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Schmitz S, Soto C, Crowe JE, Meiler J. Human-likeness of antibody biologics determined by back-translation and comparison with large antibody variable gene repertoires. MAbs 2021; 12:1758291. [PMID: 32397786 PMCID: PMC8648325 DOI: 10.1080/19420862.2020.1758291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The antibody (Ab) germline gene rearrangement of variable (V), diversity (D), and joining (J) gene segments, as well as somatic hypermutation, give rise to the human Ab variable gene sequence repertoire. It is common to characterize single nucleotide frequencies of the variable region by alignment to species-specific wildtype germline genes. The increasing application of next-generation sequencing to immune repertoire studies has led to the compilation of increasing large adaptive immunome receptor repertoire datasets. We have developed a method that maps the sequence of a target Ab onto an immunome dataset of 326 million human Ab sequences. For this purpose, we created a position- and gene-specific scoring matrix (PGSSM) and its corresponding antibody similarity score. We characterized our PGSSM score and found that it strongly correlated with the phylogenetic distance of 181,355 Ab sequences from GenBank across 20 species. The most likely human nucleotide back-translation was obtained given only PGSSMs and the amino acid sequence of an Ab achieving a nucleotide sequence recovery of 95.9% and 97.2% for human heavy and light chains, respectively. In conclusion, the scoring of our back-translation is a valuable estimate for the similarity of an Ab sequence to the natural human repertoire. As expected, Ab therapeutic molecules developed from a human source showed a higher similarity to the repertoire than engineered Abs. Thus, the PGSSM metric introduced here can be used to engineer human-like Ab therapeutics.
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Affiliation(s)
- Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Cinque Soto
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,The Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James E Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,The Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.,Institute for Drug Development, Leipzig University Medical School, Leipzig, SAC, Germany
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Claes N, Fraussen J, Stinissen P, Hupperts R, Somers V. B Cells Are Multifunctional Players in Multiple Sclerosis Pathogenesis: Insights from Therapeutic Interventions. Front Immunol 2015; 6:642. [PMID: 26734009 PMCID: PMC4685142 DOI: 10.3389/fimmu.2015.00642] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/07/2015] [Indexed: 01/07/2023] Open
Abstract
Multiple sclerosis (MS) is a severe disease of the central nervous system (CNS) characterized by autoimmune inflammation and neurodegeneration. Historically, damage to the CNS was thought to be mediated predominantly by activated pro-inflammatory T cells. B cell involvement in the pathogenesis of MS was solely attributed to autoantibody production. The first clues for the involvement of antibody-independent B cell functions in MS pathology came from positive results in clinical trials of the B cell-depleting treatment rituximab in patients with relapsing-remitting (RR) MS. The survival of antibody-secreting plasma cells and decrease in T cell numbers indicated the importance of other B cell functions in MS such as antigen presentation, costimulation, and cytokine production. Rituximab provided us with an example of how clinical trials can lead to new research opportunities concerning B cell biology. Moreover, analysis of the antibody-independent B cell functions in MS has gained interest since these trials. Limited information is present on the effects of current immunomodulatory therapies on B cell functions, although effects of both first-line (interferon, glatiramer acetate, dimethyl fumarate, and teriflunomide), second-line (fingolimod, natalizumab), and even third-line (monoclonal antibody therapies) treatments on B cell subtype distribution, expression of functional surface markers, and secretion of different cytokines by B cells have been studied to some extent. In this review, we summarize the effects of different MS-related treatments on B cell functions that have been described up to now in order to find new research opportunities and contribute to the understanding of the pathogenesis of MS.
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Affiliation(s)
- Nele Claes
- Hasselt University, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences , Diepenbeek , Belgium
| | - Judith Fraussen
- Hasselt University, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences , Diepenbeek , Belgium
| | - Piet Stinissen
- Hasselt University, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences , Diepenbeek , Belgium
| | - Raymond Hupperts
- Department of Neuroscience, School of Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands; Department of Neurology, Academic MS Center Limburg, Zuyderland Medisch Centrum, Sittard, Netherlands
| | - Veerle Somers
- Hasselt University, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences , Diepenbeek , Belgium
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Nogales-Gadea G, Saxena A, Hoffmann C, Hounjet J, Coenen D, Molenaar P, Losen M, Martinez-Martinez P. Generation of Recombinant Human IgG Monoclonal Antibodies from Immortalized Sorted B Cells. J Vis Exp 2015:e52830. [PMID: 26132628 PMCID: PMC4545184 DOI: 10.3791/52830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Finding new methods for generating human monoclonal antibodies is an active research field that is important for both basic and applied sciences, including the development of immunotherapeutics. However, the techniques to identify and produce such antibodies tend to be arduous and sometimes the heavy and light chain pair of the antibodies are dissociated. Here, we describe a relatively simple, straightforward protocol to produce human recombinant monoclonal antibodies from human peripheral blood mononuclear cells using immortalization with Epstein-Barr Virus (EBV) and Toll-like receptor 9 activation. With an adequate staining, B cells producing antibodies can be isolated for subsequent immortalization and clonal expansion. The antibody transcripts produced by the immortalized B cell clones can be amplified by PCR, sequenced as corresponding heavy and light chain pairs and cloned into immunoglobulin expression vectors. The antibodies obtained with this technique can be powerful tools to study relevant human immune responses, including autoimmunity, and create the basis for new therapeutics.
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Affiliation(s)
- Gisela Nogales-Gadea
- School for Mental Health and Neuroscience, Maastricht University; Department of Neurosciences, Institut d'Investigació Germans Trias i Pujol
| | - Abhishek Saxena
- School for Mental Health and Neuroscience, Maastricht University
| | - Carolin Hoffmann
- School for Mental Health and Neuroscience, Maastricht University
| | - Judith Hounjet
- School for Mental Health and Neuroscience, Maastricht University
| | - Daniëlle Coenen
- School for Mental Health and Neuroscience, Maastricht University
| | - Peter Molenaar
- School for Mental Health and Neuroscience, Maastricht University
| | - Mario Losen
- School for Mental Health and Neuroscience, Maastricht University
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de Bock L, Somers K, Fraussen J, Hendriks JJ, van Horssen J, Rouwette M, Hellings N, Villar LM, Álvarez-Cermeño JC, Espiño M, Hupperts R, Jongen P, Damoiseaux J, Verbeek MM, De Deyn PP, D’hooghe M, Van Wijmeersch B, Stinissen P, Somers V. Sperm-Associated Antigen 16 Is a Novel Target of the Humoral Autoimmune Response in Multiple Sclerosis. THE JOURNAL OF IMMUNOLOGY 2014; 193:2147-56. [DOI: 10.4049/jimmunol.1401166] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Vrolix K, Fraussen J, Losen M, Stevens J, Lazaridis K, Molenaar PC, Somers V, Bracho MA, Le Panse R, Stinissen P, Berrih-Aknin S, Maessen JG, Van Garsse L, Buurman WA, Tzartos SJ, De Baets MH, Martinez-Martinez P. Clonal heterogeneity of thymic B cells from early-onset myasthenia gravis patients with antibodies against the acetylcholine receptor. J Autoimmun 2014; 52:101-12. [PMID: 24439114 DOI: 10.1016/j.jaut.2013.12.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
Abstract
Myasthenia gravis (MG) with antibodies against the acetylcholine receptor (AChR-MG) is considered as a prototypic autoimmune disease. The thymus is important in the pathophysiology of the disease since thymus hyperplasia is a characteristic of early-onset AChR-MG and patients often improve after thymectomy. We hypothesized that thymic B cell and antibody repertoires of AChR-MG patients differ intrinsically from those of control individuals. Using immortalization with Epstein-Barr Virus and Toll-like receptor 9 activation, we isolated and characterized monoclonal B cell lines from 5 MG patients and 8 controls. Only 2 of 570 immortalized B cell clones from MG patients produced antibodies against the AChR (both clones were from the same patient), suggesting that AChR-specific B cells are not enriched in the thymus. Surprisingly, many B cell lines from both AChR-MG and control thymus samples displayed reactivity against striated muscle proteins. Striational antibodies were produced by 15% of B cell clones from AChR-MG versus 6% in control thymus. The IgVH gene sequence analysis showed remarkable similarities, concerning VH family gene distribution, mutation frequency and CDR3 composition, between B cells of AChR-MG patients and controls. MG patients showed clear evidence of clonal B cell expansion in contrast to controls. In this latter aspect, MG resembles multiple sclerosis and clinically isolated syndrome, but differs from systemic lupus erythematosus. Our results support an antigen driven immune response in the MG thymus, but the paucity of AChR-specific B cells, in combination with the observed polyclonal expansions suggest a more diverse immune response than expected.
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Affiliation(s)
- Kathleen Vrolix
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Judith Fraussen
- Neuroimmunology group, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Mario Losen
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Jo Stevens
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | | | - Peter C Molenaar
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Veerle Somers
- Neuroimmunology group, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Maria Alma Bracho
- Centre Superior d'Investigació en Salut Pública (CSISP), Àrea de Genòmica i Salut, Conselleria de Sanitat, Generalitat Valenciana, València, Spain; Institut "Cavanilles" de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, València, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia e Innovación, Spain
| | - Rozen Le Panse
- UPMC UM 76/INSERM U974/CNRS UMR7215/Institute of Myology, 105 Bd de l'hôpital, Paris, France
| | - Piet Stinissen
- Neuroimmunology group, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sonia Berrih-Aknin
- UPMC UM 76/INSERM U974/CNRS UMR7215/Institute of Myology, 105 Bd de l'hôpital, Paris, France
| | - Jos G Maessen
- Department of Cardiothoracic Surgery, University Hospital, Maastricht, The Netherlands
| | - Leen Van Garsse
- Department of Cardiothoracic Surgery, University Hospital, Maastricht, The Netherlands
| | - Wim A Buurman
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Socrates J Tzartos
- Department of Biochemistry, Hellenic Pasteur Institute, GR 11521 Athens, Greece
| | - Marc H De Baets
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands; Neuroimmunology group, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Pilar Martinez-Martinez
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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