. In summary, mutagenesis of a Der p 2 epitope defined by x-ray crystallography revealed an IgE Ab binding site that will be considered for the design of hypoallergens for immunotherapy.
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Affiliation(s)
- Jill Glesner
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903
| | | | | | | | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | - Eugene F DeRose
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | - Paul Wright
- University of Virginia, Charlottesville, VA 22903
| | | | | | - Lisa D Vailes
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903
| | | | - Robert E London
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | | | | | | | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903;
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21
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Ljungars A, Svensson C, Carlsson A, Birgersson E, Tornberg UC, Frendéus B, Ohlin M, Mattsson M. Deep Mining of Complex Antibody Phage Pools Generated by Cell Panning Enables Discovery of Rare Antibodies Binding New Targets and Epitopes. Front Pharmacol 2019; 10:847. [PMID: 31417405 PMCID: PMC6683657 DOI: 10.3389/fphar.2019.00847] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/02/2019] [Indexed: 01/11/2023] Open
Abstract
Phage display technology is a common approach for discovery of therapeutic antibodies. Drug candidates are typically isolated in two steps: First, a pool of antibodies is enriched through consecutive rounds of selection on a target antigen, and then individual clones are characterized in a screening procedure. When whole cells are used as targets, as in phenotypic discovery, the output phage pool typically contains thousands of antibodies, binding, in theory, hundreds of different cell surface receptors. Clonal expansion throughout the phage display enrichment process is affected by multiple factors resulting in extremely complex output phage pools where a few antibodies are highly abundant and the majority is very rare. This is a huge challenge in the screening where only a fraction of the antibodies can be tested using a conventional binding analysis, identifying mainly the most abundant clones typically binding only one or a few targets. As the expected number of antibodies and specificities in the pool is much higher, complementing methods, to reach deeper into the pool, are required, called deep mining methods. In this study, four deep mining methods were evaluated: 1) isolation of rare sub-pools of specific antibodies through selection on recombinant proteins predicted to be expressed on the target cells, 2) isolation of a sub-pool enriched for antibodies of unknown specificities through depletion of the primary phage pool on recombinant proteins corresponding to receptors known to generate many binders, 3) isolation of a sub-pool enriched for antibodies through selection on cells blocked with antibodies dominating the primary phage pool, and 4) next-generation sequencing-based analysis of isolated antibody pools followed by antibody gene synthesis and production of rare but enriched clones. We demonstrate that antibodies binding new targets and epitopes, not discovered through screening alone, can be discovered using described deep mining methods. Overall, we demonstrate the complexity of phage pools generated through selection on cells and show that a combination of conventional screening and deep mining methods are needed to fully utilize such pools. Deep mining will be important in future phenotypic antibody drug discovery efforts to increase the diversity of identified antibodies and targets.
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Affiliation(s)
- Anne Ljungars
- BioInvent International AB, Lund, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | | | | | | | | | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Glesner J, Kapingidza AB, Godzwon M, Offerman LR, Mueller GA, DeRose EF, Richardson CM, Ohlin M, Chapman MD, Chruszcz M, Pomes A. Analysis Of IgE Antigenic Determinants On Der p 2 For Design Of Immunotherapy. J Allergy Clin Immunol 2019. [DOI: 10.1016/j.jaci.2018.12.568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Thörnqvist L, Ohlin M. Critical steps for computational inference of the 3'-end of novel alleles of immunoglobulin heavy chain variable genes - illustrated by an allele of IGHV3-7. Mol Immunol 2018; 103:1-6. [PMID: 30172112 DOI: 10.1016/j.molimm.2018.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/10/2018] [Accepted: 08/18/2018] [Indexed: 01/16/2023]
Abstract
Sequencing of immunoglobulin germline gene loci is a challenging process, e.g. due to their repetitiveness and complexity, hence limiting the insight in the germline gene repertoire of humans and other species. Through next generation sequencing technology, it is possible to generate immunoglobulin transcript data sets large enough to computationally infer the germline genes from which the transcripts originate. Multiple tools for such inference have been developed and they can be used for construction of individual germline gene databases, and for discovery of new immunoglobulin germline genes and alleles. However, there are challenges associated with these methods, many of them related to the biological process through which immunoglobulin coding genes are generated. The junctional diversity introduced during rearrangement of the immunoglobulin heavy chain variable (IGHV), diversity and joining genes specifically complicates the inference of the junction regions, with implications for inference of the 3'-end of IGHV genes. With the aim of coping with such diversity, an inference software package may not be able to identify novel alleles harbouring a difference in these regions compared to their closest relatives in the starting database. In this study, we were able to computationally infer one such previously uncharacterized allele, IGHV3-7*02 A318G. However, this was possible only if a strategy was used in which different variants of IGHV3-7*02 were included in the inference-initiating database. Importantly, the presence of the novel allele, but not the standard IGHV3-7*02 sequence, in the genotype was strongly supported by the actual sequences that were assigned to the allele. We thus showed that the starting database used will impact the germline gene inference process, and that difference in the 3'-end of IGHV genes may remain undetected unless specific, non-standard procedures are used to address this matter. We suggest that inferred genes/alleles should be confirmed e.g. by examination of the nucleotide composition of the 3'-bases of the inference-supporting sequence reads.
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Affiliation(s)
| | - Mats Ohlin
- Dept. of Immunotechnology, Lund University, Lund, Sweden.
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25
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Olofsson K, Carannante V, Ohlin M, Frisk T, Kushiro K, Takai M, Lundqvist A, Önfelt B, Wiklund M. Acoustic formation of multicellular tumor spheroids enabling on-chip functional and structural imaging. Lab Chip 2018; 18:2466-2476. [PMID: 30033460 DOI: 10.1039/c8lc00537k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Understanding the complex 3D tumor microenvironment is important in cancer research. This microenvironment can be modelled in vitro by culturing multicellular tumor spheroids (MCTS). Key challenges when using MCTS in applications such as high-throughput drug screening are overcoming imaging and analytical issues encountered during functional and structural investigations. To address these challenges, we use an ultrasonic standing wave (USW) based MCTS culture platform for parallel formation, staining and imaging of 100 whole MCTS. A protein repellent amphiphilic polymer coating enables flexible production of high quality and unanchored MCTS. This enables high-content multimode analysis based on flow cytometry and in situ optical microscopy. We use HepG2 hepatocellular carcinoma, A498 and ACHN renal carcinoma, and LUTC-2 thyroid carcinoma cell lines to demonstrate (i) the importance of the ultrasound-coating combination, (ii) bright field image based automatic characterization of MTCS, (iii) detailed deep tissue confocal imaging of whole MCTS mounted in a refractive index matching solution, and (iv) single cell functional analysis through flow cytometry of single cell suspensions of disintegrated MTCS. The USW MCTS culture platform is customizable and holds great potential for detailed multimode MCTS analysis in a high-content manner.
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Affiliation(s)
- K Olofsson
- Dep.t of Applied Physics, KTH Royal Institute of Technology, Sweden.
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26
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Persson H, Kirik U, Thörnqvist L, Greiff L, Levander F, Ohlin M. In Vitro Evolution of Antibodies Inspired by In Vivo Evolution. Front Immunol 2018; 9:1391. [PMID: 29977238 PMCID: PMC6021498 DOI: 10.3389/fimmu.2018.01391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/05/2018] [Indexed: 01/16/2023] Open
Abstract
In vitro generation of antibodies often requires variable domain sequence evolution to adapt the protein in terms of affinity, specificity, or developability. Such antibodies, including those that are of interest for clinical development, may have their origins in a diversity of immunoglobulin germline genes. Others and we have previously shown that antibodies of different origins tend to evolve along different, preferred trajectories. Apart from substitutions within the complementary determining regions, evolution may also, in a germline gene-origin-defined manner, be focused to residues in the framework regions, and even to residues within the protein core, in many instances at a substantial distance from the antibody’s antigen-binding site. Examples of such germline origin-defined patterns of evolution are described. We propose that germline gene-preferred substitution patterns offer attractive alternatives that should be considered in efforts to evolve antibodies intended for therapeutic use with respect to appropriate affinity, specificity, and product developability. We also hypothesize that such germline gene-origin-defined in vitro evolution hold potential to result in products with limited immunogenicity, as similarly evolved antibodies will be parts of conventional, in vivo-generated antibody responses and thus are likely to have been seen by the immune system in the past.
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Affiliation(s)
- Helena Persson
- Drug Discovery and Development Platform, Science for Life Laboratory, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Ufuk Kirik
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Otorhinolaryngology, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden
| | | | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.,Human Antibody Therapeutics, Drug Discovery and Development Platform, Science for Life Laboratory, Lund University, Lund, Sweden
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27
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Thörnqvist L, Ohlin M. Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains. Data Brief 2018; 19:337-352. [PMID: 29892656 PMCID: PMC5992955 DOI: 10.1016/j.dib.2018.04.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/30/2018] [Indexed: 01/13/2023] Open
Abstract
The highly variable complementary determining region 3 (CDR3) of antibodies is generated through recombination of immunoglobulin heavy chain variable (IGHV), diversity, and joining genes. The codons encoding the first residues of CDR3 may be derived directly from the IGHV germline gene but they may also be generated as part of the rearrangement process. Data of the nucleotide composition of these codons of rearranged genes, an indicator of the degree of contribution of the IGHV gene to CDR3 diversity, are presented in this article. Analyzed data are presented for two unrelated sets of raw sequence data. The raw data sets consisted of sequences of antibody heavy chain-encoding transcripts of six allergic subjects (European Nucleotide Archive accession number PRJEB18926), and paired antibody heavy and light chain variable region-encoding transcripts of memory B cells of three subjects (European Nucleotide Archive accession numbers SRX709625, SRX709626, and SRX709627). The nucleotide compositions of the corresponding 5′-ends of sequences encoding the CDR3 are presented for transcripts with an origin in 47 different IGHV alleles. These data have been used (Thörnqvist and Ohlin, 2018) [1] to demonstrate the extent of incorporation of the 3′ most bases of IGHV germline genes into rearranged immunoglobulin encoding sequences, and the extent whereby any difference in incorporation affects the specificity of inference of the 3′-end of IGHV genes from immunoglobulin-encoding transcripts. They have also been used to assess the effect of observed gene differences on the composition of the ascending strand of CDR3 associated to antibodies with an origin in different IGHV genes (Thörnqvist and Ohlin, 2018) [1].
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Affiliation(s)
| | - Mats Ohlin
- Dept. of Immunotechnology, Lund University, Lund, Sweden
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28
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Thörnqvist L, Ohlin M. The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes. Mol Immunol 2018; 96:61-68. [PMID: 29499482 DOI: 10.1016/j.molimm.2018.02.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/01/2018] [Accepted: 02/18/2018] [Indexed: 12/15/2022]
Abstract
Inference of antibody gene repertoires using transcriptome data has emerged as an alternative approach to the complex process of sequencing of adaptive immune receptor germline gene loci. The diversity introduced during rearrangement of immunoglobulin heavy chain variable (IGHV), diversity, and joining genes has however been identified as potentially affecting inference specificity. In this study, we have addressed this issue by analysing the nucleotide composition of unmutated human immunoglobulin heavy chains-encoding transcripts, focusing on the 3ö most bases of 47 IGHV germline genes. Although transcripts derived from some of the germline genes predominately incorporated the germline encoded base even at position 320, the last base of most IGHV genes, transcripts originating in other genes presented other nucleotides to the same extent at this position. In transcripts derived from two of the germline genes, IGHV3-13*01 and IGHV4-30-2*01, the predominating nucleotide (G) was in fact not that of the gene (A). Hence, we suggest that inference of IGHV genes should be limited to bases preceding nucleotide 320, as inference beyond this would jeopardize the specificity of the inference process. The different degree of incorporation of the final base of the IGHV gene directly influences the distribution of amino acids of the ascending strand of the third complementarity determining region of the heavy chain. Thereby it influences the nature of this specificity-determining part of the antibody population. In addition, we also present data that indicate the existence of a common so far un-recognized allelic variant of IGHV3-7 that carries an A318G difference in relation to IGHV3-7*02.
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Affiliation(s)
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.
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Kirik U, Persson H, Levander F, Greiff L, Ohlin M. Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths. Front Immunol 2017; 8:1433. [PMID: 29180996 PMCID: PMC5694033 DOI: 10.3389/fimmu.2017.01433] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/16/2017] [Indexed: 02/04/2023] Open
Abstract
B cells produce antibodies, key effector molecules in health and disease. They mature their properties, including their affinity for antigen, through hypermutation events; processes that involve, e.g., base substitution, codon insertion and deletion, often in association with an isotype switch. Investigations of antibody evolution define modes whereby particular antibody responses are able to form, and such studies provide insight important for instance for development of efficient vaccines. Antibody evolution is also used in vitro for the design of antibodies with improved properties. To better understand the basic concepts of antibody evolution, we analyzed the mutational paths, both in terms of amino acid substitution and insertions and deletions, taken by antibodies of the IgG isotype. The analysis focused on the evolution of the heavy chain variable domain of sets of antibodies, each with an origin in 1 of 11 different germline genes representing six human heavy chain germline gene subgroups. Investigated genes were isolated from cells of human bone marrow, a major site of antibody production, and characterized by next-generation sequencing and an in-house bioinformatics pipeline. Apart from substitutions within the complementarity determining regions, multiple framework residues including those in protein cores were targets of extensive diversification. Diversity, both in terms of substitutions, and insertions and deletions, in antibodies is focused to different positions in the sequence in a germline gene-unique manner. Altogether, our findings create a framework for understanding patterns of evolution of antibodies from defined germline genes.
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Affiliation(s)
- Ufuk Kirik
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development Platform, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden.,National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.,Science for Life Laboratory, Drug Discovery and Development Platform, Human Antibody Therapeutics, Lund University, Lund, Sweden.,U-READ, Lund School of Technology, Lund University, Lund, Sweden
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Kjeldgård L, Ohlin M, Elrud R, Stigson H, Alexanderson K, Friberg E. Bicycle crashes and sickness absence - A nationwide Swedish cross-sectional study. Eur J Public Health 2017. [DOI: 10.1093/eurpub/ckx186.342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- L Kjeldgård
- Insurance Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - M Ohlin
- Insurance Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Gothenburg, Sweden
| | - R Elrud
- Insurance Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - K Alexanderson
- Insurance Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - E Friberg
- Insurance Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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31
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Hjort C, Schiøtz PO, Ohlin M, Würtzen PA, Christensen LH, Hoffmann HJ. The number and affinity of productive IgE pairs determine allergen activation of mast cells. J Allergy Clin Immunol 2017; 140:1167-1170.e2. [DOI: 10.1016/j.jaci.2017.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/18/2017] [Accepted: 04/10/2017] [Indexed: 11/30/2022]
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32
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Kirik U, Greiff L, Levander F, Ohlin M. Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery. Mol Immunol 2017; 87:12-22. [DOI: 10.1016/j.molimm.2017.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/18/2022]
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33
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Kirik U, Greiff L, Levander F, Ohlin M. Data on haplotype-supported immunoglobulin germline gene inference. Data Brief 2017; 13:620-640. [PMID: 28725665 PMCID: PMC5502703 DOI: 10.1016/j.dib.2017.06.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/26/2017] [Accepted: 06/19/2017] [Indexed: 01/03/2023] Open
Abstract
Data that defines IGHV (immunoglobulin heavy chain variable) germline gene inference using sequences of IgM-encoding transcriptomes obtained by Illumina MiSeq sequencing technology are described. Such inference is used to establish personalized germline gene sets for in-depth antibody repertoire studies and to detect new antibody germline genes from widely available immunoglobulin-encoding transcriptome data sets. Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery (DOI: 10.1016/j.molimm.2017.03.012) (Kirik et al., 2017) [1]) the inference process. This was accomplished based on analysis of the inferred germline genes’ association to the donors’ different haplotypes as defined by their different, expressed IGHJ alleles and/or IGHD genes/alleles. The data is important for development of validated germline gene databases containing entries inferred from immunoglobulin-encoding transcriptome sequencing data sets, and for generation of valid, personalized antibody germline gene repertoires.
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Affiliation(s)
- Ufuk Kirik
- Dept. of Immunotechnology, Lund University, Lund, Sweden
| | - Lennart Greiff
- Dept. of Clinical Sciences, Division of Otorhinolaryngology, Head and Neck Cancer, Lund University, Sweden.,Dept. of Otorhinolaryngology, Skåne University Hospital, Lund, Sweden
| | | | - Mats Ohlin
- Dept. of Immunotechnology, Lund University, Lund, Sweden
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34
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Huseinovic E, Ohlin M, Winkvist A, Bertz F, Sonesson U, Brekke HK. Does diet intervention in line with nutrition recommendations affect dietary carbon footprint? Results from a weight loss trial among lactating women. Eur J Clin Nutr 2017; 71:1241-1245. [PMID: 28488687 DOI: 10.1038/ejcn.2017.63] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/23/2017] [Accepted: 03/30/2017] [Indexed: 11/09/2022]
Abstract
BACKGROUND/OBJECTIVES Results from studies evaluating the sustainability of diets combining environmental and nutritional aspects have been diverse; thus, greenhouse gas emissions (that is, carbon footprint (CF)) of diets in line with dietary recommendations in free-living individuals warrants further examination. Here, changes in dietary CF related to changes in food choice during a weight loss trial among lactating women who received a 12-week diet intervention based on the Nordic Nutrition Recommendations (NNR) 2004 were analyzed. The objective of this study was to examine if a diet intervention based on NNR 2004 results in reduced dietary CF. SUBJECTS/METHODS Changes in dietary CF were analyzed among 61 lactating women participating in a weight loss trial. Food intake data from 4-day weighed diet records and results from life cycle analyses were used to examine changes in dietary CF across eight food groups during the intervention, specified in the unit carbon dioxide equivalent (CO2eq/day). Differences in changes in dietary CF between women receiving diet treatment (D-group) and women not receiving it (ND-group) were compared. RESULTS There was no difference in change in dietary CF of the overall diet between D- and ND-group (P>0.05). As for the eight food groups, D-group increased their dietary CF from fruit and vegetables (+0.06±0.13 kg CO2eq/day) compared with a decrease in ND-group (-0.01±0.01 kg CO2eq/day) during the intervention, P=0.01. CONCLUSIONS A diet intervention in line with NNR 2004 produced clinically relevant weight loss, but did not reduce dietary CF among lactating women with overweight and obesity. Dietary interventions especially designed to decrease dietary CF and their coherence with dietary recommendations need further exploration.
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Affiliation(s)
- E Huseinovic
- Department of Internal Medicine and Clinical Nutrition, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - M Ohlin
- Department of Internal Medicine and Clinical Nutrition, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - A Winkvist
- Department of Internal Medicine and Clinical Nutrition, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - F Bertz
- Department of Internal Medicine and Clinical Nutrition, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - U Sonesson
- Department of Agrifood and Bioscience, RISE- Research Institutes of Sweden, Gothenburg, Sweden
| | - H K Brekke
- Department of Internal Medicine and Clinical Nutrition, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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35
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Säll A, Persson H, Ohlin M, Borrebaeck CAK, Wingren C. Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach. N Biotechnol 2016; 33:503-13. [PMID: 26703809 DOI: 10.1016/j.nbt.2015.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/27/2015] [Accepted: 12/03/2015] [Indexed: 11/17/2022]
Abstract
Increasing the understanding of a proteome and how its protein composition is affected by for example different diseases, such as cancer, has the potential to improve strategies for early diagnosis and therapeutics. The Global Proteome Survey or GPS is a method that combines mass spectrometry and affinity enrichment with the use of antibodies. The technology enables profiling of complex proteomes in a species independent manner. The sensitivity of GPS, and other methods relying on affinity enrichment, is largely affected by the activity of the exploited affinity reagent. We here present an improvement of the GPS platform by utilizing an antibody immobilization approach which ensures a controlled immobilization process of the antibody to the magnetic bead support. More specifically, we make use of an antibody format that enables site-directed biotinylation and use this in combination with streptavidin coated magnetic beads. The performance of the expanded GPS platform was evaluated by profiling yeast proteome samples. We demonstrate that the oriented antibody immobilization strategy increases the ability of the GPS platform and results in larger fraction of functional antibodies. Additionally, we show that this new antibody format enabled in-solution capture, i.e. immobilization of the antibodies after sample incubation. A workflow has been established that permit the use of an oriented immobilization strategy for the GPS platform.
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Affiliation(s)
- Anna Säll
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden
| | - Helena Persson
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden; Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden
| | - Carl A K Borrebaeck
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden.
| | - Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden.
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36
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Säll A, Walle M, Wingren C, Müller S, Nyman T, Vala A, Ohlin M, Borrebaeck CAK, Persson H. Generation and analyses of human synthetic antibody libraries and their application for protein microarrays. Protein Eng Des Sel 2016; 29:427-437. [DOI: 10.1093/protein/gzw042] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 07/21/2016] [Indexed: 11/12/2022] Open
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37
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Levin M, Levander F, Palmason R, Greiff L, Ohlin M. Antibody-encoding repertoires of bone marrow and peripheral blood-a focus on IgE. J Allergy Clin Immunol 2016; 139:1026-1030. [PMID: 27521279 DOI: 10.1016/j.jaci.2016.06.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/21/2016] [Accepted: 06/27/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Mattias Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden; Bioinformatics Infrastructure for Life Sciences, Lund University, Lund, Sweden
| | - Robert Palmason
- Department of Hematology, Oncology and Medical Physics, Skåne University Hospital, Lund, Sweden
| | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden; Department of ORL, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.
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38
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Pomés A, Glesner J, Godzwon M, Levin M, Chapman MD, Ohlin M. Recombinant Human IgE Antibodies to Analyze Antigenic Determinants in Group 1 Mite Allergens for the Design of Immunotherapy. J Allergy Clin Immunol 2016. [DOI: 10.1016/j.jaci.2015.12.696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Levin M, King JJ, Glanville J, Jackson KJL, Looney TJ, Hoh RA, Mari A, Andersson M, Greiff L, Fire AZ, Boyd SD, Ohlin M. Persistence and evolution of allergen-specific IgE repertoires during subcutaneous specific immunotherapy. J Allergy Clin Immunol 2015; 137:1535-44. [PMID: 26559321 DOI: 10.1016/j.jaci.2015.09.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 07/24/2015] [Accepted: 09/23/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Specific immunotherapy (SIT) is the only treatment with proved long-term curative potential in patients with allergic disease. Allergen-specific IgE is the causative agent of allergic disease, and antibodies contribute to SIT, but the effects of SIT on aeroallergen-specific B-cell repertoires are not well understood. OBJECTIVE We sought to characterize the IgE sequences expressed by allergen-specific B cells and track the fate of these B-cell clones during SIT. METHODS We used high-throughput antibody gene sequencing and identification of allergen-specific IgE with combinatorial antibody fragment library technology to analyze immunoglobulin repertoires of blood and the nasal mucosa from aeroallergen-sensitized subjects before and during the first year of subcutaneous SIT. RESULTS Of 52 distinct allergen-specific IgE heavy chains from 8 allergic donors, 37 were also detected by using high-throughput antibody gene sequencing of blood samples, nasal mucosal samples, or both. The allergen-specific clones had increased persistence, higher likelihood of belonging to clones expressing other switched isotypes, and possibly larger clone size than the rest of the IgE repertoire. Clone members in nasal tissue showed close mutational relationships. CONCLUSION In the future, combining functional binding studies, deep antibody repertoire sequencing, and information on clinical outcomes in larger studies might aid assessment of SIT mechanisms and efficacy.
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Affiliation(s)
- Mattias Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Jasmine J King
- Department of Biology, Stanford University, Stanford, Calif; Department of Pathology, Stanford University, Stanford, Calif
| | - Jacob Glanville
- Department of Immunology, Stanford University, Stanford, Calif
| | | | | | - Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, Calif
| | - Adriano Mari
- Center for Molecular Allergology, IDI-IRCCS, Rome, Italy; Associated Centers for Molecular Allergology, Rome, Italy
| | - Morgan Andersson
- Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Lennart Greiff
- Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, Calif; Department of Genetics, Stanford University, Stanford, Calif
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, Calif
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.
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Fisher SZ, von Schantz L, Håkansson M, Logan DT, Ohlin M. Neutron crystallographic studies reveal hydrogen bond and water-mediated interactions between a carbohydrate-binding module and its bound carbohydrate ligand. Biochemistry 2015; 54:6435-8. [PMID: 26451738 DOI: 10.1021/acs.biochem.5b01058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Carbohydrate-binding modules (CBMs) are key components of many carbohydrate-modifying enzymes. CBMs affect the activity of these enzymes by modulating bonding and catalysis. To further characterize and study CBM-ligand binding interactions, neutron crystallographic studies of an engineered family 4-type CBM in complex with a branched xyloglucan ligand were conducted. The first neutron crystal structure of a CBM-ligand complex reported here shows numerous atomic details of hydrogen bonding and water-mediated interactions and reveals the charged state of key binding cleft amino acid side chains.
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Affiliation(s)
- S Zoë Fisher
- European Spallation Source , S-221 00 Lund, Sweden
| | - Laura von Schantz
- Department of Immunotechnology, Lund University , Medicon Village, S-223 81 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures AB , Medicon Village, S-223 81 Lund, Sweden
| | - Derek T Logan
- SARomics Biostructures AB , Medicon Village, S-223 81 Lund, Sweden.,Department of Biochemistry and Structural Biology, Lund University , S-221 00 Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University , Medicon Village, S-223 81 Lund, Sweden
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41
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Ohlin M, Söderberg-Nauclér C. Human antibody technology and the development of antibodies against cytomegalovirus. Mol Immunol 2015; 67:153-70. [DOI: 10.1016/j.molimm.2015.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 02/08/2023]
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Paës G, von Schantz L, Ohlin M. Bioinspired assemblies of plant cell wall polymers unravel the affinity properties of carbohydrate-binding modules. Soft Matter 2015; 11:6586-94. [PMID: 26189625 DOI: 10.1039/c5sm01157d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Lignocellulose-acting enzymes play a central role in the biorefinery of plant biomass to make fuels, chemicals and materials. These enzymes are often appended to carbohydrate binding modules (CBMs) that promote substrate targeting. When used in plant materials, which are complex assemblies of polymers, the binding properties of CBMs can be difficult to understand and predict, thus limiting the efficiency of enzymes. In order to gain more information on the binding properties of CBMs, some bioinspired model assemblies that contain some of the polymers and covalent interactions found in the plant cell walls have been designed. The mobility of three engineered CBMs has been investigated by FRAP in these assemblies, while varying the parameters related to the polymer concentration, the physical state of assemblies and the oligomerization state of CBMs. The features controlling the mobility of the CBMs in the assemblies have been quantified and hierarchized. We demonstrate that the parameters can have additional or opposite effects on mobility, depending on the CBM tested. We also find evidence of a relationship between the mobility of CBMs and their binding strength. Overall, bioinspired assemblies are able to reveal the unique features of affinity of CBMs. In particular, the results show that oligomerization of CBMs and the presence of ferulic acid motifs in the assemblies play an important role in the binding affinity of CBMs. Thus we propose that these features should be finely tuned when CBMs are used in plant cell walls to optimise bioprocesses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR0614 Fractionnement des AgroRessources et Environnement, 2 esplanade Roland-Garros, 51100 Reims, France.
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Ohlin M, von Schantz L, Schrader TE, Ostermann A, Logan DT, Fisher SZ. Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase. Acta Crystallogr F Struct Biol Commun 2015; 71:1072-7. [PMID: 26249702 PMCID: PMC4528944 DOI: 10.1107/s2053230x15011383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 11/10/2022] Open
Abstract
Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate-protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A of Rhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm(3)) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement using phenix.refine showed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein-carbohydrate binding interactions.
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Affiliation(s)
- Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, Building 406, 223 81 Lund, Sweden
| | - Laura von Schantz
- Department of Immunotechnology, Lund University, Medicon Village, Building 406, 223 81 Lund, Sweden
| | - Tobias E. Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Derek T. Logan
- Department of Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - S. Zoë Fisher
- Scientific Activities Division, European Spallation Source, Tunavägen 24, 221 00 Lund, Sweden
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44
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Godzwon M, Levin M, Säll A, Ohlin M. A microarray-based reaction rate analysis platform. Is there evidence of validity? J Immunol Methods 2015; 426:144-6. [PMID: 26168708 DOI: 10.1016/j.jim.2015.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
Affiliation(s)
| | | | - Anna Säll
- Dept. of Immunotechnology, Lund University, Sweden
| | - Mats Ohlin
- Dept. of Immunotechnology, Lund University, Sweden.
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45
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Levin M, Rotthus S, Wendel S, Najafi N, Källström E, Focke-Tejkl M, Valenta R, Flicker S, Ohlin M. Multiple independent IgE epitopes on the highly allergenic grass pollen allergen Phl p 5. Clin Exp Allergy 2015; 44:1409-19. [PMID: 25262820 PMCID: PMC4278554 DOI: 10.1111/cea.12423] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 07/06/2014] [Accepted: 08/15/2014] [Indexed: 11/30/2022]
Abstract
Background Group 5 allergens are small proteins that consist of two domains. They belong to the most potent respiratory allergens. Objective To determine the binding sites and to study allergic patients' IgE recognition of the group 5 allergen (Phl p 5) from timothy grass pollen using human monoclonal IgE antibodies that have been isolated from grass pollen allergic patients. Methods Using recombinant isoallergens, fragments, mutants and synthetic peptides of Phl p 5, as well as peptide-specific antibodies, the interaction of recombinant human monoclonal IgE and Phl p 5 was studied using direct binding and blocking assays. Cross-reactivity of monoclonal IgE with group 5 allergens in several grasses was studied and inhibition experiments with patients' polyclonal IgE were performed. Results Monoclonal human IgE showed extensive cross-reactivity with group 5 allergens in several grasses. Despite its small size of 29 kDa, four independent epitope clusters on isoallergen Phl p 5.0101, two in each domain, were recognized by human IgE. Isoallergen Phl p 5.0201 carried two of these epitopes. Inhibition studies with allergic patients' polyclonal IgE suggest the presence of additional IgE epitopes on Phl p 5. Conclusions & Clinical Relevance Our results reveal the presence of a large number of independent IgE epitopes on the Phl p 5 allergen explaining the high allergenic activity of this protein and its ability to induce severe allergic symptoms. High-density IgE recognition may be a general feature of many potent allergens and form a basis for the development of improved diagnostic and therapeutic procedures in allergic disease.
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Affiliation(s)
- M Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
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Levin M, Otten H, von Wachenfeldt C, Ohlin M. A folded and immunogenic IgE-hyporeactive variant of the major allergen Phl p 1 produced in Escherichia coli. BMC Biotechnol 2015; 15:52. [PMID: 26054338 PMCID: PMC4460866 DOI: 10.1186/s12896-015-0150-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 04/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Group 1 grass pollen allergens are a major cause of allergic disease. Specific immunotherapy involving controlled administration of allergens can be used as a disease-modifying treatment for such disease. Recombinant allergen variants with reduced IgE binding capacity may be used as component in such vaccines, as they may induce fewer treatment side effects than materials currently in use. A mutated variant of the immunodominant C-terminal domain of the group 1 grass pollen allergen Phl p 1 was recently established through an approach that used a set of human monoclonal IgE as a guide to identify mutations that disturbed IgE-allergen interactions. Further analysis of this domain is required to establish its potential for use in treatment. METHODS GST-tagged wild-type and mutated C-terminal domains of Phl p 1 were produced in Escherichia coli TUNER(DE3). The products were purified by affinity chromatography on immobilized glutathione. GST was removed by enzymatic cleavage and tag-free products were purified by size exclusion chromatography. Products were assessed by SDS-PAGE, circular dichroism spectroscopy, differential scanning fluorimetry and dynamic light scattering. Rats were immunized with GST-tagged and tag-free mutated C-terminal domain of Phl p 1. Antigen-binding properties of induced antibodies were assessed by immunochemical analysis. RESULTS The mutated domain has a structure very similar to that of the wild-type domain as determined by circular dichroism, but a reduced thermal stability. Immunization of rats demonstrates that this IgE-hyporeactive domain, despite its three sequence modifications (K8A, N11A, D55A), is able to induce antibodies that substantially block the binding of allergic subjects' IgE to the wild-type allergen. CONCLUSIONS It is concluded that this IgE-hyporeactive molecule can be produced in folded form and that it is able to induce an antibody response that efficiently competes with IgE recognition of Phl p 1. These findings suggest that it, or a further evolved variant thereof, is a candidate for use as a component in specific immunotherapy against grass pollen allergy.
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Affiliation(s)
- Mattias Levin
- Dept. of Immunotechnology, Lund University, Medicon Village building 406, S-223 81, Lund, Sweden.
| | - Harm Otten
- Crystallization facility at the MAX IV laboratory and Lund University, Lund, Sweden. .,Lund Protein Production Platform (LP3), Lund University, Lund, Sweden.
| | | | - Mats Ohlin
- Dept. of Immunotechnology, Lund University, Medicon Village building 406, S-223 81, Lund, Sweden.
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von Schantz L, Schagerlöf H, Nordberg Karlsson E, Ohlin M. Characterization of the substitution pattern of cellulose derivatives using carbohydrate-binding modules. BMC Biotechnol 2014; 14:113. [PMID: 25540113 PMCID: PMC4302574 DOI: 10.1186/s12896-014-0113-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/18/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Derivatized celluloses, such as methylcellulose (MC) and hydroxypropyl methylcellulose (HPMC), are of pharmaceutical importance and extensively employed in tablet matrices. Each batch of derivatized cellulose is thoroughly characterized before utilized in tablet formulations as batch-to-batch differences can affect drug release. The substitution pattern of the derivatized cellulose polymers, i.e. the mode on which the substituent groups are dispersed along the cellulose backbone, can vary from batch-to-batch and is a factor that can influence drug release. RESULTS In the present study an analytical approach for the characterization of the substitution pattern of derivatized celluloses is presented, which is based on the use of carbohydrate-binding modules (CBMs) and affinity electrophoresis. CBM4-2 from Rhodothermus marinus xylanase 10A is capable of distinguishing between batches of derivatized cellulose with different substitution patterns. This is demonstrated by a higher migration retardation of the CBM in acrylamide gels containing batches of MC and HPMC with a more heterogeneous distribution pattern. CONCLUSIONS We conclude that CBMs have the potential to characterize the substitution pattern of cellulose derivatives and anticipate that with use of CBMs with a very selective recognition capacity it will be possible to more extensively characterize and standardize important carbohydrates used for instance in tablet formulation.
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Säll A, Carlsson F, Olsson N, Wingren C, Ohlin M, Persson H, Waldemarson S. AFFIRM--a multiplexed immunoaffinity platform that combines recombinant antibody fragments and LC-SRM analysis. J Proteome Res 2014; 13:5837-47. [PMID: 25337893 DOI: 10.1021/pr500757s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Targeted measurements of low abundance proteins in complex mixtures are in high demand in many areas, not the least in clinical applications measuring biomarkers. We here present the novel platform AFFIRM (AFFInity sRM) that utilizes the power of antibody fragments (scFv) to efficiently enrich for target proteins from a complex background and the exquisite specificity of SRM-MS based detection. To demonstrate the ability of AFFIRM, three target proteins of interest were measured in a serum background in single-plexed and multiplexed experiments in a concentration range of 5-1000 ng/mL. Linear responses were demonstrated down to low ng/mL concentrations with high reproducibility. The platform allows for high throughput measurements in 96-well format, and all steps are amendable to automation and scale-up. We believe the use of recombinant antibody technology in combination with SRM MS analysis provides a powerful way to reach sensitivity, specificity, and reproducibility as well as the opportunity to build resources for fast on-demand implementation of novel assays.
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Affiliation(s)
- Anna Säll
- Department of Immunotechnology, Lund University , Medicon Village (House 406), SE-223 81 Lund, Sweden
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von Schantz L, Håkansson M, Logan DT, Nordberg-Karlsson E, Ohlin M. Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-Π interactions. Proteins 2014; 82:3466-75. [PMID: 25302425 DOI: 10.1002/prot.24700] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 09/03/2014] [Accepted: 09/19/2014] [Indexed: 12/13/2022]
Abstract
Engineering of novel carbohydrate-binding proteins that can be utilized in various biochemical and biotechnical applications would benefit from a deeper understanding of the biochemical interactions that determine protein-carbohydrate specificity. In an effort to understand further the basis for specificity we present the crystal structure of the multi-specific carbohydrate-binding module (CBM) X-2 L110F bound to a branched oligomer of xyloglucan (XXXG). X-2 L110F is an engineered CBM that can recognize xyloglucan, xylans and β-glucans. The structural observations of the present study compared with previously reported structures of X-2 L110F in complex with linear oligomers, show that the π-surface of a phenylalanine, F110, allows for interactions with hydrogen atoms on both linear (xylopentaose and cellopentaose) and branched ligands (XXXG). Furthermore, X-2 L110F is shown to have a relatively flexible binding cleft, as illustrated in binding to XXXG. This branched ligand requires a set of reorientations of protein side chains Q72, N31, and R142, although these residues have previously been determined as important for binding to xylose oligomers by mediating polar contacts. The loss of these polar contacts is compensated for in binding to XXXG by polar interactions mediated by other protein residues, T74, R115, and Y149, which interact mainly with the branching xyloses of the xyloglucan oligomer. Taken together, the present study illustrates in structural detail how CH-π interactions can influence binding specificity and that flexibility is a key feature for the multi-specificity displayed by X-2 L110F, allowing for the accommodation of branched ligands.
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Affiliation(s)
- Laura von Schantz
- Department of Immunotechnology, Lund University, Medicon Village, SE-223 81 Lund, Sweden
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Levin M, Davies AM, Liljekvist M, Carlsson F, Gould HJ, Sutton BJ, Ohlin M. Human IgE against the major allergen Bet v 1--defining an epitope with limited cross-reactivity between different PR-10 family proteins. Clin Exp Allergy 2014; 44:288-99. [PMID: 24447087 PMCID: PMC4215112 DOI: 10.1111/cea.12230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/24/2013] [Accepted: 10/25/2013] [Indexed: 02/05/2023]
Abstract
Background The interaction between IgE and allergen is a key event at the initiation of an allergic response, and its characteristics have substantial effects on the clinical manifestation. Despite this, the molecular details of the interaction between human IgE and the major birch allergen Bet v 1, one of the most potent tree allergens, still remain poorly investigated. Objective To isolate Bet v 1-specific human monoclonal IgE and characterize their interaction with the allergen. Methods Recombinant human IgE were isolated from a combinatorial antibody fragment library and their interaction with Bet v 1 assessed using various immunological assays. The structure of one such IgE in the single-chain fragment variable format was determined using X-ray crystallography. Results We present four novel Bet v 1-specific IgE, for one of which we solve the structure, all with their genetic origin in the IGHV5 germline gene, and demonstrate that they target two non-overlapping epitopes on the surface of Bet v 1, thereby fulfilling the basic criteria for FcεRI cross-linkage. We further define these epitopes and for one epitope pinpoint single amino acid residues important for the interaction with human IgE. This provides a potential explanation, at the molecular level, for the differences in recognition of isoforms of Bet v 1 and other allergens in the PR-10 protein family displayed by IgE targeting this epitope. Finally, we present the first high-resolution structure of a human allergen-specific IgE fragment in the single-chain fragment variable (scFv) format. Conclusions and Clinical Relevance We here display the usefulness of allergen-specific human monoclonal IgE as a tool in studies of the crucial molecular interaction taking place at the initiation of an allergic response. Such studies may aid us in development of better diagnostic tools and guide us in the development of new therapeutic compounds.
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Affiliation(s)
- M Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
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