1
|
|
Wang Z, Tang Q, Liu B, Zhang W, Chen Y, Ji N, Peng Y, Yang X, Cui D, Kong W, Tang X, Yang T, Zhang M, Chang X, Zhu J, Huang M, Feng Z. A SARS-CoV-2 neutralizing antibody discovery by single cell sequencing and molecular modeling. J Biomed Res 2022; 37:1. [PMID: 36992606 DOI: 10.7555/jbr.36.20220221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although vaccines have been developed, mutations of SARS-CoV-2, especially the dominant B.1.617.2 (delta) and B.1.529 (omicron) strains with more than 30 mutations on their spike protein, have caused a significant decline in prophylaxis, calling for the need for drug improvement. Antibodies are drugs preferentially used in infectious diseases and are easy to get from immunized organisms. The current study combined molecular modeling and single memory B cell sequencing to assess candidate sequences before experiments, providing a strategy for the fabrication of SARS-CoV-2 neutralizing antibodies. A total of 128 sequences were obtained after sequencing 196 memory B cells, and 42 sequences were left after merging extremely similar ones and discarding incomplete ones, followed by homology modeling of the antibody variable region. Thirteen candidate sequences were expressed, of which three were tested positive for receptor binding domain recognition but only one was confirmed as having broad neutralization against several SARS-CoV-2 variants. The current study successfully obtained a SARS-CoV-2 antibody with broad neutralizing abilities and provided a strategy for antibody development in emerging infectious diseases using single memory B cell BCR sequencing and computer assistance in antibody fabrication.
Collapse
Affiliation(s)
- Zheyue Wang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qi Tang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Bende Liu
- Department of Cardiology, the First People's Hospital of Jiangxia District, Wuhan, Hubei 430299, China
| | - Wenqing Zhang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yufeng Chen
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ningfei Ji
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yan Peng
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaohui Yang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Daixun Cui
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Weiyu Kong
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaojun Tang
- Department of Rheumatology and Immunology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Tingting Yang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Mingshun Zhang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xinxia Chang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jin Zhu
- Huadong Medical Institute of Biotechniques, Nanjing, Jiangsu 210028, China
| | - Mao Huang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Zhenqing Feng
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| |
Collapse
|
2
|
|
Abstract
The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.
Collapse
Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Paula Lam
- CellVec Private Limited, 118518, Singapore; National University of Singapore, Department of Physiology, 117597, Singapore; Duke-NUS Graduate Medical School, Cancer and Stem Cells Biology Program, 169857, Singapore
| | - Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
3
|
|
Barreto K, Maruthachalam BV, Hill W, Hogan D, Sutherland AR, Kusalik A, Fonge H, DeCoteau JF, Geyer CR. Next-generation sequencing-guided identification and reconstruction of antibody CDR combinations from phage selection outputs. Nucleic Acids Res 2019; 47:e50. [PMID: 30854567 DOI: 10.1093/nar/gkz131] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 12/12/2018] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have been employed in several phage display platforms for analyzing natural and synthetic antibody sequences and for identifying and reconstructing single-chain variable fragments (scFv) and antigen-binding fragments (Fab) not found by conventional ELISA screens. In this work, we developed an NGS-assisted antibody discovery platform by integrating phage-displayed, single-framework, synthetic Fab libraries. Due to limitations in attainable read and amplicon lengths, NGS analysis of Fab libraries and selection outputs is usually restricted to either VH or VL. Since this information alone is not sufficient for high-throughput reconstruction of Fabs, we developed a rapid and simple method for linking and sequencing all diversified CDRs in phage Fab pools. Our method resulted in a reliable and straightforward platform for converting NGS information into Fab clones. We used our NGS-assisted Fab reconstruction method to recover low-frequency rare clones from phage selection outputs. While previous studies chose rare clones for rescue based on their relative frequencies in sequencing outputs, we chose rare clones for reconstruction from less-frequent CDRH3 lengths. In some cases, reconstructed rare clones (frequency ∼0.1%) showed higher affinity and better specificity than high-frequency top clones identified by Sanger sequencing, highlighting the significance of NGS-based approaches in synthetic antibody discovery.
Collapse
Affiliation(s)
- Kris Barreto
- Department of Pathology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | | | - Wayne Hill
- Department of Pathology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Daniel Hogan
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada
| | - Ashley R Sutherland
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada
| | - Humphrey Fonge
- Department of Medical Imaging, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - John F DeCoteau
- Department of Pathology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - C Ronald Geyer
- Department of Pathology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| |
Collapse
|
4
|
|
Ryvkin A, Ashkenazy H, Weiss-Ottolenghi Y, Piller C, Pupko T, Gershoni JM. Phage display peptide libraries: deviations from randomness and correctives. Nucleic Acids Res 2018; 46:e52. [PMID: 29420788 DOI: 10.1093/nar/gky077] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study, we demonstrate that the UAG over-representation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by mass spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications.
Collapse
Affiliation(s)
- Arie Ryvkin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yael Weiss-Ottolenghi
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Piller
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan M Gershoni
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
5
|
|
Lim CC, Woo PCY, Lim TS. Development of a Phage Display Panning Strategy Utilizing Crude Antigens: Isolation of MERS-CoV Nucleoprotein human antibodies. Sci Rep 2019; 9:6088. [PMID: 30988390 DOI: 10.1038/s41598-019-42628-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
Antibody phage display has been pivotal in the quest to generate human monoclonal antibodies for biomedical and research applications. Target antigen preparation is a main bottleneck associated with the panning process. This includes production complexity, downstream purification, quality and yield. In many instances, purified antigens are preferred for panning but this may not be possible for certain difficult target antigens. Here, we describe an improved procedure of affinity selection against crude or non-purified antigen by saturation of non-binders with blocking agents to promote positive binder enrichment termed as Yin-Yang panning. A naïve human scFv library with kappa light chain repertoire with a library size of 109 was developed. The improved Yin-Yang biopanning process was able to enrich monoclonal antibodies specific to the MERS-CoV nucleoprotein. Three unique monoclonal antibodies were isolated in the process. The Yin-Yang biopanning method highlights the possibility of utilizing crude antigens for the isolation of monoclonal antibodies by phage display.
Collapse
Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia. .,Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| |
Collapse
|
6
|
|
Gueneau F, Ravn U, Fischer N. Round optimization for improved discovery of native bispecific antibodies. Methods 2019; 154:51-9. [PMID: 30448477 DOI: 10.1016/j.ymeth.2018.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 01/07/2023] Open
Abstract
The assembly of bispecific antibodies (bsAb) that retain the structure of a standard IgG can be challenging as the correct pairing of the different heavy and light chains has to be ensured while unwanted side products kept to a minimum. The use of antibodies sharing a common chain facilitates assembly of such bsAb formats but requires additional efforts during the initial discovery phase. We have developed a native bsAb format called κλ body based on antibodies that, while being specific for different antigens, share the same heavy chain. Such antibodies can readily be isolated from antibody libraries incorporating a single VH combined with light chain diversity. However, in order to improve the discovery process of such fixed VH antibodies, we developed a method to optimize populations of light chains by recovering and shuffling CDRL3 sequences that have been enriched for antigen binding by phage display selection. This approach allowed for the isolation of a more diverse and potent panel of antibodies blocking the interaction between PD-1 and PD-L1 when compared to our standard in vitro selection approach, thus providing better building blocks for subsequent bsAb generation.
Collapse
Affiliation(s)
- F Gueneau
- Novimmune SA, 14 chemin des Aulx, 1228 Plan-les-Ouates, Switzerland
| | - U Ravn
- Novimmune SA, 14 chemin des Aulx, 1228 Plan-les-Ouates, Switzerland
| | - N Fischer
- Novimmune SA, 14 chemin des Aulx, 1228 Plan-les-Ouates, Switzerland.
| |
Collapse
|
7
|
|
D'Angelo S, Ferrara F, Naranjo L, Erasmus MF, Hraber P, Bradbury ARM. Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding. Front Immunol 2018; 9:395. [PMID: 29568296 DOI: 10.3389/fimmu.2018.00395] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022] Open
Abstract
Because of its great potential for diversity, the immunoglobulin heavy-chain complementarity-determining region 3 (HCDR3) is taken as an antibody molecule’s most important component in conferring binding activity and specificity. For this reason, HCDR3s have been used as unique identifiers to investigate adaptive immune responses in vivo and to characterize in vitro selection outputs where display systems were employed. Here, we show that many different HCDR3s can be identified within a target-specific antibody population after in vitro selection. For each identified HCDR3, a number of different antibodies bearing differences elsewhere can be found. In such selected populations, all antibodies with the same HCDR3 recognize the target, albeit at different affinities. In contrast, within unselected populations, the majority of antibodies with the same HCDR3 sequence do not bind the target. In one HCDR3 examined in depth, all target-specific antibodies were derived from the same VDJ rearrangement, while non-binding antibodies with the same HCDR3 were derived from many different V and D gene rearrangements. Careful examination of previously published in vivo datasets reveals that HCDR3s shared between, and within, different individuals can also originate from rearrangements of different V and D genes, with up to 26 different rearrangements yielding the same identical HCDR3 sequence. On the basis of these observations, we conclude that the same HCDR3 can be generated by many different rearrangements, but that specific target binding is an outcome of unique rearrangements and VL pairing: the HCDR3 is necessary, albeit insufficient, for specific antibody binding.
Collapse
Affiliation(s)
| | | | | | | | - Peter Hraber
- Los Alamos National Laboratory, Los Alamos, NM, United States
| | | |
Collapse
|
8
|
|
Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology 2018; 153:31-41. [PMID: 28898398 DOI: 10.1111/imm.12838] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high-throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high-throughput sequencing has made it possible to obtain large-scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high-throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high-throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.
Collapse
Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Life Science Zurich Graduate School, Systems Biology, ETH Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| |
Collapse
|
9
|
|
Fagète S, Botas-perez L, Rossito-borlat I, Adea K, Gueneau F, Ravn U, Rousseau F, Kosco-vilbois M, Fischer N, Hartley O. Dual display: phage selection driven by co-engagement of two targets by two different antibody fragments. Protein Eng Des Sel 2017; 30:575-82. [DOI: 10.1093/protein/gzx021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 04/13/2017] [Indexed: 01/03/2023] Open
|
10
|
|
Christiansen A, Kringelum JV, Hansen CS, Bøgh KL, Sullivan E, Patel J, Rigby NM, Eiwegger T, Szépfalusi Z, de Masi F, Nielsen M, Lund O, Dufva M. High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum. Sci Rep 2015; 5:12913. [PMID: 26246327 DOI: 10.1038/srep12913] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022] Open
Abstract
Phage display is a prominent screening technique with a multitude of applications including therapeutic antibody development and mapping of antigen epitopes. In this study, phages were selected based on their interaction with patient serum and exhaustively characterised by high-throughput sequencing. A bioinformatics approach was developed in order to identify peptide motifs of interest based on clustering and contrasting to control samples. Comparison of patient and control samples confirmed a major issue in phage display, namely the selection of unspecific peptides. The potential of the bioinformatic approach was demonstrated by identifying epitopes of a prominent peanut allergen, Ara h 1, in sera from patients with severe peanut allergy. The identified epitopes were confirmed by high-density peptide micro-arrays. The present study demonstrates that high-throughput sequencing can empower phage display by (i) enabling the analysis of complex biological samples, (ii) circumventing the traditional laborious picking and functional testing of individual phage clones and (iii) reducing the number of selection rounds.
Collapse
Affiliation(s)
- Anders Christiansen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jens V Kringelum
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian S Hansen
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Katrine L Bøgh
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Eric Sullivan
- Roche NimbleGen, Madison, Wisconsin, the United States of America
| | - Jigar Patel
- Roche NimbleGen, Madison, Wisconsin, the United States of America
| | - Neil M Rigby
- Institute of Food Research, Norwich, United Kingdom
| | - Thomas Eiwegger
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | - Zsolt Szépfalusi
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | - Federico de Masi
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Morten Nielsen
- 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark [2] Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Ole Lund
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
11
|
|
Levin M, Rotthus S, Wendel S, Najafi N, Källström E, Focke-Tejkl M, Valenta R, Flicker S, Ohlin M. Multiple independent IgE epitopes on the highly allergenic grass pollen allergen Phl p 5. Clin Exp Allergy 2014; 44:1409-19. [PMID: 25262820 DOI: 10.1111/cea.12423] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 07/06/2014] [Accepted: 08/15/2014] [Indexed: 11/30/2022]
Abstract
Background Group 5 allergens are small proteins that consist of two domains. They belong to the most potent respiratory allergens. Objective To determine the binding sites and to study allergic patients' IgE recognition of the group 5 allergen (Phl p 5) from timothy grass pollen using human monoclonal IgE antibodies that have been isolated from grass pollen allergic patients. Methods Using recombinant isoallergens, fragments, mutants and synthetic peptides of Phl p 5, as well as peptide-specific antibodies, the interaction of recombinant human monoclonal IgE and Phl p 5 was studied using direct binding and blocking assays. Cross-reactivity of monoclonal IgE with group 5 allergens in several grasses was studied and inhibition experiments with patients' polyclonal IgE were performed. Results Monoclonal human IgE showed extensive cross-reactivity with group 5 allergens in several grasses. Despite its small size of 29 kDa, four independent epitope clusters on isoallergen Phl p 5.0101, two in each domain, were recognized by human IgE. Isoallergen Phl p 5.0201 carried two of these epitopes. Inhibition studies with allergic patients' polyclonal IgE suggest the presence of additional IgE epitopes on Phl p 5. Conclusions & Clinical Relevance Our results reveal the presence of a large number of independent IgE epitopes on the Phl p 5 allergen explaining the high allergenic activity of this protein and its ability to induce severe allergic symptoms. High-density IgE recognition may be a general feature of many potent allergens and form a basis for the development of improved diagnostic and therapeutic procedures in allergic disease.
Collapse
Affiliation(s)
- M Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
|
Haka J, Niemi MH, Iljin K, Reddy VS, Takkinen K, Laukkanen ML. Isolation of Mal d 1 and Api g 1 - specific recombinant antibodies from mouse IgG Fab fragment libraries - Mal d 1-specific antibody exhibits cross-reactivity against Bet v 1. BMC Biotechnol 2015; 15:34. [PMID: 26013405 DOI: 10.1186/s12896-015-0157-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/01/2015] [Indexed: 11/12/2022] Open
Abstract
Background Around 3–5% of the population suffer from IgE-mediated food allergies in Western countries and the number of food-allergenic people is increasing. Individuals with certain pollen allergies may also suffer from a sensitisation to proteins in the food products. As an example a person sensitised to the major birch pollen allergen, Bet v 1, is often sensitised to its homologues, such as the major allergens of apple, Mal d 1, and celery, Api g 1, as well. Development of tools for the reliable, sensitive and quick detection of allergens present in various food products is essential for allergic persons to prevent the consumption of substances causing mild and even life-threatening immune responses. The use of monoclonal antibodies would ensure the specific detection of the harmful food content for a sensitised person. Methods Mouse IgG antibody libraries were constructed from immunised mice and specific recombinant antibodies for Mal d 1 and Api g 1 were isolated from the libraries by phage display. More detailed characterisation of the resulting antibodies was carried out using ELISA, SPR experiments and immunoprecipitation assays. Results The allergen-specific Fab fragments exhibited high affinity towards the target recombinant allergens. Furthermore, the Fab fragments also recognised native allergens from natural sources. Interestingly, isolated Mal d 1-specific antibody bound also to Bet v 1, the main allergen eliciting the cross-reactivity syndrome between the birch pollen and apple. Despite the similarities in Api g 1 and Bet v 1 tertiary structures, the isolated Api g 1-specific antibodies showed no cross-reactivity to Bet v 1. Conclusions Here, high-affinity allergen-specific recombinant antibodies were isolated with interesting binding properties. With further development, these antibodies can be utilised as tools for the specific and reliable detection of allergens from different consumable products. This study gives new preliminary insights to elucidate the mechanism behind the pollen-food syndrome and to study the IgG epitope of the allergens.
Collapse
Affiliation(s)
- Jaana Haka
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, Espoo, FI-02044 VTT, Finland.
| | - Merja H Niemi
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, P.O. Box 111, Joensuu, FI-80101, Finland.
| | - Kristiina Iljin
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, Espoo, FI-02044 VTT, Finland.
| | - Vanga Siva Reddy
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Kristiina Takkinen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, Espoo, FI-02044 VTT, Finland.
| | - Marja-Leena Laukkanen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, Espoo, FI-02044 VTT, Finland.
| |
Collapse
|
13
|
|
Bonvin P, Venet S, Kosco-vilbois M, Fischer N. Purpose-Oriented Antibody Libraries Incorporating Tailored CDR3 Sequences. Antibodies (Basel) 2015; 4:103-122. [DOI: 10.3390/antib4020103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
14
|
|
Levin M, Davies AM, Liljekvist M, Carlsson F, Gould HJ, Sutton BJ, Ohlin M. Human IgE against the major allergen Bet v 1--defining an epitope with limited cross-reactivity between different PR-10 family proteins. Clin Exp Allergy 2014; 44:288-99. [PMID: 24447087 DOI: 10.1111/cea.12230] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/24/2013] [Accepted: 10/25/2013] [Indexed: 02/05/2023]
Abstract
Background The interaction between IgE and allergen is a key event at the initiation of an allergic response, and its characteristics have substantial effects on the clinical manifestation. Despite this, the molecular details of the interaction between human IgE and the major birch allergen Bet v 1, one of the most potent tree allergens, still remain poorly investigated. Objective To isolate Bet v 1-specific human monoclonal IgE and characterize their interaction with the allergen. Methods Recombinant human IgE were isolated from a combinatorial antibody fragment library and their interaction with Bet v 1 assessed using various immunological assays. The structure of one such IgE in the single-chain fragment variable format was determined using X-ray crystallography. Results We present four novel Bet v 1-specific IgE, for one of which we solve the structure, all with their genetic origin in the IGHV5 germline gene, and demonstrate that they target two non-overlapping epitopes on the surface of Bet v 1, thereby fulfilling the basic criteria for FcεRI cross-linkage. We further define these epitopes and for one epitope pinpoint single amino acid residues important for the interaction with human IgE. This provides a potential explanation, at the molecular level, for the differences in recognition of isoforms of Bet v 1 and other allergens in the PR-10 protein family displayed by IgE targeting this epitope. Finally, we present the first high-resolution structure of a human allergen-specific IgE fragment in the single-chain fragment variable (scFv) format. Conclusions and Clinical Relevance We here display the usefulness of allergen-specific human monoclonal IgE as a tool in studies of the crucial molecular interaction taking place at the initiation of an allergic response. Such studies may aid us in development of better diagnostic tools and guide us in the development of new therapeutic compounds.
Collapse
Affiliation(s)
- M Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | | | | | | | | | | |
Collapse
|
15
|
|
Farajnia S, Ahmadzadeh V, Tanomand A, Veisi K, Khosroshahi SA, Rahbarnia L. Development trends for generation of single-chain antibody fragments. Immunopharmacol Immunotoxicol 2014; 36:297-308. [DOI: 10.3109/08923973.2014.945126] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
16
|
|
Valdés-Alemán J, Téllez-Sosa J, Ovilla-Muñoz M, Godoy-Lozano E, Velázquez-Ramírez D, Valdovinos-Torres H, Gómez-Barreto RE, Martinez-Barnetche J. Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing. MAbs 2014; 6:493-501. [PMID: 24492293 DOI: 10.4161/mabs.27435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.
Collapse
Affiliation(s)
- Javier Valdés-Alemán
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México; Programa de Ingeniería en Biotecnología; Universidad Politécnica del Estado de Morelos; Jiutepec, México
| | - Juan Téllez-Sosa
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Marbella Ovilla-Muñoz
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Elizabeth Godoy-Lozano
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Daniel Velázquez-Ramírez
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Humberto Valdovinos-Torres
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Rosa E Gómez-Barreto
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Jesús Martinez-Barnetche
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| |
Collapse
|
17
|
|
Abstract
IgE is a key mediator in allergic diseases. However, in strong contrast to other antibody isotypes, many details of the composition of the human IgE repertoire are poorly defined. The low levels of human IgE in the circulation and the rarity of IgE-producing B cells are important reasons for this lack of knowledge. In this review, we summarize the current knowledge on these repertoires both in terms of their complexity and activity, i.e. knowledge which despite the difficulties encountered when studying the molecular details of human IgE has been acquired in recent years. We also take a look at likely future developments, for instance through improvements in sequencing technology and methodology that allow the isolation of additional allergen-specific human antibodies mimicking IgE, as this certainly will support our understanding of human IgE in the context of human disease in the years to come.
Collapse
Affiliation(s)
- Elisabeth Gadermaier
- Division of Immunopathology, Department of Pathophysiology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | | | | |
Collapse
|
18
|
|
Venet S, Kosco-Vilbois M, Fischer N. Comparing CDRH3 diversity captured from secondary lymphoid organs for the generation of recombinant human antibodies. MAbs 2013; 5:690-8. [PMID: 23924800 DOI: 10.4161/mabs.25592] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The plasticity of natural immunoglobulin repertoires can be exploited for the generation of phage display libraries. Secondary lymphoid organs, such as the spleen and the lymph nodes, constitute interesting sources of diversity because they are rich in B cells, part of which can be affinity matured. These organs, however, differ in their anatomical structure, reflecting the different fluids they drain, which affects the B cell repertoires. The CDRH3 repertoires from these organs, extracted from naïve or immunized mice, were compared in the context of phage display libraries using human antibody framework families. Deep sequencing analysis revealed that all libraries displayed different CDRH3 repertoires, but the one derived from lymph nodes of naïve mice was the most diverse. Library performance was assessed by in vitro selection. For both organs, immunization increased substantially the frequency of molecules able to bind to the immunogen. The library derived from lymph nodes from naïve mice, however, was the most effective in generating diverse and high affinity candidates. These results illustrate that the use of a biased CDRH3 repertoire increases the performance of libraries, but reduces the clonal diversity, which may be detrimental for certain strategies.
Collapse
|
19
|
|
Tiller T, Schuster I, Deppe D, Siegers K, Strohner R, Herrmann T, Berenguer M, Poujol D, Stehle J, Stark Y, Heßling M, Daubert D, Felderer K, Kaden S, Kölln J, Enzelberger M, Urlinger S. A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties. MAbs 2013; 5:445-70. [PMID: 23571156 DOI: 10.4161/mabs.24218] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds.
Collapse
|
20
|
|
Ravn U, Didelot G, Venet S, Ng KT, Gueneau F, Rousseau F, Calloud S, Kosco-Vilbois M, Fischer N. Deep sequencing of phage display libraries to support antibody discovery. Methods 2013; 60:99-110. [PMID: 23500657 DOI: 10.1016/j.ymeth.2013.03.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 02/18/2013] [Accepted: 03/01/2013] [Indexed: 11/18/2022] Open
Abstract
The use of next generation sequencing (NGS) for the analysis of antibody sequences both in phage display libraries and during in vitro selection processes has become increasingly popular in the last few years. Here, our methods developed for DNA preparation, sequencing and data analysis are presented. A key parameter has also been to develop new software designed for high throughput antibody sequence analysis that is used in combination with publicly available tools. As an example of our methods, we provide data from the extensive analysis of five scFv libraries generated using different heavy chain CDR3 diversification strategies. The results not only confirm that the library designs were correct but also reveal differences in quality not easily identified by standard DNA sequencing approaches. The very large number of reads permits extensive sequence coverage after the selection process. Furthermore, as samples can be multiplexed, costs decrease and more information is gained per NGS run. Using examples of results obtained post phage display selections against two antigens, frequency and clustering analysis identified novel antibody fragments that were then shown to be specific for the target antigen. In summary, the methods described here demonstrate how NGS analysis enhances quality control of complex antibody libraries as well as facilitates the antibody discovery process.
Collapse
Affiliation(s)
- Ulla Ravn
- NovImmune S.A., 14 Chemin des Aulx, CH-1228 Plan-les-Ouates, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|