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Matsunaga R, Tsumoto K. Accelerating antibody discovery and optimization with high-throughput experimentation and machine learning. J Biomed Sci 2025; 32:46. [PMID: 40346589 PMCID: PMC12063268 DOI: 10.1186/s12929-025-01141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 04/23/2025] [Indexed: 05/11/2025] Open
Abstract
The integration of high-throughput experimentation and machine learning is transforming data-driven antibody engineering, revolutionizing the discovery and optimization of antibody therapeutics. These approaches employ extensive datasets comprising antibody sequences, structures, and functional properties to train predictive models that enable rational design. This review highlights the significant advancements in data acquisition and feature extraction, emphasizing the necessity of capturing both sequence and structural information. We illustrate how machine learning models, including protein language models, are used not only to enhance affinity but also to optimize other crucial therapeutic properties, such as specificity, stability, viscosity, and manufacturability. Furthermore, we provide practical examples and case studies to demonstrate how the synergy between experimental and computational approaches accelerates antibody engineering. Finally, this review discusses the remaining challenges in fully realizing the potential of artificial intelligence (AI)-powered antibody discovery pipelines to expedite therapeutic development.
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Affiliation(s)
- Ryo Matsunaga
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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2
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Walimbwa SI, Maly P, Kafkova LR, Raska M. Beyond glycan barriers: non-cognate ligands and protein mimicry approaches to elicit broadly neutralizing antibodies for HIV-1. J Biomed Sci 2024; 31:83. [PMID: 39169357 PMCID: PMC11337606 DOI: 10.1186/s12929-024-01073-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) vaccine immunogens capable of inducing broadly neutralizing antibodies (bNAbs) remain obscure. HIV-1 evades immune responses through enormous diversity and hides its conserved vulnerable epitopes on the envelope glycoprotein (Env) by displaying an extensive immunodominant glycan shield. In elite HIV-1 viremic controllers, glycan-dependent bNAbs targeting conserved Env epitopes have been isolated and are utilized as vaccine design templates. However, immunological tolerance mechanisms limit the development of these antibodies in the general population. The well characterized bNAbs monoclonal variants frequently exhibit extensive levels of somatic hypermutation, a long third heavy chain complementary determining region, or a short third light chain complementarity determining region, and some exhibit poly-reactivity to autoantigens. This review elaborates on the obstacles to engaging and manipulating the Env glycoprotein as an effective immunogen and describes an alternative reverse vaccinology approach to develop a novel category of bNAb-epitope-derived non-cognate immunogens for HIV-1 vaccine design.
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Affiliation(s)
- Stephen Ian Walimbwa
- Department of Immunology, University Hospital Olomouc, Zdravotníků 248/7, 77900, Olomouc, Czech Republic.
| | - Petr Maly
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Leona Raskova Kafkova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 3, 779 00, Olomouc, Czech Republic
| | - Milan Raska
- Department of Immunology, University Hospital Olomouc, Zdravotníků 248/7, 77900, Olomouc, Czech Republic.
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 3, 779 00, Olomouc, Czech Republic.
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3
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Wang Q, Feng D, Jia S, Lu Q, Zhao M. B-Cell Receptor Repertoire: Recent Advances in Autoimmune Diseases. Clin Rev Allergy Immunol 2024; 66:76-98. [PMID: 38459209 DOI: 10.1007/s12016-024-08984-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
In the field of contemporary medicine, autoimmune diseases (AIDs) are a prevalent and debilitating group of illnesses. However, they present extensive and profound challenges in terms of etiology, pathogenesis, and treatment. A major reason for this is the elusive pathophysiological mechanisms driving disease onset. Increasing evidence suggests the indispensable role of B cells in the pathogenesis of autoimmune diseases. Interestingly, B-cell receptor (BCR) repertoires in autoimmune diseases display a distinct skewing that can provide insights into disease pathogenesis. Over the past few years, advances in high-throughput sequencing have provided powerful tools for analyzing B-cell repertoire to understand the mechanisms during the period of B-cell immune response. In this paper, we have provided an overview of the mechanisms and analytical methods for generating BCR repertoire diversity and summarize the latest research progress on BCR repertoire in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), primary Sjögren's syndrome (pSS), multiple sclerosis (MS), and type 1 diabetes (T1D). Overall, B-cell repertoire analysis is a potent tool to understand the involvement of B cells in autoimmune diseases, facilitating the creation of innovative therapeutic strategies targeting specific B-cell clones or subsets.
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Affiliation(s)
- Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Sujie Jia
- Department of Pharmacy, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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Feng F, Yuen R, Wang Y, Hua A, Kepler TB, Wetzler LM. Characterizing adjuvants' effects at murine immunoglobulin repertoire level. iScience 2024; 27:108749. [PMID: 38269092 PMCID: PMC10805652 DOI: 10.1016/j.isci.2023.108749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/29/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024] Open
Abstract
Generating large-scale, high-fidelity sequencing data is challenging and, furthermore, not much has been done to characterize adjuvants' effects at the repertoire level. Thus, we introduced an IgSeq pipeline that standardized library prep protocols and data analysis functions for accurate repertoire profiling. We then studied systemically effects of CpG and Alum on the Ig heavy chain repertoire using the ovalbumin (OVA) murine model. Ig repertoires of different tissues (spleen and bone marrow) and isotypes (IgG and IgM) were examined and compared in IGHV mutation, gene usage, CDR3 length, clonal diversity, and clonal selection. We found Ig repertoires of different compartments exhibited distinguishable profiles at the non-immunized steady state, and distinctions became more pronounced upon adjuvanted immunizations. Notably, Alum and CpG effects exhibited different tissue- and isotype-preferences. The former led to increased diversity of abundant clones in bone marrow, and the latter promoted the selection of IgG clones in both tissues.
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Affiliation(s)
- Feng Feng
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Rachel Yuen
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Yumei Wang
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Axin Hua
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Thomas B. Kepler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Mathematics and Statistics, Boston University, Boston, MA 02118, USA
| | - Lee M. Wetzler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
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5
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Stamatatos L. 'Immunization during ART and ATI for HIV-1 vaccine discovery/development'. Curr Opin HIV AIDS 2023; 18:309-314. [PMID: 37712859 PMCID: PMC10552831 DOI: 10.1097/coh.0000000000000817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
PURPOSE OF REVIEW Explore whether immunization with germline-targeting Env immunogens during ART, followed by ATI, leads to the identification of viral envelope glycoproteins (Envs) that promote and guide the full maturation of broadly neutralizing antibody responses. RECENT FINDINGS The HIV-1 envelope glycoprotein (Env) does not efficiently engage the germline precursors of broadly neutralizing antibodies (bnAbs). However, Env-derived proteins specifically designed to precisely do that, have been recently developed. These 'germline-targeting' Env immunogens activate naïve B cells that express the germline precursors of bnAbs but by themselves cannot guide their maturation towards their broadly neutralizing forms. This requires sequential immunizations with heterologous sets of Envs. These 'booster' Envs are currently unknown. SUMMARY Combining germline-targeting Env immunization approaches during ART with ATI could lead to the identification of natural Envs that are responsible for the maturation of broadly neutralizing antibody responses during infection. Such Envs could then serve as booster immunogens to guide the maturation of glBCRs that have become activated by germline-targeting immunogens in uninfected subjects.
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Affiliation(s)
- Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center and University of Washington, Department of Global Health, Seattle, WA, USA
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Lowden MJ, Lei EK, Hussack G, Henry KA. Applications of High-Throughput DNA Sequencing to Single-Domain Antibody Discovery and Engineering. Methods Mol Biol 2023; 2702:489-540. [PMID: 37679637 DOI: 10.1007/978-1-0716-3381-6_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Next-generation DNA sequencing (NGS) technologies have made it possible to interrogate antibody repertoires to unprecedented depths, typically via sequencing of cDNAs encoding immunoglobulin variable domains. In the absence of heavy-light chain pairing, the variable domains of heavy chain-only antibodies (HCAbs), referred to as single-domain antibodies (sdAbs), are uniquely amenable to NGS analyses. In this chapter, we provide simple and rapid protocols for producing and sequencing multiplexed immunoglobulin variable domain (VHH, VH, or VL) amplicons derived from a variety of sources using the Illumina MiSeq platform. Generation of such amplicon libraries is relatively inexpensive, requiring no specialized equipment and only a limited set of PCR primers. We also present several applications of NGS to sdAb discovery and engineering, including: (1) evaluation of phage-displayed sdAb library sequence diversity and monitoring of panning experiments; (2) identification of sdAbs of predetermined epitope specificity following competitive elution of phage-displayed sdAb libraries; (3) direct selection of B cells expressing antigen-specific, membrane-bound HCAb using antigen-coupled magnetic beads and identification of antigen-specific sdAbs, and (4) affinity maturation of lead sdAbs using tandem phage display selection and NGS. These methods can easily be adapted to other types of proteins and libraries and expand the utility of in vitro display technology.
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Affiliation(s)
- Michael J Lowden
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Eric K Lei
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.
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A key F27I substitution within HCDR1 facilitates the rapid maturation of P2C-1F11-like neutralizing antibodies in a SARS-CoV-2-infected donor. Cell Rep 2022; 40:111335. [PMID: 36057256 PMCID: PMC9395280 DOI: 10.1016/j.celrep.2022.111335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/20/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
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Brooks BD, Beland A, Aguero G, Taylor N, Towne FD. Moving beyond Titers. Vaccines (Basel) 2022; 10:vaccines10050683. [PMID: 35632439 PMCID: PMC9144832 DOI: 10.3390/vaccines10050683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 01/27/2023] Open
Abstract
Vaccination to prevent and even eliminate disease is amongst the greatest achievements of modern medicine. Opportunities remain in vaccine development to improve protection across the whole population. A next step in vaccine development is the detailed molecular characterization of individual humoral immune responses against a pathogen, especially the rapidly evolving pathogens. New technologies such as sequencing the immune repertoire in response to disease, immunogenomics/vaccinomics, particularly the individual HLA variants, and high-throughput epitope characterization offer new insights into disease protection. Here, we highlight the emerging technologies that could be used to identify variation within the human population, facilitate vaccine discovery, improve vaccine safety and efficacy, and identify mechanisms of generating immunological memory. In today’s vaccine-hesitant climate, these techniques used individually or especially together have the potential to improve vaccine effectiveness and safety and thus vaccine uptake rates. We highlight the importance of using these techniques in combination to understand the humoral immune response as a whole after vaccination to move beyond neutralizing titers as the standard for immunogenicity and vaccine efficacy, especially in clinical trials.
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Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58103, USA
- Correspondence: ; Tel.: +1-(435)-222-1304
| | - Alexander Beland
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Gabriel Aguero
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Nicholas Taylor
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Francina D. Towne
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
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9
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Liu H, Pan W, Tang C, Tang Y, Wu H, Yoshimura A, Deng Y, He N, Li S. The methods and advances of adaptive immune receptors repertoire sequencing. Theranostics 2021; 11:8945-8963. [PMID: 34522220 PMCID: PMC8419057 DOI: 10.7150/thno.61390] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.
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Affiliation(s)
- Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Congli Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Yujie Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hu-nan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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Kaku Y, Kuwata T, Zahid HM, Hashiguchi T, Noda T, Kuramoto N, Biswas S, Matsumoto K, Shimizu M, Kawanami Y, Shimura K, Onishi C, Muramoto Y, Suzuki T, Sasaki J, Nagasaki Y, Minami R, Motozono C, Toyoda M, Takahashi H, Kishi H, Fujii K, Tatsuke T, Ikeda T, Maeda Y, Ueno T, Koyanagi Y, Iwagoe H, Matsushita S. Resistance of SARS-CoV-2 variants to neutralization by antibodies induced in convalescent patients with COVID-19. Cell Rep 2021; 36:109385. [PMID: 34237284 PMCID: PMC8226103 DOI: 10.1016/j.celrep.2021.109385] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/16/2021] [Accepted: 06/18/2021] [Indexed: 12/20/2022] Open
Abstract
Administration of convalescent plasma or neutralizing monoclonal antibodies (mAbs) is a potent therapeutic option for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, SARS-CoV-2 variants with mutations in the spike protein have emerged in many countries. To evaluate the efficacy of neutralizing antibodies induced in convalescent patients against emerging variants, we isolate anti-spike mAbs from two convalescent COVID-19 patients infected with prototypic SARS-CoV-2 by single-cell sorting of immunoglobulin-G-positive (IgG+) memory B cells. Anti-spike antibody induction is robust in these patients, and five mAbs have potent neutralizing activities. The efficacy of most neutralizing mAbs and convalescent plasma samples is maintained against B.1.1.7 and mink cluster 5 variants but is significantly decreased against variants B.1.351 from South Africa and P.1 from Brazil. However, mAbs with a high affinity for the receptor-binding domain remain effective against these neutralization-resistant variants. Rapid spread of these variants significantly impacts antibody-based therapies and vaccine strategies against SARS-CoV-2.
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Affiliation(s)
- Yu Kaku
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takeo Kuwata
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan.
| | - Hasan Md Zahid
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takao Hashiguchi
- Labolatory of Medical Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Noriko Kuramoto
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shashwata Biswas
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Kaho Matsumoto
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mikiko Shimizu
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yoko Kawanami
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Kazuya Shimura
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Chiho Onishi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yukiko Muramoto
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Tateki Suzuki
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Jiei Sasaki
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoji Nagasaki
- Division of Infectious Diseases, Clinical Research Institute, National Hospitalization Organization, Kyushu Medical Center, Fukuoka, Japan
| | - Rumi Minami
- Internal Medicine, Clinical Research Institute, National Hospital Organization, Kyushu Medical Center, Fukuoka, Japan
| | - Chihiro Motozono
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mako Toyoda
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hiroshi Takahashi
- Department of Respiratory Medicine, Kumamoto City Hospital, Kumamoto 862-8505, Japan
| | - Hiroto Kishi
- Department of Respiratory Medicine, Kumamoto City Hospital, Kumamoto 862-8505, Japan
| | - Kazuhiko Fujii
- Department of Respiratory Medicine, Kumamoto City Hospital, Kumamoto 862-8505, Japan
| | - Tsuneyuki Tatsuke
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yosuke Maeda
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takamasa Ueno
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Hajime Iwagoe
- Department of Infectious Disease, Kumamoto City Hospital, Kumamoto 862-8505, Japan
| | - Shuzo Matsushita
- Division of Clinical Retrovirology, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 860-0811, Japan.
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11
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Johansson G, Kaltak M, Rîmniceanu C, Singh AK, Lycke J, Malmeström C, Hühn M, Vaarala O, Cardell S, Ståhlberg A. Ultrasensitive DNA Immune Repertoire Sequencing Using Unique Molecular Identifiers. Clin Chem 2021; 66:1228-1237. [PMID: 32814950 DOI: 10.1093/clinchem/hvaa159] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Immune repertoire sequencing of the T-cell receptor can identify clonotypes that have expanded as a result of antigen recognition or hematological malignancies. However, current sequencing protocols display limitations with nonuniform amplification and polymerase-induced errors during sequencing. Here, we developed a sequencing method that overcame these issues and applied it to γδ T cells, a cell type that plays a unique role in immunity, autoimmunity, homeostasis of intestine, skin, adipose tissue, and cancer biology. METHODS The ultrasensitive immune repertoire sequencing method used PCR-introduced unique molecular identifiers. We constructed a 32-panel assay that captured the full diversity of the recombined T-cell receptor delta loci in γδ T cells. The protocol was validated on synthetic reference molecules and blood samples of healthy individuals. RESULTS The 32-panel assay displayed wide dynamic range, high reproducibility, and analytical sensitivity with single-nucleotide resolution. The method corrected for sequencing-depended quantification bias and polymerase-induced errors and could be applied to both enriched and nonenriched cells. Healthy donors displayed oligoclonal expansion of γδ T cells and similar frequencies of clonotypes were detected in both enrichment and nonenriched samples. CONCLUSIONS Ultrasensitive immune repertoire sequencing strategy enables quantification of individual and specific clonotypes in a background that can be applied to clinical as well as basic application areas. Our approach is simple, flexible, and can easily be implemented in any molecular laboratory.
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Affiliation(s)
- Gustav Johansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Translational Science & Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), Gothenburg, Sweden
| | - Melita Kaltak
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Cristiana Rîmniceanu
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Avadhesh K Singh
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Jan Lycke
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Clas Malmeström
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Michael Hühn
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), Gothenburg, Sweden
| | - Outi Vaarala
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Susanna Cardell
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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12
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[Isolation of anti-SARS-CoV-2 neutralizing monoclonal antibodies cross effective to variants aiming at antibody therapy]. Uirusu 2021; 71:163-168. [PMID: 37245978 DOI: 10.2222/jsv.71.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We isolated five mAbs with potent neutralizing activities against SARS-CoV-2 from two convalescent COVID-19 patients infected with prototype virus. Among them, the 9-105 antibody that have a highest affinity for the receptor-binding domain (RBD), cross-neutralize variants, such as B.1.1.7 (alfa), mink cluster 5 variant, B.1.351 (beta), P.1 (gamma), C.37 (lambda), B.1.617.1 (kappa), B.1.617.2 (delta) and B.1.621 (mu). A single amino acid mutation at K417 of RBD decreased neutralization sensitivity of 9-105. A 9-105 homology model revealed that 9-105 light chain binds to RBD including K417 by the same angle as ACE2.
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13
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Yang X, Tipton CM, Woodruff MC, Zhou E, Lee FEH, Sanz I, Qiu P. GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data. BMC Genomics 2020; 21:583. [PMID: 32900378 PMCID: PMC7488003 DOI: 10.1186/s12864-020-06936-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background B cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind antigens. Lineage trees are used to describe this microevolution of B cell immunoglobulin genes. In a lineage tree, each node is one BCR sequence that mutated from the germinal center and each directed edge represents a single base mutation, insertion or deletion. In BCR sequencing data, the observed data only contains a subset of BCR sequences in this microevolution process. Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. Results We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree nodes. Through comparison using simulated and real data, GLaMST outperforms existing algorithms in simulations with high rates of mutation, insertion and deletion, and generates lineage trees with smaller size and closer to ground truth according to tree features that highly correlated with selection pressure. Conclusions GLaMST outperforms state-of-art in reconstruction of the BCR lineage tree in both efficiency and accuracy. Integrating it into existing BCR sequencing analysis frameworks can significant improve lineage tree reconstruction aspect of the analysis.
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Affiliation(s)
- Xingyu Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Christopher M Tipton
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, USA
| | - Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, USA
| | - Enlu Zhou
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, USA
| | | | - Inãki Sanz
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, USA
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, USA.
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14
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Kumar S, Ju B, Shapero B, Lin X, Ren L, Zhang L, Li D, Zhou Z, Feng Y, Sou C, Mann CJ, Hao Y, Sarkar A, Hou J, Nunnally C, Hong K, Wang S, Ge X, Su B, Landais E, Sok D, Zwick MB, He L, Zhu J, Wilson IA, Shao Y. A V H1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite. SCIENCE ADVANCES 2020; 6:eabb1328. [PMID: 32938661 PMCID: PMC7494343 DOI: 10.1126/sciadv.abb1328] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/31/2020] [Indexed: 05/03/2023]
Abstract
An oligomannose patch around the V3 base of HIV-1 envelope glycoprotein (Env) is recognized by multiple classes of broadly neutralizing antibodies (bNAbs). Here, we investigated the bNAb response to the V3 glycan supersite in an HIV-1-infected Chinese donor by Env-specific single B cell sorting, structural and functional studies, and longitudinal analysis of antibody and virus repertoires. Monoclonal antibodies 438-B11 and 438-D5 were isolated that potently neutralize HIV-1 with moderate breadth, are encoded by the VH1-69 germline gene, and have a disulfide-linked long HCDR3 loop. Crystal structures of Env-bound and unbound antibodies revealed heavy chain-mediated recognition of the glycan supersite with a unique angle of approach and a critical role of the intra-HCDR3 disulfide. The mechanism of viral escape was examined via single-genome amplification/sequencing and glycan mutations around the N332 supersite. Our findings further emphasize the V3 glycan supersite as a prominent target for Env-based vaccine design.
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Affiliation(s)
- Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bin Ju
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
| | - Benjamin Shapero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Li Ren
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Lei Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Zehua Zhou
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colin J Mann
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yanling Hao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiali Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Christian Nunnally
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kunxue Hong
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Shuo Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Xiangyang Ge
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui Province 230601, China
| | - Elise Landais
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Devin Sok
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China.
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
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15
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Wen GP, He L, Tang ZM, Wang SL, Zhang X, Chen YZ, Lin X, Liu C, Chen JX, Ying D, Chen ZH, Wang YB, Luo WX, Huang SJ, Li SW, Zhang J, Zheng ZZ, Zhu J, Xia NS. Quantitative evaluation of protective antibody response induced by hepatitis E vaccine in humans. Nat Commun 2020; 11:3971. [PMID: 32769993 PMCID: PMC7414844 DOI: 10.1038/s41467-020-17737-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/14/2020] [Indexed: 12/18/2022] Open
Abstract
Efficacy evaluation through human trials is crucial for advancing a vaccine candidate to clinics. Next-generation sequencing (NGS) can be used to quantify B cell repertoire response and trace antibody lineages during vaccination. Here, we demonstrate this application with a case study of Hecolin®, the licensed vaccine for hepatitis E virus (HEV). Four subjects are administered the vaccine following a standard three-dose schedule. Vaccine-induced antibodies exhibit a high degree of clonal diversity, recognize five conformational antigenic sites of the genotype 1 HEV p239 antigen, and cross-react with other genotypes. Unbiased repertoire sequencing is performed for seven time points over six months of vaccination, with maturation pathways characterize for a set of vaccine-induced antibodies. In addition to dynamic repertoire profiles, NGS analysis reveals differential patterns of HEV-specific antibody lineages and highlights the necessity of the long vaccine boost. Together, our study presents a quantitative strategy for vaccine evaluation in small-scale human studies.
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Affiliation(s)
- Gui-Ping Wen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Zi-Min Tang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Si-Ling Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Xu Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Yuan-Zhi Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Jia-Xin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Dong Ying
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Zi-Hao Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Ying-Bin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Wen-Xin Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Shou-Jie Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Shao-Wei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Zi-Zheng Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China.
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Ning-Shao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China.
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China.
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16
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Brochu HN, Tseng E, Smith E, Thomas MJ, Jones AM, Diveley KR, Law L, Hansen SG, Picker LJ, Gale M, Peng X. Systematic Profiling of Full-Length Ig and TCR Repertoire Diversity in Rhesus Macaque through Long Read Transcriptome Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:3434-3444. [PMID: 32376650 PMCID: PMC7276939 DOI: 10.4049/jimmunol.1901256] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
The diversity of Ig and TCR repertoires is a focal point of immunological studies. Rhesus macaques (Macaca mulatta) are key for modeling human immune responses, placing critical importance on the accurate annotation and quantification of their Ig and TCR repertoires. However, because of incomplete reference resources, the coverage and accuracy of the traditional targeted amplification strategies for profiling rhesus Ig and TCR repertoires are largely unknown. In this study, using long read sequencing, we sequenced four Indian-origin rhesus macaque tissues and obtained high-quality, full-length sequences for over 6000 unique Ig and TCR transcripts, without the need for sequence assembly. We constructed, to our knowledge, the first complete reference set for the constant regions of all known isotypes and chain types of rhesus Ig and TCR repertoires. We show that sequence diversity exists across the entire variable regions of rhesus Ig and TCR transcripts. Consequently, existing strategies using targeted amplification of rearranged variable regions comprised of V(D)J gene segments miss a significant fraction (27-53% and 42-49%) of rhesus Ig/TCR diversity. To overcome these limitations, we designed new rhesus-specific assays that remove the need for primers conventionally targeting variable regions and allow single cell level Ig and TCR repertoire analysis. Our improved approach will enable future studies to fully capture rhesus Ig and TCR repertoire diversity and is applicable for improving annotations in any model organism.
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Affiliation(s)
- Hayden N Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | | | - Elise Smith
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Matthew J Thomas
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
| | - Aiden M Jones
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Genetics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Kayleigh R Diveley
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Genetics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
- Washington National Primate Research Center, University of Washington, Seattle, WA 98121; and
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607;
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695
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17
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Targeting broadly neutralizing antibody precursors: a naïve approach to vaccine design. Curr Opin HIV AIDS 2020; 14:294-301. [PMID: 30946041 DOI: 10.1097/coh.0000000000000548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW It is believed that broadly neutralizing antibodies (bNAbs) will be an important component of an effective HIV-1 vaccine. Several immunogens have been designed that can target specific precursor B cells as a first step in a vaccine strategy to elicit bNAbs. RECENT FINDINGS Germline-targeting immunogens have been developed that specifically engage precursors of reproducible classes of anti-HIV antibodies, such as VRC01-class and apex-directed bNAbs. However, these precursors represent only a small portion of the immune repertoire and any antigen will inherently present off-target epitopes to the immune system that may confound bNAb development. Novel animal models are being utilized to understand the competitive fitness of bNAb precursors in the context of immunization with germline-targeting immunogens. In parallel, immunogen design efforts are being pursued to favor the development of bNAb responses over off-target responses following immunization. New studies of bNAb precursor interactions with glycosylated Env variants can inform prime-boost regimens geared towards accelerating bNAb development. SUMMARY Germline-targeting immunogens hold promise as a first step in eliciting a bNAb response through vaccination. A better understating of how efficiently germline-targeting immunogens can specifically target rare bNAb precursors is emerging. In addition, a more comprehensive structure-based understanding of critical barriers to bNAb elicitation, as well as commonalities between bNAb classes can further inform vaccine design.
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18
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Matsuda K, Huang J, Zhou T, Sheng Z, Kang BH, Ishida E, Griesman T, Stuccio S, Bolkhovitinov L, Wohlbold TJ, Chromikova V, Cagigi A, Leung K, Andrews S, Cheung CSF, Pullano AA, Plyler J, Soto C, Zhang B, Yang Y, Joyce MG, Tsybovsky Y, Wheatley A, Narpala SR, Guo Y, Darko S, Bailer RT, Poole A, Liang CJ, Smith J, Alexander J, Gurwith M, Migueles SA, Koup RA, Golding H, Khurana S, McDermott AB, Shapiro L, Krammer F, Kwong PD, Connors M. Prolonged evolution of the memory B cell response induced by a replicating adenovirus-influenza H5 vaccine. Sci Immunol 2020; 4:4/34/eaau2710. [PMID: 31004012 DOI: 10.1126/sciimmunol.aau2710] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 03/18/2019] [Indexed: 12/23/2022]
Abstract
Induction of an antibody response capable of recognizing highly diverse strains is a major obstacle to the development of vaccines for viruses such as HIV and influenza. Here, we report the dynamics of B cell expansion and evolution at the single-cell level after vaccination with a replication-competent adenovirus type 4 recombinant virus expressing influenza H5 hemagglutinin. Fluorescent H1 or H5 probes were used to quantitate and isolate peripheral blood B cells and their antigen receptors. We observed increases in H5-specific antibody somatic hypermutation and potency for several months beyond the period of active viral replication that was not detectable at the serum level. Individual broad and potent antibodies could be isolated, including one stem-specific antibody that is part of a new multidonor class. These results demonstrate prolonged evolution of the B cell response for months after vaccination and should be considered in efforts to evaluate or boost vaccine-induced immunity.
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Affiliation(s)
- Kenta Matsuda
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jinghe Huang
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Zukerman Institute of Mind Brain Behavior, Columbia University, New York, NY 10032, USA
| | - Byong H Kang
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Elise Ishida
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Trevor Griesman
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sarah Stuccio
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Lyuba Bolkhovitinov
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Teddy J Wohlbold
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Veronika Chromikova
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alberto Cagigi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sarah Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Crystal S F Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Alyssa A Pullano
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jason Plyler
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Cinque Soto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Adam Wheatley
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sandeep R Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Yicheng Guo
- Department of Biochemistry and Molecular Biophysics, Zukerman Institute of Mind Brain Behavior, Columbia University, New York, NY 10032, USA
| | - Sam Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - April Poole
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - C Jason Liang
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jon Smith
- Emergent Biosolutions Inc., Gaithersburg, MD 20879, USA
| | | | - Marc Gurwith
- Emergent Biosolutions Inc., Gaithersburg, MD 20879, USA
| | - Stephen A Migueles
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Admnistration, Silver Spring, MD 20993, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Admnistration, Silver Spring, MD 20993, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Zukerman Institute of Mind Brain Behavior, Columbia University, New York, NY 10032, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mark Connors
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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19
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Joyce C, Burton DR, Briney B. Comparisons of the antibody repertoires of a humanized rodent and humans by high throughput sequencing. Sci Rep 2020; 10:1120. [PMID: 31980672 PMCID: PMC6981180 DOI: 10.1038/s41598-020-57764-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/12/2019] [Indexed: 11/10/2022] Open
Abstract
The humanization of animal model immune systems by genetic engineering has shown great promise for antibody discovery, tolerance studies and for the evaluation of vaccines. Assessment of the baseline antibody repertoires of unimmunized model animals will be useful as a benchmark for future immunization experiments. We characterized the heavy chain and kappa light chain antibody repertoires of a model animal, the OmniRat, by high throughput antibody sequencing and made use of two novel datasets for comparison to human repertoires. Intra-animal and inter-animal repertoire comparisons reveal a high level of conservation in antibody diversity between the lymph node and spleen and between members of the species. Multiple differences were found in both the heavy and kappa chain repertoires between OmniRats and humans including gene segment usage, CDR3 length distributions, class switch recombination, somatic hypermutation levels and in features of V(D)J recombination. The Inference and Generation of Repertoires (IGoR) software tool was used to model recombination in VH regions which allowed for the quantification of some of these differences. Diversity estimates of the OmniRat heavy chain repertoires almost reached that of humans, around two orders of magnitude less. Despite variation between the species repertoires, a high frequency of OmniRat clonotypes were also found in the human repertoire. These data give insights into the development and selection of humanized animal antibodies and provide actionable information for use in vaccine studies.
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Affiliation(s)
- Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Human Vaccines Project, New York, NY, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Human Vaccines Project, New York, NY, USA.
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, USA.
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20
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Kreer C, Gruell H, Mora T, Walczak AM, Klein F. Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies. Vaccines (Basel) 2020; 8:vaccines8010013. [PMID: 31906351 PMCID: PMC7157687 DOI: 10.3390/vaccines8010013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/22/2022] Open
Abstract
The human antibody repertoire is generated by the recombination of different gene segments as well as by processes of somatic mutation. Together these mechanisms result in a tremendous diversity of antibodies that are able to combat various pathogens including viruses and bacteria, or malignant cells. In this review, we summarize the opportunities and challenges that are associated with the analyses of the B cell receptor repertoire and the antigen-specific B cell response. We will discuss how recent advances have increased our understanding of the antibody response and how repertoire analyses can be exploited to inform on vaccine strategies, particularly against HIV-1.
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Affiliation(s)
- Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure (PSL University), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France; (T.M.); (A.M.W.)
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure (PSL University), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France; (T.M.); (A.M.W.)
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Correspondence:
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21
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Zhang L, Irimia A, He L, Landais E, Rantalainen K, Leaman DP, Vollbrecht T, Stano A, Sands DI, Kim AS, Poignard P, Burton DR, Murrell B, Ward AB, Zhu J, Wilson IA, Zwick MB. An MPER antibody neutralizes HIV-1 using germline features shared among donors. Nat Commun 2019; 10:5389. [PMID: 31772165 PMCID: PMC6879610 DOI: 10.1038/s41467-019-12973-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/11/2019] [Indexed: 11/09/2022] Open
Abstract
The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC50). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.
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Affiliation(s)
- Lei Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- CTK Biotech, Inc., 3855 Stowe Drive, Poway, California, 92064, USA
| | - Adriana Irimia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Lingling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative, New York, New York, 10004, USA
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel P Leaman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Thomas Vollbrecht
- Department of Medicine, University of California, San Diego, California, 92093, USA
| | - Armando Stano
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel I Sands
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Arthur S Kim
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- Departments of Medicine, Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Pascal Poignard
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative, New York, New York, 10004, USA
- Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044, Grenoble, France
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachussetts, 02114, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, California, 92093, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Jiang Zhu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.
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22
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Cashman KS, Jenks SA, Woodruff MC, Tomar D, Tipton CM, Scharer CD, Lee EH, Boss JM, Sanz I. Understanding and measuring human B-cell tolerance and its breakdown in autoimmune disease. Immunol Rev 2019; 292:76-89. [PMID: 31755562 PMCID: PMC6935423 DOI: 10.1111/imr.12820] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022]
Abstract
The maintenance of immunological tolerance of B lymphocytes is a complex and critical process that must be implemented as to avoid the detrimental development of autoreactivity and possible autoimmunity. Murine models have been invaluable to elucidate many of the key components in B-cell tolerance; however, translation to human homeostatic and pathogenic immune states can be difficult to assess. Functional autoreactive, flow cytometric, and single-cell cloning assays have proven to be critical in deciphering breaks in B-cell tolerance within autoimmunity; however, newer approaches to assess human B-cell tolerance may prove to be vital in the further exploration of underlying tolerance defects. In this review, we supply a comprehensive overview of human immune tolerance checkpoints with associated mechanisms of enforcement, and highlight current and future methodologies which are likely to benefit future studies into the mechanisms that become defective in human autoimmune conditions.
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Affiliation(s)
- Kevin S. Cashman
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Scott A. Jenks
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Matthew C. Woodruff
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Deepak Tomar
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Christopher M. Tipton
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Eun-Hyung Lee
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Emory University, Atlanta, Georgia, USA
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
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23
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Gao F, Lin X, He L, Wang R, Wang H, Shi X, Zhang F, Yin C, Zhang L, Zhu J, Yu L. Development of a Potent and Protective Germline-Like Antibody Lineage Against Zika Virus in a Convalescent Human. Front Immunol 2019; 10:2424. [PMID: 31708914 PMCID: PMC6821881 DOI: 10.3389/fimmu.2019.02424] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/27/2019] [Indexed: 12/31/2022] Open
Abstract
Zika virus (ZIKV) specific neutralizing antibodies hold great promise for antibody-based interventions and vaccine design against ZIKV infection. However, their development in infected patients remains unclear. Here, we applied next-generation sequencing (NGS) to probe the dynamic development of a potent and protective ZIKV E DIII-specific antibody ZK2B10 isolated from a ZIKV convalescent individual. The unbiased repertoire analysis showed dramatic changes in the usage of antibody variable region germline genes. However, lineage tracing of ZK2B10 revealed limited somatic hypermutation and transient expansion during the 12 months following the onset of symptoms. The NGS-derived, germline-like ZK2B10 somatic variants neutralized ZIKV potently and protected mice from lethal challenge of ZIKV without detectable cross-reactivity with Dengue virus (DENV). Site-directed mutagenesis identified two residues within the λ chain, N31 and S91, that are essential to the functional maturation of ZK2B10. The repertoire and lineage features unveiled here will help elucidate the developmental process and protective potential of E DIII-directed antibodies against ZIKV infection.
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Affiliation(s)
- Fei Gao
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Linling He
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Ruoke Wang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Han Wang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Xuanling Shi
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Fuchun Zhang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chibiao Yin
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Linqi Zhang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Lei Yu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
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24
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Abstract
Immune repertoire is a collection of enormously diverse adaptive immune cells within an individual. As the repertoire shapes and represents immunological conditions, identification of clones and characterization of diversity are critical for understanding how to protect ourselves against various illness such as infectious diseases and cancers. Over the past several years, fast growing technologies for high throughput sequencing have facilitated rapid advancement of repertoire research, enabling us to observe the diversity of repertoire at an unprecedented level. Here, we focus on B cell receptor (BCR) repertoire and review approaches to B cell isolation and sequencing library construction. These experiments should be carefully designed according to BCR regions to be interrogated, such as heavy chain full length, complementarity determining regions, and isotypes. We also highlight preprocessing steps to remove sequencing and PCR errors with unique molecular index and bioinformatics techniques. Due to the nature of massive sequence variation in BCR, caution is warranted when interpreting repertoire diversity from error-prone sequencing data. Furthermore, we provide a summary of statistical frameworks and bioinformatics tools for clonal evolution and diversity. Finally, we discuss limitations of current BCR-seq technologies and future perspectives on advances in repertoire sequencing.
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Affiliation(s)
- Daeun Kim
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, Korea
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, Korea
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25
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Li R, Fu F, Feng L, Liu P. Next-generation sequencing and single-cell RT-PCR reveal a distinct variable gene usage of porcine antibody repertoire following PEDV vaccination. SCIENCE CHINA-LIFE SCIENCES 2019; 63:1240-1250. [PMID: 31321668 PMCID: PMC7088813 DOI: 10.1007/s11427-019-9576-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/12/2019] [Indexed: 11/24/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is the most common diarrhea-causing pathogen in newborn piglets. The clarifications of the overall antibody repertoire and antigen-specific antibody repertoire are essential to provide important insights into the B-cell response and reshape new vaccines. Here, we applied next-generation sequencing (NGS) technology to investigate immunoglobulin (Ig) variable (V) gene segment usage of swine B-cells from peripheral blood lymphocytes (PBL) and mesenteric lymph node (MLN) cells following PEDV vaccination. We identified the transcripts of all functional Ig V-genes in antibody repertoire. IgHV1S2, IgKV1-11, and IgLV3-4 were the most prevalent gene segments for heavy, kappa, and lambda chains, respectively, in PBL and MLN. Unlike previous studies, IgKV1, instead of IgKV2, and IgLV3, instead of IgLV8, were the prevalent Ig V-gene families for kappa and lambda light chains, respectively. We further examined the antibody repertoire of PEDV spike-specific B cells by single-cell RT-PCR. In contrast to the overall antibody repertoire, Ig V-gene segments of PEDV spike-specific B cells preferentially adopted IgHV1-4 and IgHV1-14 for heavy chain, IgKV1-11 for kappa chain, and IgLV3-3 for lambda chain. These results represent a comprehensive analysis to characterize the Ig V-gene segment usage in the overall and PEDV spike-specific antibody repertoire in PBL and MLN.
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Affiliation(s)
- Ren Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Fang Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - PingHuang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
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26
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Feng J, Shaw DA, Minin VN, Simon N, Matsen FA. Survival analysis of DNA mutation motifs with penalized proportional hazards. Ann Appl Stat 2019; 13:1268-1294. [PMID: 33214798 PMCID: PMC7673484 DOI: 10.1214/18-aoas1233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Antibodies, an essential part of our immune system, develop through an intricate process to bind a wide array of pathogens. This process involves randomly mutating DNA sequences encoding these antibodies to find variants with improved binding, though mutations are not distributed uniformly across sequence sites. Immunologists observe this nonuniformity to be consistent with "mutation motifs", which are short DNA subsequences that affect how likely a given site is to experience a mutation. Quantifying the effect of motifs on mutation rates is challenging: a large number of possible motifs makes this statistical problem high dimensional, while the unobserved history of the mutation process leads to a nontrivial missing data problem. We introduce an ℓ 1-penalized proportional hazards model to infer mutation motifs and their effects. In order to estimate model parameters, our method uses a Monte Carlo EM algorithm to marginalize over the unknown ordering of mutations. We show that our method performs better on simulated data compared to current methods and leads to more parsimonious models. The application of proportional hazards to mutation processes is, to our knowledge, novel and formalizes the current methods in a statistical framework that can be easily extended to analyze the effect of other biological features on mutation rates.
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Affiliation(s)
- Jean Feng
- Department of Biostatistics, University of Washington Seattle, WA, USA
| | - David A. Shaw
- Computational Biology Program, Fred Hutchinson Cancer Research Center Seattle, WA, USA
| | - Vladimir N. Minin
- Department of Statistics, University of California, Irvine, Irvine, CA, USA
| | - Noah Simon
- Department of Biostatistics, University of Washington Seattle, WA, USA
| | - Frederick A. Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center Seattle, WA, USA
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27
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Vázquez Bernat N, Corcoran M, Hardt U, Kaduk M, Phad GE, Martin M, Karlsson Hedestam GB. High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis. Front Immunol 2019; 10:660. [PMID: 31024532 PMCID: PMC6459949 DOI: 10.3389/fimmu.2019.00660] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Next generation sequencing (NGS) of immunoglobulin (Ig) repertoires (Rep-seq) enables examination of the adaptive immune system at an unprecedented level. Applications include studies of expressed repertoires, gene usage, somatic hypermutation levels, Ig lineage tracing and identification of genetic variation within the Ig loci through inference methods. All these applications require starting libraries that allow the generation of sequence data with low error rate and optimal representation of the expressed repertoire. Here, we provide detailed protocols for the production of libraries suitable for human Ig germline gene inference and Ig repertoire studies. Various parameters used in the process were tested in order to demonstrate factors that are critical to obtain high quality libraries. We demonstrate an improved 5'RACE technique that reduces the length constraints of Illumina MiSeq based Rep-seq analysis but allows for the acquisition of sequences upstream of Ig V genes, useful for primer design. We then describe a 5' multiplex method for library preparation, which yields full length V(D)J sequences suitable for genotype identification and novel gene inference. We provide comprehensive sets of primers targeting IGHV, IGKV, and IGLV genes. Using the optimized protocol, we produced IgM, IgG, IgK, and IgL libraries and analyzed them using the germline inference tool IgDiscover to identify expressed germline V alleles. This process additionally uncovered three IGHV, one IGKV, and six IGLV novel alleles in a single individual, which are absent from the IMGT reference database, highlighting the need for further study of Ig genetic variation. The library generation protocols presented here enable a robust means of analyzing expressed Ig repertoires, identifying novel alleles and producing individualized germline gene databases from humans.
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Affiliation(s)
- Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Uta Hardt
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Rheumatology, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Mateusz Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ganesh E. Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marcel Martin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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28
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Jayaraman S, Harris C, Paxton E, Donachie AM, Vaikkinen H, McCulloch R, Hall JPJ, Kenny J, Lenzi L, Hertz-Fowler C, Cobbold C, Reeve R, Michoel T, Morrison LJ. Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS Negl Trop Dis 2019; 13:e0007262. [PMID: 30943202 PMCID: PMC6464242 DOI: 10.1371/journal.pntd.0007262] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/15/2019] [Accepted: 02/25/2019] [Indexed: 12/31/2022] Open
Abstract
Antigenic variation is employed by many pathogens to evade the host immune response, and Trypanosoma brucei has evolved a complex system to achieve this phenotype, involving sequential use of variant surface glycoprotein (VSG) genes encoded from a large repertoire of ~2,000 genes. T. brucei express multiple, sometimes closely related, VSGs in a population at any one time, and the ability to resolve and analyse this diversity has been limited. We applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from batches of mice sacrificed at time points (days 3, 6, 10 and 12) post-infection with T. brucei TREU927. The data showed that long read sequencing is reliable for resolving variant differences between VSGs, and demonstrated that there is significant expressed diversity (449 VSGs detected across 20 mice) and across the timeframe of study there was a clear semi-reproducible pattern of expressed diversity (median of 27 VSGs per sample at day 3 post infection (p.i.), 82 VSGs at day 6 p.i., 187 VSGs at day 10 p.i. and 132 VSGs by day 12 p.i.). There was also consistent detection of one VSG dominating expression across replicates at days 3 and 6, and emergence of a second dominant VSG across replicates by day 12. The innovative application of ecological diversity analysis to VSG reads enabled characterisation of hierarchical VSG expression in the dataset, and resulted in a novel method for analysing such patterns of variation. Additionally, the long read approach allowed detection of mosaic VSG expression from very few reads–the earliest in infection that such events have been detected. Therefore, our results indicate that long read analysis is a reliable tool for resolving diverse gene expression profiles, and provides novel insights into the complexity and nature of VSG expression in trypanosomes, revealing significantly higher diversity than previously shown and the ability to identify mosaic gene formation early during the infection process. Antigenic variation is a system whereby pathogens switch identity of a protein that is exposed to the host adaptive immune response as a way of remaining one step ahead and avoiding being detected. African trypanosomes have evolved a spectacularly elaborate system of antigenic variation, with variants being used from a library of ~2,000 genes. Our ability to understand how this rich repository is used has been hampered by the resolution of available technologies to discriminate between what can be closely related gene variants. We have applied a long read sequencing technology, which generates sequence information for the whole length of the antigen gene variants, thereby avoiding having to try and piece together antigen sequences from lots of small fragments, the pitfall of standard sequencing. Applying this technology to material taken at specific time points from batches of mice infected with trypanosomes reveals that the diversity of variants is much higher than previously suspected, and that there is a clear semi-predictable pattern in the gene expression. Additionally, using this technology we have been able to detect the presence of ‘mosaic’ genes, which are created by stitching together fragments from several donor genes in the library, much earlier in infection than has been shown previously. Therefore, we shed new light on the complexity of antigenic variation and show that long read sequencing will be a very useful tool in analysing and understanding the expression patterns of closely related genes, and how pathogens use them to cause persistent infections and disease.
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Affiliation(s)
- Siddharth Jayaraman
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Claire Harris
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Edith Paxton
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Anne-Marie Donachie
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Heli Vaikkinen
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard McCulloch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Christiane Hertz-Fowler
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Christina Cobbold
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tom Michoel
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Liam J. Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- * E-mail:
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29
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Tzarum N, Giang E, Kong L, He L, Prentoe J, Augestad E, Hua Y, Castillo S, Lauer GM, Bukh J, Zhu J, Wilson IA, Law M. Genetic and structural insights into broad neutralization of hepatitis C virus by human V H1-69 antibodies. SCIENCE ADVANCES 2019; 5:eaav1882. [PMID: 30613781 PMCID: PMC6314831 DOI: 10.1126/sciadv.aav1882] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/27/2018] [Indexed: 05/19/2023]
Abstract
An effective vaccine to the antigenically diverse hepatitis C virus (HCV) must target conserved immune epitopes. Here, we investigate cross-neutralization of HCV genotypes by broadly neutralizing antibodies (bNAbs) encoded by the relatively abundant human gene family V H 1-69. We have deciphered the molecular requirements for cross-neutralization by this unique class of human antibodies from crystal structures of HCV E2 in complex with bNAbs. An unusually high binding affinity is found for germ line-reverted versions of VH1-69 precursor antibodies, and neutralization breadth is acquired during affinity maturation. Deep sequencing analysis of an HCV-immune B cell repertoire further demonstrates the importance of the V H 1-69 gene family in the generation of HCV bNAbs. This study therefore provides critical insights into immune recognition of HCV with important implications for rational vaccine design.
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Affiliation(s)
- Netanel Tzarum
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erick Giang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Leopold Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jannick Prentoe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elias Augestad
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yuanzi Hua
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shaun Castillo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Georg M. Lauer
- Gastrointestinal Unit and Liver Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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30
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Kovaltsuk A, Krawczyk K, Kelm S, Snowden J, Deane CM. Filtering Next-Generation Sequencing of the Ig Gene Repertoire Data Using Antibody Structural Information. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 201:3694-3704. [PMID: 30397033 PMCID: PMC6485405 DOI: 10.4049/jimmunol.1800669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/02/2018] [Indexed: 01/29/2023]
Abstract
Next-generation sequencing of the Ig gene repertoire (Ig-seq) produces large volumes of information at the nucleotide sequence level. Such data have improved our understanding of immune systems across numerous species and have already been successfully applied in vaccine development and drug discovery. However, the high-throughput nature of Ig-seq means that it is afflicted by high error rates. This has led to the development of error-correction approaches. Computational error-correction methods use sequence information alone, primarily designating sequences as likely to be correct if they are observed frequently. In this work, we describe an orthogonal method for filtering Ig-seq data, which considers the structural viability of each sequence. A typical natural Ab structure requires the presence of a disulfide bridge within each of its variable chains to maintain the fold. Our Ab Sequence Selector (ABOSS) uses the presence/absence of this bridge as a way of both identifying structurally viable sequences and estimating the sequencing error rate. On simulated Ig-seq datasets, ABOSS is able to identify more than 99% of structurally viable sequences. Applying our method to six independent Ig-seq datasets (one mouse and five human), we show that our error calculations are in line with previous experimental and computational error estimates. We also show how ABOSS is able to identify structurally impossible sequences missed by other error-correction methods.
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Affiliation(s)
- Aleksandr Kovaltsuk
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | | | | | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
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31
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Simon JS, Botero S, Simon SM. Sequencing the peripheral blood B and T cell repertoire - Quantifying robustness and limitations. J Immunol Methods 2018; 463:137-147. [PMID: 30312601 DOI: 10.1016/j.jim.2018.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 12/27/2022]
Abstract
The adaptive immune response generates a large repertoire of T cells with T-cell receptors (TCRalpha and TCRbeta) and B cells with immunoglobulins (Ig). The repertoire changes in response to antigen stimulation both through amplification of specific cells (clonal expansion) as well as somatic hypermutation of immunoglobulins. Alterations of the immune repertoire have been observed in response to acute disease, such as external pathogens, or chronic diseases, such as autoimmunity and cancer. Here we establish experimental and analytical protocols for quantifying the peripheral blood of healthy human individuals by profiling the immune repertoire for the Complementarity determining region 3 (CDR3) of the variable regions of TCRbeta (CDRβ3) and the IgG heavy chain (CDRH1, CDRH2, CDRH3). The results demonstrate that 40 ml of blood are sufficient to reliably capture the 10,000 most common TCRbeta and 1000 most common IgG and determine their relative frequency in the circulation. We conclude that by using an accessible sample size of human PBMC one is able to robustly monitor alterations in the immune repertoire.
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Affiliation(s)
- Joel S Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sergio Botero
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States.
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32
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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: 3] [Impact Index Per Article: 0.4] [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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33
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Migalska M, Sebastian A, Radwan J. Profiling of the TCRβ repertoire in non-model species using high-throughput sequencing. Sci Rep 2018; 8:11613. [PMID: 30072736 PMCID: PMC6072738 DOI: 10.1038/s41598-018-30037-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 07/19/2018] [Indexed: 02/06/2023] Open
Abstract
In recent years, immune repertoire profiling with high-throughput sequencing (HTS) has advanced our understanding of adaptive immunity. However, fast progress in the field applied mostly to human and mouse research, with only few studies devoted to other model vertebrates. We present the first in-depth characterization of the T-cell receptor (TCR) repertoire in a non-model mammal (bank vole, Myodes glareolus), widely used in ecological and evolutionary research. We used RNA from spleens, 5′RACE and HTS to describe V and J segments of TCRβ, qualitatively characterize preferential V–J segment usage and CDR3 length distribution. Overall orthology to murine genes was preserved, with 11 J and 37 V genes found in voles (although 3 V genes lacked a close orthologue). Further, we implemented unique molecular identifiers for quantitative analysis of CDR3 repertoire with stringent error correction. A conservative, lower bound estimation of the TCRβ repertoire was similar to that found for mice (1.7–2.3 × 105 clonotypes). We hope that by providing an easy-to-follow molecular protocol and on-line bioinformatics tools that do not require reference sequences (AmpliTCR and AmpliCDR3), we will encourage HTS immune repertoire profiling in other non-model vertebrates, thus opening new research avenues in e.g. comparative immunology, ecology and evolutionary biology.
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Affiliation(s)
- Magdalena Migalska
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
| | - Alvaro Sebastian
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.,Instituto Aragonés de Empleo (INAEM), c/Royo Villanova 1, 50007, Zaragoza, Spain
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
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34
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Bürckert JP, Faison WJ, Mustin DE, Dubois ARSX, Sinner R, Hunewald O, Wienecke-Baldacchino A, Brieger A, Muller CP. High-throughput sequencing of murine immunoglobulin heavy chain repertoires using single side unique molecular identifiers on an Ion Torrent PGM. Oncotarget 2018; 9:30225-30239. [PMID: 30100985 PMCID: PMC6084394 DOI: 10.18632/oncotarget.25493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/07/2018] [Indexed: 11/25/2022] Open
Abstract
With the advent of high-throughput sequencing (HTS), profiling immunoglobulin (IG) repertoires has become an essential part of immunological research. Advances in sequencing technology enable the IonTorrent Personal Genome Machine (PGM) to cover the full-length of IG mRNA transcripts. Nucleotide insertions and deletions (indels) are the dominant errors of the PGM sequencing platform and can critically influence IG repertoire assessments. Here, we present a PGM-tailored IG repertoire sequencing approach combining error correction through unique molecular identifier (UID) barcoding and indel detection through ImMunoGeneTics (IMGT), the most commonly used sequence alignment database for IG sequences. Using artificially falsified sequences for benchmarking, we found that IMGT's underlying algorithms efficiently detect 98% of the introduced indels. Undetected indels are either located at the end of the sequences or produce masked frameshifts with an insertion and deletion in close proximity. The complementary determining regions 3 (CDR3s) are returned correct for up to 3 insertions or 3 deletions through conservative culling. We further show, that our PGM-tailored unique molecular identifiers result in highly accurate HTS data if combined with the presented processing strategy. In this regard, considering sequences with at least two copies from datasets with UID families of minimum 3 reads result in correct sequences with over 99% confidence. Finally, we show that the protocol can readily be used to generate homogenous datasets for bulk sequencing of murine bone marrow samples. Taken together, this approach will help to establish benchtop-scale sequencing of IG heavy chain transcripts in the field of IG repertoire research.
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Affiliation(s)
- Jean-Philippe Bürckert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - William J Faison
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Danielle E Mustin
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Axel R S X Dubois
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Regina Sinner
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | | | - Anne Brieger
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
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35
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Waltari E, Jia M, Jiang CS, Lu H, Huang J, Fernandez C, Finzi A, Kaufmann DE, Markowitz M, Tsuji M, Wu X. 5' Rapid Amplification of cDNA Ends and Illumina MiSeq Reveals B Cell Receptor Features in Healthy Adults, Adults With Chronic HIV-1 Infection, Cord Blood, and Humanized Mice. Front Immunol 2018; 9:628. [PMID: 29632541 PMCID: PMC5879793 DOI: 10.3389/fimmu.2018.00628] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/13/2018] [Indexed: 12/17/2022] Open
Abstract
Using 5′ rapid amplification of cDNA ends, Illumina MiSeq, and basic flow cytometry, we systematically analyzed the expressed B cell receptor (BCR) repertoire in 14 healthy adult PBMCs, 5 HIV-1+ adult PBMCs, 5 cord blood samples, and 3 HIS-CD4/B mice, examining the full-length variable region of μ, γ, α, κ, and λ chains for V-gene usage, somatic hypermutation (SHM), and CDR3 length. Adding to the known repertoire of healthy adults, Illumina MiSeq consistently detected small fractions of reads with high mutation frequencies including hypermutated μ reads, and reads with long CDR3s. Additionally, the less studied IgA repertoire displayed similar characteristics to that of IgG. Compared to healthy adults, the five HIV-1 chronically infected adults displayed elevated mutation frequencies for all μ, γ, α, κ, and λ chains examined and slightly longer CDR3 lengths for γ, α, and λ. To evaluate the reconstituted human BCR sequences in a humanized mouse model, we analyzed cord blood and HIS-CD4/B mice, which all lacked the typical SHM seen in the adult reference. Furthermore, MiSeq revealed identical unmutated IgM sequences derived from separate cell aliquots, thus for the first time demonstrating rare clonal members of unmutated IgM B cells by sequencing.
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Affiliation(s)
- Eric Waltari
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Manxue Jia
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Caroline S Jiang
- Hospital Biostatistics, The Rockefeller University, New York, NY, United States
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Jing Huang
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Cristina Fernandez
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, United States
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Moriya Tsuji
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
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36
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Zhou T, Zheng A, Baxa U, Chuang GY, Georgiev IS, Kong R, O'Dell S, Shahzad-Ul-Hussan S, Shen CH, Tsybovsky Y, Bailer RT, Gift SK, Louder MK, McKee K, Rawi R, Stevenson CH, Stewart-Jones GBE, Taft JD, Waltari E, Yang Y, Zhang B, Shivatare SS, Shivatare VS, Lee CCD, Wu CY, Mullikin JC, Bewley CA, Burton DR, Polonis VR, Shapiro L, Wong CH, Mascola JR, Kwong PD, Wu X. A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope. Immunity 2018; 48:500-513.e6. [PMID: 29548671 PMCID: PMC6421865 DOI: 10.1016/j.immuni.2018.02.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/22/2017] [Accepted: 02/15/2018] [Indexed: 01/26/2023]
Abstract
Virtually the entire surface of the HIV-1-envelope trimer is recognized by neutralizing antibodies, except for a highly glycosylated region at the center of the "silent face" on the gp120 subunit. From an HIV-1-infected donor, #74, we identified antibody VRC-PG05, which neutralized 27% of HIV-1 strains. The crystal structure of the antigen-binding fragment of VRC-PG05 in complex with gp120 revealed an epitope comprised primarily of N-linked glycans from N262, N295, and N448 at the silent face center. Somatic hypermutation occurred preferentially at antibody residues that interacted with these glycans, suggesting somatic development of glycan recognition. Resistance to VRC-PG05 in donor #74 involved shifting of glycan-N448 to N446 or mutation of glycan-proximal residue E293. HIV-1 neutralization can thus be achieved at the silent face center by glycan-recognizing antibody; along with other known epitopes, the VRC-PG05 epitope completes coverage by neutralizing antibody of all major exposed regions of the prefusion closed trimer.
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Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Anqi Zheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ulrich Baxa
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Vanderbilt Vaccine Center, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, and Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Syed Shahzad-Ul-Hussan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Syna K Gift
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Catherine H Stevenson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Justin D Taft
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Eric Waltari
- Aaron Diamond AIDS Research Center, Affiliate of the Rockefeller University, New York, NY 10016, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Sachin S Shivatare
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Vidya S Shivatare
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Chang-Chun D Lee
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - James C Mullikin
- NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, IAVI Neutralizing Antibody Center, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Affiliate of the Rockefeller University, New York, NY 10016, USA.
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37
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HIV Broadly Neutralizing Antibodies: VRC01 and Beyond. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1075:53-72. [PMID: 30030789 DOI: 10.1007/978-981-13-0484-2_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Developing an effective prophylaxis HIV-1 vaccine is likely to require the elicitation of broadly neutralizing antibodies (bnAbs). As the HIV-1 envelope (Env) glycoprotein - the sole target of bnAbs - has evolved multiple mechanisms to evade antibody neutralization, the processes for bnAb generation are highly selective and time-consuming. Benefiting from antibody isolation technologies of single B cell culturing and direct single B cell sorting and cloning, a new generation of monoclonal bnAbs has been isolated since 2009, exhibiting remarkable breadths and potencies, thus breaking through a nearly 20-year-long limit of four monoclonal bnAbs with moderate breadth and potency. The discovery of a long list of monoclonal bnAbs has provided in-depth understanding of the sites of vulnerability on the HIV-1 Env and the complexity of human B cell immunology to generate such responses, thus presenting both guidance and challenges to move the Env immunogen design effort forward.
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Next-Generation DNA Sequencing of V H/V L Repertoires: A Primer and Guide to Applications in Single-Domain Antibody Discovery. Methods Mol Biol 2018; 1701:425-446. [PMID: 29116520 DOI: 10.1007/978-1-4939-7447-4_24] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Immunogenetic analyses of expressed antibody repertoires are becoming increasingly common experimental investigations and are critical to furthering our understanding of autoimmunity, infectious disease, and cancer. Next-generation DNA sequencing (NGS) technologies have now made it possible to interrogate antibody repertoires to unprecedented depths, typically by sequencing of cDNAs encoding immunoglobulin variable domains. In this chapter, we describe simple, fast, and reliable methods for producing and sequencing multiplex PCR amplicons derived from the variable regions (VH, VHH or VL) of rearranged immunoglobulin heavy and light chain genes using the Illumina MiSeq platform. We include complete protocols and primer sets for amplicon sequencing of VH/VHH/VL repertoires directly from human, mouse, and llama lymphocytes as well as from phage-displayed VH/VHH/VL libraries; these can be easily be adapted to other types of amplicons with little modification. The resulting amplicons are diverse and representative, even using as few as 103 input B cells, and their generation is relatively inexpensive, requiring no special equipment and only a limited set of primers. In the absence of heavy-light chain pairing, single-domain antibodies are uniquely amenable to NGS analyses. We present a number of applications of NGS technology useful in discovery of single-domain antibodies from phage display libraries, including: (i) assessment of library functionality; (ii) confirmation of desired library randomization; (iii) estimation of library diversity; and (iv) monitoring the progress of panning experiments. While the case studies presented here are of phage-displayed single-domain antibody libraries, the principles extend to other types of in vitro display libraries.
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Kovaltsuk A, Krawczyk K, Galson JD, Kelly DF, Deane CM, Trück J. How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data. Front Immunol 2017; 8:1753. [PMID: 29276518 PMCID: PMC5727015 DOI: 10.3389/fimmu.2017.01753] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/27/2017] [Indexed: 12/24/2022] Open
Abstract
Next-generation sequencing of immunoglobulin gene repertoires (Ig-seq) allows the investigation of large-scale antibody dynamics at a sequence level. However, structural information, a crucial descriptor of antibody binding capability, is not collected in Ig-seq protocols. Developing systematic relationships between the antibody sequence information gathered from Ig-seq and low-throughput techniques such as X-ray crystallography could radically improve our understanding of antibodies. The mapping of Ig-seq datasets to known antibody structures can indicate structurally, and perhaps functionally, uncharted areas. Furthermore, contrasting naïve and antigenically challenged datasets using structural antibody descriptors should provide insights into antibody maturation. As the number of antibody structures steadily increases and more and more Ig-seq datasets become available, the opportunities that arise from combining the two types of information increase as well. Here, we review how these data types enrich one another and show potential for advancing our knowledge of the immune system and improving antibody engineering.
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Affiliation(s)
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jacob D Galson
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
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40
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Yacoob C, Pancera M, Vigdorovich V, Oliver BG, Glenn JA, Feng J, Sather DN, McGuire AT, Stamatatos L. Differences in Allelic Frequency and CDRH3 Region Limit the Engagement of HIV Env Immunogens by Putative VRC01 Neutralizing Antibody Precursors. Cell Rep 2017; 17:1560-1570. [PMID: 27806295 DOI: 10.1016/j.celrep.2016.10.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/14/2016] [Accepted: 10/05/2016] [Indexed: 12/26/2022] Open
Abstract
Elicitation of broadly neutralizing antibodies remains a long-standing goal of HIV vaccine research. Although such antibodies can arise during HIV-1 infection, gaps in our knowledge of their germline, pre-immune precursor forms, as well as on their interaction with viral Env, limit our ability to elicit them through vaccination. Studies of broadly neutralizing antibodies from the VRC01-class provide insight into progenitor B cell receptors (BCRs) that could develop into this class of antibodies. Here, we employed high-throughput heavy chain variable region (VH)/light chain variable region (VL) deep sequencing, combined with biophysical, structural, and modeling antibody analyses, to interrogate circulating potential VRC01-progenitor BCRs in healthy individuals. Our study reveals that not all humans are equally predisposed to generate VRC01-class antibodies, not all predicted progenitor VRC01-expressing B cells can bind to Env, and the CDRH3 region of germline VRC01 antibodies influence their ability to recognize HIV-1. These findings will be critical to the design of optimized immunogens that should consider CDRH3 interactions.
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Affiliation(s)
- Christina Yacoob
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Vladimir Vigdorovich
- Center for Infectious Disease Research, 307 Westlake Avenue North #500, Seattle, WA 98109, USA
| | - Brian G Oliver
- Center for Infectious Disease Research, 307 Westlake Avenue North #500, Seattle, WA 98109, USA
| | - Jolene A Glenn
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Junli Feng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - D Noah Sather
- Center for Infectious Disease Research, 307 Westlake Avenue North #500, Seattle, WA 98109, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Department of Global Health, University of Washington, 1410 Northeast Campus Parkway, Seattle, WA 98195, USA.
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41
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Salinas I, Magadán S. Omics in fish mucosal immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:99-108. [PMID: 28235585 DOI: 10.1016/j.dci.2017.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 05/22/2023]
Abstract
The mucosal immune system of fish is a complex network of immune cells and molecules that are constantly surveilling the environment and protecting the host from infection. A number of "omics" tools are now available and utilized to understand the complexity of mucosal immune systems in non-traditional animal models. This review summarizes recent advances in the implementation of "omics" tools pertaining to the four mucosa-associated lymphoid tissues in teleosts. Genomics, transcriptomics, proteomics, and "omics" in microbiome research require interdisciplinary collaboration and careful experimental design. The data-rich datasets generated are proving really useful at discovering new innate immune players in fish mucosal secretions, identifying novel markers of specific mucosal immune responses, unraveling the diversity of the B and T cell repertoires and characterizing the diversity of the microbial communities present in teleost mucosal surfaces. Bioinformatics, data analysis and storage platforms should be developed to facilitate rapid processing of large datasets, especially when mammalian tools such as bioinformatics analysis software are not available in fishes.
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Affiliation(s)
- Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Susana Magadán
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA; Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Campus Lagoas Marcosende, Vigo, Pontevedra 36310, Spain.
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42
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Alenko A, Fleming AM, Burrows CJ. Reverse Transcription Past Products of Guanine Oxidation in RNA Leads to Insertion of A and C opposite 8-Oxo-7,8-dihydroguanine and A and G opposite 5-Guanidinohydantoin and Spiroiminodihydantoin Diastereomers. Biochemistry 2017; 56:5053-5064. [PMID: 28845978 DOI: 10.1021/acs.biochem.7b00730] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reactive oxygen species, both endogenous and exogenous, can damage nucleobases of RNA and DNA. Among the nucleobases, guanine has the lowest redox potential, making it a major target of oxidation. Although RNA is more prone to oxidation than DNA is, oxidation of guanine in RNA has been studied to a significantly lesser extent. One of the reasons for this is that many tools that were previously developed to study oxidation of DNA cannot be used on RNA. In the study presented here, the lack of a method for seeking sites of modification in RNA where oxidation occurs is addressed. For this purpose, reverse transcription of RNA containing major products of guanine oxidation was used. Extension of a DNA primer annealed to an RNA template containing 8-oxo-7,8-dihydroguanine (OG), 5-guanidinohydantoin (Gh), or the R and S diastereomers of spiroiminodihydantoin (Sp) was studied under standing start conditions. SuperScript III reverse transcriptase is capable of bypassing these lesions in RNA inserting predominantly A opposite OG, predominantly G opposite Gh, and almost an equal mixture of A and G opposite the Sp diastereomers. These data should allow RNA sequencing of guanine oxidation products by following characteristic mutation signatures formed by the reverse transcriptase during primer elongation past G oxidation sites in the template RNA strand.
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Affiliation(s)
- Anton Alenko
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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43
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He L, Lin X, de Val N, Saye-Francisco KL, Mann CJ, Augst R, Morris CD, Azadnia P, Zhou B, Sok D, Ozorowski G, Ward AB, Burton DR, Zhu J. Hidden Lineage Complexity of Glycan-Dependent HIV-1 Broadly Neutralizing Antibodies Uncovered by Digital Panning and Native-Like gp140 Trimer. Front Immunol 2017; 8:1025. [PMID: 28883821 PMCID: PMC5573810 DOI: 10.3389/fimmu.2017.01025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/08/2017] [Indexed: 11/30/2022] Open
Abstract
Germline precursors and intermediates of broadly neutralizing antibodies (bNAbs) are essential to the understanding of humoral response to HIV-1 infection and B-cell lineage vaccine design. Using a native-like gp140 trimer probe, we examined antibody libraries constructed from donor-17, the source of glycan-dependent PGT121-class bNAbs recognizing the N332 supersite on the HIV-1 envelope glycoprotein. To facilitate this analysis, a digital panning method was devised that combines biopanning of phage-displayed antibody libraries, 900 bp long-read next-generation sequencing, and heavy/light (H/L)-paired antibodyomics. In addition to single-chain variable fragments resembling the wild-type bNAbs, digital panning identified variants of PGT124 (a member of the PGT121 class) with a unique insertion in the heavy chain complementarity-determining region 1, as well as intermediates of PGT124 exhibiting notable affinity for the native-like trimer and broad HIV-1 neutralization. In a competition assay, these bNAb intermediates could effectively compete with mouse sera induced by a scaffolded BG505 gp140.681 trimer for the N332 supersite. Our study thus reveals previously unrecognized lineage complexity of the PGT121-class bNAbs and provides an array of library-derived bNAb intermediates for evaluation of immunogens containing the N332 supersite. Digital panning may prove to be a valuable tool in future studies of bNAb diversity and lineage development.
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Affiliation(s)
- Linling He
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Xiaohe Lin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Karen L Saye-Francisco
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Colin J Mann
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Ryan Augst
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Charles D Morris
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Parisa Azadnia
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Bin Zhou
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States
| | - Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jiang Zhu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
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Abstract
In 2009, Dimitrov's group reported that the inferred germline (iGL) forms of several HIV-1 broadly neutralizing antibodies (bNAbs) did not display measurable binding to a recombinant gp140 Env protein (derived from the dual-tropic 89.6 virus), which was efficiently recognized by the mature (somatically mutated) antibodies. At that time, a small number of bNAbs were available, but in the following years, the implementation of high-throughput B-cell isolation and sequencing assays and of screening methodologies facilitated the isolation of greater numbers of bNAbs from infected subjects. Using these newest bNAbs, and a wide range of diverse recombinant Envs, we and others confirmed the observations made by Dimitrov's group. The results from these studies created a paradigm shift in our collective thinking as to why recombinant Envs are ineffective in eliciting bNAbs and has led to the "germline-targeting" immunization approach. Here we discuss this approach in detail: what has been done so far, the advantages and limitations of the current germline-targeting immunogens and of the animal models used to test them, and we conclude with a few thoughts about future directions in this area of research.
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Affiliation(s)
- Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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45
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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: 2.6] [Reference Citation Analysis] [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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46
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Specific microRNA library of IFN-τ on bovine endometrial epithelial cells. Oncotarget 2017; 8:61487-61498. [PMID: 28977879 PMCID: PMC5617439 DOI: 10.18632/oncotarget.18470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/14/2017] [Indexed: 12/02/2022] Open
Abstract
IFN-τ is specifically secreted by the conceptus in ruminants during early pregnancy, and it plays a vital role in the immunological function of pregnancy. However, its mechanism involving microRNA (miRNA) is still not well understood. Deep sequencing was used to explore the specific miRNA library of IFN-τ on bovine endometrial epithelial cells (bEECs). The results showed that 574 known bovine miRNAs and 109 novel miRNAs were identified. We found 74 differentially expressed miRNAs, including 30 commonly expressed miRNAs in the experiment. Then, qPCR verification of six selected miRNAs showed that they corresponded with the sequencing data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed significant enrichment of predicted target genes of differentially expressed miRNAs, including influenza A, herpes simplex infection, antigen processing and presentation, viral myocarditis, TNF signaling pathway, graft-versus-host disease, and allograft rejection. These results may provide important contributions to the immune response during early pregnancy in ruminants, but further studies are need to verify the proposed cellular/immunological effects and role of specific miRNA as biomarkers in vivo.
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47
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Shagin DA, Turchaninova MA, Shagina IA, Shugay M, Zaretsky AR, Zueva OI, Bolotin DA, Lukyanov S, Chudakov DM. Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries. BMC Genomics 2017; 18:440. [PMID: 28583065 PMCID: PMC5460480 DOI: 10.1186/s12864-017-3815-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 05/24/2017] [Indexed: 12/18/2022] Open
Abstract
Background Recently we proposed efficient method to exclude undesirable primers at any stage of amplification reaction, here termed NOPE (NOnsense-mediated Primer Exclusion). According to this method, added oligonucleotide overlapping with the 3′-end of unwanted amplification primer (NOPE oligo) simultaneously provides a template for its elongation. This elongation disrupts specificity of unwanted primer, preventing its further participation in PCR. The suggested approach allows to rationally manage the course of PCR reactions in order to facilitate analysis of complex DNA mixtures as well as to perform multistage PCR bypassing intermediate purification steps. Results Here we apply NOPE method to DNA library preparation for the high-throughput sequencing (HTS) with the PCR-based introduction of unique molecular identifiers (UMI). We show that NOPE oligo efficiently neutralizes UMI-containing oligonucleotides after introduction of UMI into sample DNA molecules, thus allowing to proceed with further amplification steps without purification and associated loss of starting material. At the same time, NOPE oligo does not affect the efficiency of target PCR amplification. Conclusion We describe a simple, robust and cheap modification of UMI-labeled HTS libraries preparation procedure, that allows to bypass purification step and thus to preserve starting material which may be limited, e.g. circulating tumor DNA, circulating fetal DNA, or small amounts of isolated cells of interest. Furthermore, demonstrated simplicity and robustness of NOPE method should make it popular in various PCR protocols.
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Affiliation(s)
- Dmitriy A Shagin
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Maria A Turchaninova
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andrew R Zaretsky
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Olga I Zueva
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Dmitriy A Bolotin
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Dmitriy M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia. .,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic. .,Skolkovo Institute of Science and Technology, Moscow, Russia.
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48
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Xia L, Tang A, Meng W, Freed DC, He L, Wang D, Li F, Li L, Xiong W, Gui X, Schultz RD, Chen H, He X, Swoyer R, Ha S, Liu Y, Morris CD, Zhou Y, Wang IM, Zhao Q, Luo W, Xia N, Espeseth AS, Hazuda DJ, Rupp RE, Barrett AD, Zhang N, Zhu J, Fu TM, An Z. Active evolution of memory B-cells specific to viral gH/gL/pUL128/130/131 pentameric complex in healthy subjects with silent human cytomegalovirus infection. Oncotarget 2017; 8:73654-73669. [PMID: 29088734 PMCID: PMC5650289 DOI: 10.18632/oncotarget.18359] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 05/19/2017] [Indexed: 01/16/2023] Open
Abstract
Human cytomegalovirus (HCMV) can cause life-threatening infection in immunosuppressed patients, and in utero infection that may lead to birth defects. No vaccine is currently available. HCMV infection in healthy subjects is generally asymptomatic, and virus persists as latent infection for life. Host immunity is effective against reactivation and super-infection with another strain. Thus, vaccine candidates able to elicit immune responses similar to those of natural infection may confer protection. Since neutralization is essential for prophylactic vaccines, it is important to understand how antiviral antibodies are developed in natural infection. We hypothesized that the developmental path of antibodies in seropositive subjects could be unveiled by interrogating host B-cell repertoires using unique genetic signature sequences of mAbs. Towards this goal, we isolated 56 mAbs from three healthy donors with different neutralizing titers. Antibodies specific to the gH/gL/pUL128/130/131 pentameric complex were more potent in neutralization than those to gB. Using these mAbs as probes, patterns of extended lineage development for B-cells and evidence of active antibody maturation were revealed in two donors with higher neutralizing titers. Importantly, such patterns were limited to mAbs specific to the pentamer, but none to gB. Thus, memory B-cells with antiviral function such as neutralization were active during latent infection in the two donors, and this activity was responsible for their higher neutralizing titers. Our results indicated that memory B-cells of neutralizing capacity could be frequently mobilized in host, probably responding to silent viral episodes, further suggesting that neutralizing antibodies could play a role in control of recurrent infection.
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Affiliation(s)
- Lin Xia
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
| | - Aimin Tang
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Weixu Meng
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Daniel C Freed
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Linling He
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Dai Wang
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Fengsheng Li
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Leike Li
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Wei Xiong
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xun Gui
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Robbie D Schultz
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Haotai Chen
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xi He
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ryan Swoyer
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Sha Ha
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Yaping Liu
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Charles D Morris
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Yu Zhou
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - I-Ming Wang
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Qinjian Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
| | - Wenxin Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
| | - Amy S Espeseth
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Daria J Hazuda
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Richard E Rupp
- Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
| | - Alan D Barrett
- Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jiang Zhu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tong-Ming Fu
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
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49
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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: 34] [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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50
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MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. PLoS Comput Biol 2017; 13:e1005480. [PMID: 28475621 PMCID: PMC5419444 DOI: 10.1371/journal.pcbi.1005480] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/24/2017] [Indexed: 12/16/2022] Open
Abstract
Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants. Using an extensive set of benchmark datasets including gold-standard biological samples with known variant frequencies, cell-free DNA from tumor patient blood samples and publicly available UMI-encoded datasets we demonstrate that our method is both robust and efficient in calling rare variants. The versatility of our software is supported by accurate results obtained for both tumor DNA and viral RNA samples in datasets prepared using three different UMI-based protocols.
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