1
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Fahad AS, Madan B, DeKosky BJ. Bioinformatic Analysis of Natively Paired VH:VL Antibody Repertoires for Antibody Discovery. Methods Mol Biol 2023; 2552:447-463. [PMID: 36346608 DOI: 10.1007/978-1-0716-2609-2_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Next-generation DNA sequencing (NGS) of human antibody repertoires has been extensively implemented to discover novel antibody drugs, to analyze B-cell developmental features, and to investigate antibody responses to infectious diseases and vaccination. Because the antibody repertoire encoded by human B cells is highly diverse, NGS analyses of antibody genes have provided a new window into understanding antibody responses for basic immunology, biopharmaceutical drug discovery, and immunotherapy. However, many antibody discovery protocols analyze the heavy and light chains separately due to the short-read nature of most NGS technologies, whereas paired heavy and light chain data are required for complete antibody characterization. Here, we describe a computational workflow to process millions of paired antibody heavy and light chain DNA sequence reads using the Illumina MiSeq 2x300 NGS platform. In this workflow, we describe raw NGS read processing and initial quality filtering, the annotation and assembly of antibody clonotypes relating to paired heavy and light chain antibody lineages, and the generation of complete heavy+light consensus sequences for the downstream cloning and expression of human antibody proteins.
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Affiliation(s)
- Ahmed S Fahad
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Bharat Madan
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Brandon J DeKosky
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, USA.
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2
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Martos-Folgado I, del Monte-Monge A, Lorenzo C, Busse CE, Delgado P, Mur SM, Cobos-Figueroa L, Escolà-Gil JC, Martín-Ventura JL, Wardemann H, Ramiro AR. MDA-LDL vaccination induces athero-protective germinal-center-derived antibody responses. Cell Rep 2022; 41:111468. [DOI: 10.1016/j.celrep.2022.111468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/13/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
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3
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Wahl I, Obraztsova AS, Puchan J, Hundsdorfer R, Chakravarty S, Sim BKL, Hoffman SL, Kremsner PG, Mordmüller B, Wardemann H. Clonal evolution and TCR specificity of the human T FH cell response to Plasmodium falciparum CSP. Sci Immunol 2022; 7:eabm9644. [PMID: 35687696 DOI: 10.1126/sciimmunol.abm9644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
T follicular helper (TFH) cells play a crucial role in the development of long-lived, high-quality B cell responses after infection and vaccination. However, little is known about how antigen-specific TFH cells clonally evolve in response to complex pathogens and what guides the targeting of different epitopes. Here, we assessed the cell phenotype, clonal dynamics, and T cell receptor (TCR) specificity of human circulating TFH (cTFH) cells during successive malaria immunizations with radiation-attenuated Plasmodium falciparum (Pf) sporozoites. Repeated parasite exposures induced a dynamic, polyclonal cTFH response with high frequency of cells specific to a small number of epitopes in Pf circumsporozoite protein (PfCSP), the primary sporozoite surface protein and well-defined vaccine target. Human leukocyte antigen (HLA) restrictions and differences in TCR generation probability were associated with differences in the epitope targeting frequency and indicated the potential of amino acids 311 to 333 in the Th2R/T* region as a T cell supertope. But most of vaccine-induced anti-amino acid 311 to 333 TCRs, including convergent TCRs with high sequence similarity, failed to tolerate natural polymorphisms in their target peptide sequence, thus demonstrating that the TFH cell response was limited to the vaccine strain. These data suggest that the high parasite diversity in endemic areas will limit boosting of the vaccine-induced TFH cell response by natural infections. Our findings may guide the further design of PfCSP-based malaria vaccines able to induce potent T helper cell responses for broad, long-lasting antibody responses.
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Affiliation(s)
- Ilka Wahl
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany.,Biosciences Faculty, University of Heidelberg, Heidelberg, Germany
| | - Anna S Obraztsova
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany.,Biosciences Faculty, University of Heidelberg, Heidelberg, Germany
| | - Julia Puchan
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Rebecca Hundsdorfer
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | | | | | | | - Peter G Kremsner
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Benjamin Mordmüller
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Tübingen, Germany.,Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hedda Wardemann
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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4
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Wahl I, Hoffmann S, Hundsdorfer R, Puchan J, Hoffman SL, Kremsner PG, Mordmüller B, Busse CE, Wardemann H. An efficient single-cell based method for linking human T cell phenotype to T cell receptor sequence and specificity. Eur J Immunol 2021; 52:237-246. [PMID: 34710239 DOI: 10.1002/eji.202149392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/16/2021] [Accepted: 10/26/2021] [Indexed: 11/12/2022]
Abstract
Single-cell antigen-receptor gene amplification and sequencing platforms have been used to characterize T cell receptor (TCR) repertoires but typically fail to generate paired full-length gene products for direct expression cloning and do not enable linking this data to cell phenotype information. To overcome these limitations, we established a high-throughput platform for the quantitative and qualitative analysis of human TCR repertoires that provides insights into the clonal and functional composition of human CD4+ and CD8+ αβ T cells at the molecular and cellular level. The strategy is a powerful tool to qualitatively assess differences between antigen receptors of phenotypically defined αβ T cell subsets, e.g. in immune responses to cancer, vaccination, or infection, and in autoimmune diseases.
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Affiliation(s)
- Ilka Wahl
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany.,Biosciences Faculty, University of Heidelberg, Heidelberg, Germany
| | - Sandro Hoffmann
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | | | - Julia Puchan
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | | | - Peter G Kremsner
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Benjamin Mordmüller
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Tübingen, Germany.,Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian E Busse
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Hedda Wardemann
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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5
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Lorenzo C, Delgado P, Busse CE, Sanz-Bravo A, Martos-Folgado I, Bonzon-Kulichenko E, Ferrarini A, Gonzalez-Valdes IB, Mur SM, Roldán-Montero R, Martinez-Lopez D, Martin-Ventura JL, Vázquez J, Wardemann H, Ramiro AR. ALDH4A1 is an atherosclerosis auto-antigen targeted by protective antibodies. Nature 2020; 589:287-292. [PMID: 33268892 DOI: 10.1038/s41586-020-2993-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 10/05/2020] [Indexed: 12/19/2022]
Abstract
Cardiovascular disease (CVD) is the leading cause of mortality in the world, with most CVD-related deaths resulting from myocardial infarction or stroke. The main underlying cause of thrombosis and cardiovascular events is atherosclerosis, an inflammatory disease that can remain asymptomatic for long periods. There is an urgent need for therapeutic and diagnostic options in this area. Atherosclerotic plaques contain autoantibodies1,2, and there is a connection between atherosclerosis and autoimmunity3. However, the immunogenic trigger and the effects of the autoantibody response during atherosclerosis are not well understood3-5. Here we performed high-throughput single-cell analysis of the atherosclerosis-associated antibody repertoire. Antibody gene sequencing of more than 1,700 B cells from atherogenic Ldlr-/- and control mice identified 56 antibodies expressed by in-vivo-expanded clones of B lymphocytes in the context of atherosclerosis. One-third of the expanded antibodies were reactive against atherosclerotic plaques, indicating that various antigens in the lesion can trigger antibody responses. Deep proteomics analysis identified ALDH4A1, a mitochondrial dehydrogenase involved in proline metabolism, as a target antigen of one of these autoantibodies, A12. ALDH4A1 distribution is altered during atherosclerosis, and circulating ALDH4A1 is increased in mice and humans with atherosclerosis, supporting the potential use of ALDH4A1 as a disease biomarker. Infusion of A12 antibodies into Ldlr-/- mice delayed plaque formation and reduced circulating free cholesterol and LDL, suggesting that anti-ALDH4A1 antibodies can protect against atherosclerosis progression and might have therapeutic potential in CVD.
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Affiliation(s)
- Cristina Lorenzo
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Pilar Delgado
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Alejandro Sanz-Bravo
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | | | - Elena Bonzon-Kulichenko
- Cardiovascular Proteomics Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Alessia Ferrarini
- Cardiovascular Proteomics Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Ileana B Gonzalez-Valdes
- Cardiovascular Proteomics Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Sonia M Mur
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Raquel Roldán-Montero
- Vascular Pathology Lab, IIS-Fundación Jiménez Díaz-Universidad Autónoma, Madrid, Spain
| | - Diego Martinez-Lopez
- Vascular Pathology Lab, IIS-Fundación Jiménez Díaz-Universidad Autónoma, Madrid, Spain
| | - Jose L Martin-Ventura
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Vascular Pathology Lab, IIS-Fundación Jiménez Díaz-Universidad Autónoma, Madrid, Spain
| | - Jesús Vázquez
- Cardiovascular Proteomics Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Hedda Wardemann
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Almudena R Ramiro
- B Lymphocyte Biology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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6
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IGLV3-21*01 is an inherited risk factor for CLL through the acquisition of a single-point mutation enabling autonomous BCR signaling. Proc Natl Acad Sci U S A 2020; 117:4320-4327. [PMID: 32047037 PMCID: PMC7049113 DOI: 10.1073/pnas.1913810117] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CLL is characterized by autonomous B cell receptor (BCR) signaling. CLL subsets are empirically defined by sequence similarities of the BCR heavy chain. However, in the unfavorable subset 2, an acquired mutation (termed R110) in the light chain stimulates autonomous BCR signaling. This study demonstrates that the oncogenic R110 mutation dictates the unfavorable prognosis and is not restricted to the conventional subset 2. Interestingly, carriers of a particular light-chain allele (IGLV3-21*01) are predisposed to develop CLL because this allele enables autonomous BCR signaling by R110 as a single-point mutation. Monoclonal antibodies permit convenient screening for R110-expressing CLL, showing that it is the largest immunologically defined CLL subset and an example of functional rather than empirical CLL subclassification. The prognosis of chronic lymphocytic leukemia (CLL) depends on different markers, including cytogenetic aberrations, oncogenic mutations, and mutational status of the immunoglobulin (Ig) heavy-chain variable (IGHV) gene. The number of IGHV mutations distinguishes mutated (M) CLL with a markedly superior prognosis from unmutated (UM) CLL cases. In addition, B cell antigen receptor (BCR) stereotypes as defined by IGHV usage and complementarity-determining regions (CDRs) classify ∼30% of CLL cases into prognostically important subsets. Subset 2 expresses a BCR with the combination of IGHV3-21–derived heavy chains (HCs) with IGLV3-21–derived light chains (LCs), and is associated with an unfavorable prognosis. Importantly, the subset 2 LC carries a single-point mutation, termed R110, at the junction between the variable and constant LC regions. By analyzing 4 independent clinical cohorts through BCR sequencing and by immunophenotyping with antibodies specifically recognizing wild-type IGLV3-21 and R110-mutated IGLV3-21 (IGLV3-21R110), we show that IGLV3-21R110–expressing CLL represents a distinct subset with poor prognosis independent of IGHV mutations. Compared with other alleles, only IGLV3-21*01 facilitates effective homotypic BCR–BCR interaction that results in autonomous, oncogenic BCR signaling after acquiring R110 as a single-point mutation. Presumably, this mutation acts as a standalone driver that transforms IGLV3-21*01–expressing B cells to develop CLL. Thus, we propose to expand the conventional definition of CLL subset 2 to subset 2L by including all IGLV3-21R110–expressing CLL cases regardless of IGHV mutational status. Moreover, the generation of monoclonal antibodies recognizing IGLV3-21 or mutated IGLV3-21R110 facilitates the recognition of B cells carrying this mutation in CLL patients or healthy donors.
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7
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Kreer C, Döring M, Lehnen N, Ercanoglu MS, Gieselmann L, Luca D, Jain K, Schommers P, Pfeifer N, Klein F. openPrimeR for multiplex amplification of highly diverse templates. J Immunol Methods 2020; 480:112752. [PMID: 31991148 DOI: 10.1016/j.jim.2020.112752] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/19/2019] [Accepted: 01/24/2020] [Indexed: 12/28/2022]
Abstract
To study the diversity of immune receptors and pathogens, multiplex PCR has become a central approach in research and diagnostics. However, insufficient primer design against highly diverse templates often prevents amplification and therefore limits the correct understanding of biological processes. Here, we present openPrimeR, an R-based tool for evaluating and designing multiplex PCR primers. openPrimeR provides a functional and intuitive interface and uses either a greedy algorithm or an integer linear program to compute the minimal set of primers that performs full target coverage. As proof of concept, we used openPrimeR to find optimal primer sets for the amplification of highly mutated immunoglobulins. Comprehensive analyses on specifically generated immunoglobulin variable gene segment libraries resulted in the composition of highly effective primer sets (oPR-IGHV, oPR-IGKV and oPR-IGLV) that demonstrated to be particularly suitable for the isolation of novel human antibodies.
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Affiliation(s)
- Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Matthias Döring
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Nathalie Lehnen
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Meryem S Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Domnica Luca
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Kanika Jain
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany; Methods in Medical Informatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany; Medical Faculty, University of Tübingen, 72076 Tübingen, Germany; German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany.
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8
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Minervina A, Pogorelyy M, Mamedov I. T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity. Transpl Int 2019; 32:1111-1123. [DOI: 10.1111/tri.13475] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/09/2019] [Accepted: 06/25/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Anastasia Minervina
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
| | - Mikhail Pogorelyy
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
- Institute of Translational Medicine Pirogov Russian National Research Medical University Moscow Russia
| | - Ilgar Mamedov
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
- Institute of Translational Medicine Pirogov Russian National Research Medical University Moscow Russia
- Laboratory of Molecular Biology Rogachev Federal Scientific and Clinical Centre of Pediatric Hematology Oncology and Immunology Moscow Russia
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9
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Ludwig J, Huber AK, Bartsch I, Busse CE, Wardemann H. High-throughput single-cell sequencing of paired TCRα and TCRβ genes for the direct expression-cloning and functional analysis of murine T-cell receptors. Eur J Immunol 2019; 49:1269-1277. [PMID: 31017295 PMCID: PMC6767390 DOI: 10.1002/eji.201848030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/11/2019] [Accepted: 04/15/2019] [Indexed: 12/01/2022]
Abstract
Precise clonal and functional assessments of the T cell receptor (TCR) repertoire diversity require paired TCRα and TCRβ gene sequence information at monoclonal level. However, available single‐cell strategies are typically limited in throughput and often do not provide full‐length DNA templates for direct gene cloning. Here, we describe a high‐throughput strategy for the unbiased amplification and automated sequence analysis of paired TCRα and TCRβ genes from primary mouse T cells. The platform links cell phenotype and TCR gene sequence information at single‐cell level. Furthermore, it enables direct functional analyses through the efficient cloning of both genes and the generation of stable TCR expressing cell lines. This highly efficient workflow is a powerful tool to determine the diversity and quality of the murine T‐cell repertoire in various settings, for example in vaccine development, infectious diseases, autoimmunity, or cancer.
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Affiliation(s)
- Julia Ludwig
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Ann-Kathrin Huber
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Ilka Bartsch
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Christian E Busse
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Hedda Wardemann
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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10
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Abstract
The majority of lymphomas originate from B cells at the germinal center stage. Preferential selection of B-cell clones by a limited set of antigens has been suggested to drive lymphoma development. While recent studies in chronic lymphocytic leukemia have shown that self-reactive B-cell receptors (BCR) can generate cell-autonomous signaling and proliferation, our knowledge about the role of BCRs for the development or survival of other lymphomas remains limited. Here, we describe a strategy to characterize the antibody reactivity of human B cells. The approach allows the unbiased characterization of the human antibody repertoire at single-cell level through the generation of recombinant monoclonal antibodies from single primary human B cells of defined origin. This protocol offers a detailed description of the method starting from the flow-cytometric isolation of single human B cells to the reverse transcription-polymerase chain reaction (RT-PCR)-based amplification of the expressed immunoglobulin (Ig) transcripts (IGH, IGK, and IGL) and their subsequent cloning into expression vectors for the in vitro production of recombinant monoclonal antibodies. The strategy may be used to obtain information on the clonal evolution of B-cell lymphomas by single-cell sequencing of Ig transcripts and on the antibody reactivity of human lymphoma B cells.
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Affiliation(s)
- Hedda Wardemann
- Division of B-Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Christian E Busse
- Division of B-Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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11
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Sequencing and Affinity Determination of Antigen-Specific B Lymphocytes from Peripheral Blood. Methods Mol Biol 2018. [PMID: 30196503 DOI: 10.1007/978-1-4939-8648-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Here we describe methods for screening human blood to isolate peripheral blood mononuclear cells (PBMCs) capable of binding fluorescently labeled antigen, as well as methods for the amplification and sequencing of B cell receptor (BCR) heavy and light chain genes. Detailed protocols are provided for transient mammalian expression in a hexahistidine-tagged Fab format, purification by immobilized metal affinity chromatography (IMAC), and affinity determination by BioLayer interferometry (BLI).
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12
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Breden F, Watson CT. Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1053:245-263. [PMID: 29549643 DOI: 10.1007/978-3-319-72077-7_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High throughput sequencing (HTS) approaches have only recently been applied to describing the antibody/B-cell repertoire in fine detail, but these data sets have already become critical to the design of vaccines and therapeutics, and monitoring of cancer immunotherapy. As a case study, we describe the potential and present limitations of HTS studies of the Ab repertoire during infection with HIV-1. Most of the present studies restrict their analyses to lineages of specific bnAbs. We discuss future initiatives to expand this type of analysis to more complete repertoires and to improve comparing and sharing of these Ab repertoire data across studies and institutions.
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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13
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Rosenfeld AM, Meng W, Chen DY, Zhang B, Granot T, Farber DL, Hershberg U, Luning Prak ET. Computational Evaluation of B-Cell Clone Sizes in Bulk Populations. Front Immunol 2018; 9:1472. [PMID: 30008715 PMCID: PMC6034424 DOI: 10.3389/fimmu.2018.01472] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 06/13/2018] [Indexed: 12/27/2022] Open
Abstract
B cell clones expand and contract during adaptive immune responses and can persist or grow uncontrollably in lymphoproliferative disorders. One way to monitor and track B cell clones is to perform large-scale sampling of bulk cell populations, amplifying, and sequencing antibody gene rearrangements by next-generation sequencing (NGS). Here, we describe a series of computational approaches for estimating B cell clone size in NGS immune repertoire profiling data of antibody heavy chain gene rearrangements. We define three different measures of B cell clone size-copy numbers, instances, and unique sequences-and show how these measures can be used to rank clones, analyze their diversity, and study their distribution within and between individuals. We provide a detailed, step-by-step procedure for performing these analyses using two different data sets of spleen samples from human organ donors. In the first data set, 19 independently generated biological replicates from a single individual are analyzed for B cell clone size, diversity and sampling sufficiency for clonal overlap analysis. In the second data set, B cell clones are compared in eight different organ donors. We comment upon frequently encountered pitfalls and offer practical advice with alternative approaches. Overall, we provide a series of pragmatic analytical approaches and show how different clone size measures can be used to study the clonal landscape in bulk B cell immune repertoire profiling data.
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Affiliation(s)
- Aaron M. Rosenfeld
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Dora Y. Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bochao Zhang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | - Tomer Granot
- Columbia Center for Translational Immunology, Columbia University, New York, NY, United States
| | - Donna L. Farber
- Columbia Center for Translational Immunology, Columbia University, New York, NY, United States
| | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
- Department of Microbiology and Immunology, Drexel College of Medicine, Drexel University, Philadelphia, PA, United States
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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14
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Imkeller K, Wardemann H. Assessing human B cell repertoire diversity and convergence. Immunol Rev 2018; 284:51-66. [DOI: 10.1111/imr.12670] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Hedda Wardemann
- German Cancer Research Center; B Cell Immunology; Heidelberg Germany
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15
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Rollenske T, Szijarto V, Lukasiewicz J, Guachalla LM, Stojkovic K, Hartl K, Stulik L, Kocher S, Lasitschka F, Al-Saeedi M, Schröder-Braunstein J, von Frankenberg M, Gaebelein G, Hoffmann P, Klein S, Heeg K, Nagy E, Nagy G, Wardemann H. Cross-specificity of protective human antibodies against Klebsiella pneumoniae LPS O-antigen. Nat Immunol 2018; 19:617-624. [PMID: 29760533 DOI: 10.1038/s41590-018-0106-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/26/2018] [Indexed: 11/09/2022]
Abstract
Humoral immune responses to microbial polysaccharide surface antigens can prevent bacterial infection but are typically strain specific and fail to mediate broad protection against different serotypes. Here we describe a panel of affinity-matured monoclonal human antibodies from peripheral blood immunoglobulin M-positive (IgM+) and IgA+ memory B cells and clonally related intestinal plasmablasts, directed against the lipopolysaccharide (LPS) O-antigen of Klebsiella pneumoniae, an opportunistic pathogen and major cause of antibiotic-resistant nosocomial infections. The antibodies showed distinct patterns of in vivo cross-specificity and protection against different clinically relevant K. pneumoniae serotypes. However, cross-specificity was not limited to K. pneumoniae, as K. pneumoniae-specific antibodies recognized diverse intestinal microbes and neutralized not only K. pneumoniae LPS but also non-K. pneumoniae LPS. Our data suggest that the recognition of minimal glycan epitopes abundantly expressed on microbial surfaces might serve as an efficient humoral immunological mechanism to control invading pathogens and the large diversity of the human microbiota with a limited set of cross-specific antibodies.
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Affiliation(s)
- Tim Rollenske
- Max Planck Research Group Molecular Immunology, Max Planck Institute for Infection Biology, Berlin, Germany.,Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | | | - Jolanta Lukasiewicz
- Department of Immunochemistry, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy Polish Academy of Sciences, Wroclaw, Poland
| | | | - Katarina Stojkovic
- Department of Immunochemistry, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy Polish Academy of Sciences, Wroclaw, Poland
| | | | | | - Simone Kocher
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mohammed Al-Saeedi
- Department of General and Transplant Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Moritz von Frankenberg
- Department of General, Abdominal and Minimal Invasive Surgery, Hospital Salem, Heidelberg, Germany
| | - Gereon Gaebelein
- Department of Visceral, Transplantation, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany.,Department of General, Visceral, Vascular and Pediatric Surgery, Saarland University Medical Center, Homburg, Germany
| | - Peter Hoffmann
- Department of Gastroenterology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sabrina Klein
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Klaus Heeg
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Hedda Wardemann
- Max Planck Research Group Molecular Immunology, Max Planck Institute for Infection Biology, Berlin, Germany. .,Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany.
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16
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Murugan R, Buchauer L, Triller G, Kreschel C, Costa G, Pidelaserra Martí G, Imkeller K, Busse CE, Chakravarty S, Sim BKL, Hoffman SL, Levashina EA, Kremsner PG, Mordmüller B, Höfer T, Wardemann H. Clonal selection drives protective memory B cell responses in controlled human malaria infection. Sci Immunol 2018; 3:3/20/eaap8029. [DOI: 10.1126/sciimmunol.aap8029] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/30/2017] [Indexed: 01/20/2023]
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17
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Scally SW, Murugan R, Bosch A, Triller G, Costa G, Mordmüller B, Kremsner PG, Sim BKL, Hoffman SL, Levashina EA, Wardemann H, Julien JP. Rare PfCSP C-terminal antibodies induced by live sporozoite vaccination are ineffective against malaria infection. J Exp Med 2017; 215:63-75. [PMID: 29167197 PMCID: PMC5748854 DOI: 10.1084/jem.20170869] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/30/2017] [Accepted: 10/11/2017] [Indexed: 11/16/2022] Open
Abstract
Scally et al. show the molecular, structural, and functional characterization of human antibodies against the C-terminal domain of Plasmodium falciparum (Pf) circumsporozoite (CSP [C-PfCSP]) and reveal that its arrangement on the Pf sporozoite surface and epitope polymorphism contribute to poor C-PfCSP immunogenicity and ineffective humoral responses in volunteers protected against Pf malaria. Antibodies against the central repeat of the Plasmodium falciparum (Pf) circumsporozoite protein (CSP) inhibit parasite activity and correlate with protection from malaria. However, the humoral response to the PfCSP C terminus (C-PfCSP) is less well characterized. Here, we describe B cell responses to C-PfCSP from European donors who underwent immunization with live Pf sporozoites (PfSPZ Challenge) under chloroquine prophylaxis (PfSPZ-CVac), and were protected against controlled human malaria infection. Out of 215 PfCSP-reactive monoclonal antibodies, only two unique antibodies were specific for C-PfCSP, highlighting the rare occurrence of C-PfCSP–reactive B cells in PfSPZ-CVac–induced protective immunity. These two antibodies showed poor sporozoite binding and weak inhibition of parasite traversal and development, and did not protect mice from infection with PfCSP transgenic Plasmodium berghei sporozoites. Structural analyses demonstrated that one antibody interacts with a polymorphic region overlapping two T cell epitopes, suggesting that variability in C-PfCSP may benefit parasite escape from humoral and cellular immunity. Our data identify important features underlying C-PfCSP shortcomings as a vaccine target.
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Affiliation(s)
- Stephen W Scally
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Rajagopal Murugan
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Alexandre Bosch
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Gianna Triller
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Giulia Costa
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Benjamin Mordmüller
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Tübingen, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Tübingen, Germany
| | | | | | - Elena A Levashina
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Hedda Wardemann
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Jean-Philippe Julien
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada .,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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18
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Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology 2017; 153:31-41. [PMID: 28898398 DOI: 10.1111/imm.12838] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high-throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high-throughput sequencing has made it possible to obtain large-scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high-throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high-throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Life Science Zurich Graduate School, Systems Biology, ETH Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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19
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Rodríguez-Vicente AE, Bikos V, Hernández-Sánchez M, Malcikova J, Hernández-Rivas JM, Pospisilova S. Next-generation sequencing in chronic lymphocytic leukemia: recent findings and new horizons. Oncotarget 2017; 8:71234-71248. [PMID: 29050359 PMCID: PMC5642634 DOI: 10.18632/oncotarget.19525] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/12/2017] [Indexed: 11/25/2022] Open
Abstract
The rapid progress in next-generation sequencing technologies has significantly contributed to our knowledge of the genetic events associated with the development, progression and treatment resistance of chronic lymphocytic leukemia patients. Together with the discovery of new driver mutations, next-generation sequencing has revealed an immense degree of both intra- and inter-tumor heterogeneity and enabled us to describe marked clonal evolution. Advances in immunogenetics may be implemented to detect minimal residual disease more sensitively and to track clonal B cell populations, their dynamics and molecular characteristics. The interpretation of these aspects is indispensable to thoroughly examine the genetic background of chronic lymphocytic leukemia. We review and discuss the recent results provided by the different next-generation sequencing techniques used in studying the chronic lymphocytic leukemia genome, as well as future perspectives in the methodologies and applications.
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Affiliation(s)
- Ana E Rodríguez-Vicente
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom.,IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca, CSIC, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Vasilis Bikos
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - María Hernández-Sánchez
- IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca, CSIC, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Jitka Malcikova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Medical Faculty MU and University Hospital, Brno, Czech Republic
| | - Jesús-María Hernández-Rivas
- IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca, CSIC, Hospital Universitario de Salamanca, Salamanca, Spain.,Hematology Department, Hospital Universitario, Salamanca, Spain.,Department of Medicine, Universidad de Salamanca, Salamanca, Spain
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Medical Faculty MU and University Hospital, Brno, Czech Republic
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20
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Novel Approaches to Analyze Immunoglobulin Repertoires. Trends Immunol 2017; 38:471-482. [PMID: 28566130 DOI: 10.1016/j.it.2017.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/25/2017] [Accepted: 05/04/2017] [Indexed: 11/21/2022]
Abstract
Analysis of immunoglobulin (Ig) repertoires aims to comprehend Ig diversity with the goal of predicting humoral immune responses in the context of infection, vaccination, autoimmunity, and malignancies. The first next-generation sequencing (NGS) analyses of bulk B cell populations dramatically advanced sampling depth over previous low-throughput single-cell-based protocols, albeit at the expense of accuracy and loss of chain-pairing information. In recent years the field has substantially differentiated, with bulk analyses becoming more accurate while single-cell approaches have gained in throughput. Additionally, new platforms striving to combine high throughput and chain pairing have been developed as well as various computational tools for analysis. Here we review the developments of the past 4-5 years and discuss the open challenges.
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21
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Exploring Human Antimicrobial Antibody Responses on a Single B Cell Level. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00544-16. [PMID: 28356257 DOI: 10.1128/cvi.00544-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Analysis of monoclonal antibodies (MAbs) derived from single B cell cloning has been highly beneficial for antimicrobial immunotherapy, vaccine design, and advancing our understanding of pathogen-triggered effects on the human immunoglobulin repertoire. Sequencing of variable domains of single B cells, and characterization of binding and functional activities of MAbs derived from those sequences, provides in-depth insight not only into sites of susceptibility for antibody-mediated neutralization or opsonization of the pathogen but also into the dynamics of protective antibody evolution during infection. This information can be utilized to rapidly develop novel immunotherapies of completely human origin and provides a roadmap for structure-based vaccine design that aims to elicit similar protective antibody responses. Here, we summarize recent aspects of the single B cell cloning approach.
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22
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Friedensohn S, Khan TA, Reddy ST. Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires. Trends Biotechnol 2016; 35:203-214. [PMID: 28341036 DOI: 10.1016/j.tibtech.2016.09.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/19/2016] [Accepted: 09/30/2016] [Indexed: 11/19/2022]
Abstract
In recent years, major efforts have been made to develop sophisticated experimental and bioinformatic workflows for sequencing adaptive immune repertoires. The immunological insight gained has been applied to fields as varied as lymphocyte biology, immunodiagnostics, vaccines, cancer immunotherapy, and antibody engineering. In this review, we provide a detailed overview of these advanced methodologies, focusing specifically on strategies to reduce sequencing errors and bias and to achieve high-throughput pairing of variable regions (e.g., heavy-light or alpha-beta chains). In addition, we highlight recent technologies for single-cell transcriptome sequencing that can be integrated with immune repertoires. Finally, we provide a perspective on advanced immune repertoire sequencing and its ability to impact basic immunology, biopharmaceutical drug discovery and development, and cancer immunotherapy.
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Affiliation(s)
- Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Tarik A Khan
- Pharmaceutical Development & Supplies Biologics Europe, F. Hoffman-La Roche Ltd, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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23
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Gristick HB, von Boehmer L, West AP, Schamber M, Gazumyan A, Golijanin J, Seaman MS, Fätkenheuer G, Klein F, Nussenzweig MC, Bjorkman PJ. Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site. Nat Struct Mol Biol 2016; 23:906-915. [PMID: 27617431 DOI: 10.1038/nsmb.3291] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/10/2016] [Indexed: 12/14/2022]
Abstract
HIV-1 vaccine design is informed by structural studies elucidating mechanisms by which broadly neutralizing antibodies (bNAbs) recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env). Variability in high-mannose and complex-type Env glycoforms leads to heterogeneity that usually precludes visualization of the native glycan shield. We present 3.5-Å- and 3.9-Å-resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation, revealing a glycan shield of high-mannose and complex-type N-glycans, which we used to define complete epitopes of two bNAbs. Env trimer was complexed with 10-1074 (against the V3-loop) and IOMA, a new CD4-binding site (CD4bs) antibody. Although IOMA derives from VH1-2*02, the germline gene of CD4bs-targeting VRC01-class bNAbs, its light chain lacks the short CDRL3 that defines VRC01-class bNAbs. Thus IOMA resembles 8ANC131-class/VH1-46-derived CD4bs bNAbs, which have normal-length CDRL3s. The existence of bNAbs that combine features of VRC01-class and 8ANC131-class antibodies has implications for immunization strategies targeting VRC01-like bNAbs.
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Affiliation(s)
- Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Lotta von Boehmer
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Michael Schamber
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Gerd Fätkenheuer
- Department of Internal Medicine I, University Hospital of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Florian Klein
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.,Laboratory of Experimental Immunology, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Internal Medicine I, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
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24
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Imkeller K, Arndt PF, Wardemann H, Busse CE. sciReptor: analysis of single-cell level immunoglobulin repertoires. BMC Bioinformatics 2016; 17:67. [PMID: 26847109 PMCID: PMC4743164 DOI: 10.1186/s12859-016-0920-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/29/2016] [Indexed: 11/10/2022] Open
Abstract
Background The sequencing of immunoglobulin (Ig) transcripts from single B cells yields essential information about Ig heavy:light chain pairing, which is lost in conventional bulk sequencing experiments. The previously limited throughput of single-cell approaches has recently been overcome by the introduction of multiple next-generation sequencing (NGS)-based platforms. Furthermore, single-cell techniques allow the assignment of additional data types (e.g. cell surface marker expression), which are crucial for biological interpretation. However, the currently available computational tools are not designed to handle single-cell data and do not provide integral solutions for linking of sequence data to other biological data. Results Here we introduce sciReptor, a flexible toolkit for the processing and analysis of antigen receptor repertoire sequencing data at single-cell level. The software combines bioinformatics tools for immunoglobulin sequence annotation with a relational database, where raw data and analysis results are stored and linked. sciReptor supports attribution of additional data categories such as cell surface marker expression or immunological metadata. Furthermore, it comprises a quality control module as well as basic repertoire visualization tools. Conclusion sciReptor is a flexible framework for standardized sequence analysis of antigen receptor repertoires on single-cell level. The relational database allows easy data sharing and downstream analyses as well as immediate comparisons between different data sets. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0920-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katharina Imkeller
- Division of B Cell Immunology, German Cancer Research Center, Feld 280, Heidelberg, 69120, Germany.
| | - Peter F Arndt
- Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin, 14195, Germany.
| | - Hedda Wardemann
- Division of B Cell Immunology, German Cancer Research Center, Feld 280, Heidelberg, 69120, Germany.
| | - Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center, Feld 280, Heidelberg, 69120, Germany.
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25
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Catani M, Walther D, Christie MR, McLaughlin KA, Bonifacio E, Eugster A. Isolation of human monoclonal autoantibodies derived from pancreatic lymph node and peripheral blood B cells of islet autoantibody-positive patients. Diabetologia 2016; 59:294-8. [PMID: 26493188 DOI: 10.1007/s00125-015-3792-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/30/2015] [Indexed: 12/17/2022]
Abstract
AIMS/HYPOTHESIS Autoantibodies against pancreatic islets and infections by enteroviruses are associated with type 1 diabetes, but the specificity of immune responses within the type 1 diabetic pancreas is poorly characterised. We investigated whether pancreatic lymph nodes could provide a source of antigen-specific B cells for analysis of immune responses within the (pre)diabetic pancreas. METHODS Human IgG antibodies were cloned from single B lymphocytes sorted from pancreatic lymph node cells of three organ donors positive for islet autoantibodies, and from the peripheral blood of a patient with type 1 diabetes. Antibodies to insulinoma-associated antigen 2 (IA-2), GAD65, zinc transporter 8 (ZnT8) and Coxsackie B virus proteins were assayed by immunoprecipitation and by immunofluorescence on pancreatic sections. RESULTS Human IgG antibodies (863) were successfully cloned and produced from 4,092 single B cells from lymph nodes and peripheral blood. Reactivity to the protein tyrosine phosphatase domain of the IA-2 autoantigen was detected in two cloned antibodies: one derived from a pancreatic lymph node and one from peripheral blood. Epitopes for these two antibodies were similar to each other and to those for circulating antibodies in type 1 diabetes. The remaining 861 antibodies were negative for reactivity to IA-2, GAD65 or ZnT8 by both assays tested. Reactivity to a Coxsackie viral protein 2 was detected in one antibody derived from a peripheral blood B cell, but not from lymph nodes. CONCLUSIONS/INTERPRETATION We show evidence for the infrequent presence of autoantigen-specific IgG+ B lymphocytes in the pancreatic-draining lymph nodes of islet autoantibody-positive individuals.
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