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Lee HE, Cho AH, Hwang JH, Kim JW, Yang HR, Ryu T, Jung Y, Lee S. Development, High-Throughput Profiling, and Biopanning of a Large Phage Display Single-Domain Antibody Library. Int J Mol Sci 2024; 25:4791. [PMID: 38732011 PMCID: PMC11083953 DOI: 10.3390/ijms25094791] [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: 03/20/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Immunoglobulin G-based monoclonal antibodies (mAbs) have been effective in treating various diseases, but their large molecular size can limit their penetration of tissue and efficacy in multifactorial diseases, necessitating the exploration of alternative forms. In this study, we constructed a phage display library comprising single-domain antibodies (sdAbs; or "VHHs"), known for their small size and remarkable stability, using a total of 1.6 × 109 lymphocytes collected from 20 different alpacas, resulting in approximately 7.16 × 1010 colonies. To assess the quality of the constructed library, next-generation sequencing-based high-throughput profiling was performed, analyzing approximately 5.65 × 106 full-length VHH sequences, revealing 92% uniqueness and confirming the library's diverse composition. Systematic characterization of the library revealed multiple sdAbs with high affinity for three therapeutically relevant antigens. In conclusion, our alpaca sdAb phage display library provides a versatile resource for diagnostics and therapeutics. Furthermore, the library's vast natural VHH antibody repertoire offers insights for generating humanized synthetic sdAb libraries, further advancing sdAb-based therapeutics.
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Affiliation(s)
- Hee Eon Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ah Hyun Cho
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Jae Hyeon Hwang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ji Woong Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul 08507, Republic of Korea; (T.R.); (Y.J.)
| | - Yushin Jung
- ATG Lifetech Inc., Seoul 08507, Republic of Korea; (T.R.); (Y.J.)
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul 02707, Republic of Korea
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Matsuda T, Akazawa-Ogawa Y, Komaba LK, Kiyose N, Miyazaki N, Mizuguchi Y, Fukuta T, Ito Y, Hagihara Y. Prediction of antigen-responding VHH antibodies by tracking the evolution of antibody along the time course of immunization. Front Immunol 2024; 14:1335462. [PMID: 38292485 PMCID: PMC10825579 DOI: 10.3389/fimmu.2023.1335462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/22/2023] [Indexed: 02/01/2024] Open
Abstract
Antibody maturation is the central function of the adaptive immune response. This process is driven by the repetitive selection of mutations that increase the affinity toward antigens. We hypothesized that a precise observation of this process by high-throughput sequencing along the time course of immunization will enable us to predict the antibodies reacting to the immunized antigen without any additional in vitro screening. An alpaca was immunized with IgG fragments using multiple antigen injections, and the antibody repertoire development was traced via high-throughput sequencing periodically for months. The sequences were processed into clusters, and the antibodies in the 16 most abundant clusters were generated to determine whether the clusters included antigen-binding antibodies. The sequences of most antigen-responsive clusters resembled those of germline cells in the early stages. These sequences were observed to accumulate significant mutations and also showed a continuous sequence turnover throughout the experimental period. The foregoing characteristics gave us >80% successful prediction of clusters composed of antigen-responding VHHs against IgG fragment. Furthermore, when the prediction method was applied to the data from other alpaca immunized with epidermal growth factor receptor, the success rate exceeded 80% as well, confirming the general applicability of the prediction method. Superior to previous studies, we identified the immune-responsive but very rare clusters or sequences from the immunized alpaca without any empirical screening data.
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Affiliation(s)
- Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Japan
| | - Yoko Akazawa-Ogawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Lilian-Kaede Komaba
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Norihiko Kiyose
- Division of Antibody Operations, ARK Resource. Co., Ltd., Kumamoto, Japan
| | - Nobuo Miyazaki
- Division of Antibody Operations, ARK Resource. Co., Ltd., Kumamoto, Japan
| | | | | | - Yuji Ito
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Yoshihisa Hagihara
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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3
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Yong Joon Kim J, Sang Z, Xiang Y, Shen Z, Shi Y. Nanobodies: Robust miniprotein binders in biomedicine. Adv Drug Deliv Rev 2023; 195:114726. [PMID: 36754285 DOI: 10.1016/j.addr.2023.114726] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/30/2022] [Accepted: 02/02/2023] [Indexed: 02/10/2023]
Abstract
Variable domains of heavy chain-only antibodies (VHH), also known as nanobodies (Nbs), are monomeric antigen-binding domains derived from the camelid heavy chain-only antibodies. Nbs are characterized by small size, high target selectivity, and marked solubility and stability, which collectively facilitate high-quality drug development. In addition, Nbs are readily expressed from various expression systems, including E. coli and yeast cells. For these reasons, Nbs have emerged as preferred antibody fragments for protein engineering, disease diagnosis, and treatment. To date, two Nb-based therapies have been approved by the U.S. Food and Drug Administration (FDA). Numerous candidates spanning a wide spectrum of diseases such as cancer, immune disorders, infectious diseases, and neurodegenerative disorders are under preclinical and clinical investigation. Here, we discuss the structural features of Nbs that allow for specific, versatile, and strong target binding. We also summarize emerging technologies for identification, structural analysis, and humanization of Nbs. Our main focus is to review recent advances in using Nbs as a modular scaffold to facilitate the engineering of multivalent polymers for cutting-edge applications. Finally, we discuss remaining challenges for Nb development and envision new opportunities in Nb-based research.
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Affiliation(s)
- Jeffrey Yong Joon Kim
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA; Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhe Sang
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA
| | - Yufei Xiang
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA
| | - Zhuolun Shen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi Shi
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA.
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4
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Wang M, Wei L, Xiang H, Ren B, Liu X, Jiang L, Yang N, Shi J. A megadiverse naïve library derived from numerous camelids for efficient and rapid development of VHH antibodies. Anal Biochem 2022; 657:114871. [PMID: 36108795 DOI: 10.1016/j.ab.2022.114871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 07/20/2022] [Accepted: 08/17/2022] [Indexed: 11/01/2022]
Abstract
The field of antibody development is under pressure to meet rising demands for speed, cost-effectiveness, efficacy, reliability, and large-scale production. It is costly and time-consuming to immunize animals and build a single-domain antibody (sdAb) library for each target. Using the variable domain (VHH) of heavy-chain only antibodies (HcAbs) derived from blood samples of 75 non-immunized camelid animals (51 alpacas, 13 llamas, 11 Bactrian camels), and spleens from two Bactrian camels, a naïve sdAb library with extensive megadiversity and reusability was constructed. The library was evaluated using next-generation DNA sequencing (NGS) and was found to contain hundreds of billions of unique clones. To confirm the availability of target-specific VHHs, a naive library was screened for a variety of targets. At least two VHH candidates were extracted for each target using a 20-day selection pipeline. Some binders had ultrahigh potencies, with binding affinities in the nanomolar range. This naïve library, in particular, offers the possibility of acquiring unique antibodies targeting antigens of interest with low feasible dissociation constant (kD) without the time, effort, and price associated in producing antibodies in animals via antigen injection. Overall, the study shows that the megadiverse naïve library provides a rapid, adaptable, and easy platform for antibody creation, emphasizing its therapeutic and diagnostic implications.
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Affiliation(s)
- Meiniang Wang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Likun Wei
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; Biotechnology and Health Centre, City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Bingzhao Ren
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaopan Liu
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Lin Jiang
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; Complete Genomics, Inc., 2904 Orchard Parkway, San Jose, CA, 95134, USA.
| | - Jiahai Shi
- Synthetic Biology Translational Research Programmes, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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5
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Khalaf HE, Al-Bouqaee H, Hwijeh M, Abbady AQ. Characterization of rabbit polyclonal antibody against camel recombinant nanobodies. Open Life Sci 2022; 17:659-675. [PMID: 35800073 PMCID: PMC9202535 DOI: 10.1515/biol-2022-0065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/02/2022] [Accepted: 03/12/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Nanobodies (Nbs) are recombinant single-domain fragments derived from camelids’ heavy-chain antibodies (HCAbs). Nanobodies are increasingly used in numerous biotechnological and medical applications because of their high stability, solubility, and yield. However, one major obstacle prohibiting Nb expansion is the affordability of specific detector antibodies for their final revelation. In this work, the production of a specific anti-Nb antibody as a general detector for camel antibodies, conventional cIgG, and HCAb, and their derived Nbs was sought. Thus, a T7 promoter plasmid was constructed and used to highly express six different Nbs that were used in a successful rabbit immunization. Affinity-purified rabbit anti-Nb rIgG was able to detect immobilized or antigen-bound Nbs via enzyme-linked immunosorbent assay, and its performance was comparable to that of a commercial anti-6× His antibody. Its capacities in dosing impure Nbs, detecting Nbs displayed on M13 phages, and revealing denatured Nbs in immune blotting were all proven. As expected, and because of shared epitopes, rabbit anti-Nb cross-reacted with cIgG, HCAbs, and 6× His-tagged proteins, and the percentage of each fraction within anti-Nb rIgG was determined. Anti-Nb is a promising tool for the checkpoints throughout the recombinant Nb technology.
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Affiliation(s)
- Houssam-Eddin Khalaf
- Division of Molecular Biomedicine, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS) , P. O. Box 6091 , Damascus , Syria
| | - Hassan Al-Bouqaee
- Division of Molecular Biomedicine, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS) , P. O. Box 6091 , Damascus , Syria
| | - Manal Hwijeh
- Division of Molecular Biomedicine, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS) , P. O. Box 6091 , Damascus , Syria
| | - Abdul Qader Abbady
- Division of Molecular Biomedicine, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS) , P. O. Box 6091 , Damascus , Syria
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Oliinyk OS, Baloban M, Clark CL, Carey E, Pletnev S, Nimmerjahn A, Verkhusha VV. Single-domain near-infrared protein provides a scaffold for antigen-dependent fluorescent nanobodies. Nat Methods 2022; 19:740-750. [PMID: 35606446 DOI: 10.1038/s41592-022-01467-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/24/2022] [Indexed: 12/16/2022]
Abstract
Small near-infrared (NIR) fluorescent proteins (FPs) are much needed as protein tags for imaging applications. We developed a 17 kDa NIR FP, called miRFP670nano3, which brightly fluoresces in mammalian cells and enables deep-brain imaging. By exploring miRFP670nano3 as an internal tag, we engineered 32 kDa NIR fluorescent nanobodies, termed NIR-Fbs, whose stability and fluorescence strongly depend on the presence of specific intracellular antigens. NIR-Fbs allowed background-free visualization of endogenous proteins, detection of viral antigens, labeling of cells expressing target molecules and identification of double-positive cell populations with bispecific NIR-Fbs against two antigens. Applying NIR-Fbs as destabilizing fusion partners, we developed molecular tools for directed degradation of targeted proteins, controllable protein expression and modulation of enzymatic activities. Altogether, NIR-Fbs enable the detection and manipulation of a variety of cellular processes based on the intracellular protein profile.
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Affiliation(s)
- Olena S Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikhail Baloban
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Charles L Clark
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Erin Carey
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Vladislav V Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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7
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Mills C, Campbell K. A new chapter for anti-idiotypes in low molecular weight compound immunoassays. Trends Biotechnol 2022; 40:1102-1120. [DOI: 10.1016/j.tibtech.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 11/25/2022]
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8
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Deszyński P, Młokosiewicz J, Volanakis A, Jaszczyszyn I, Castellana N, Bonissone S, Ganesan R, Krawczyk K. INDI-integrated nanobody database for immunoinformatics. Nucleic Acids Res 2022; 50:D1273-D1281. [PMID: 34747487 PMCID: PMC8728276 DOI: 10.1093/nar/gkab1021] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/30/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Nanobodies, a subclass of antibodies found in camelids, are versatile molecular binding scaffolds composed of a single polypeptide chain. The small size of nanobodies bestows multiple therapeutic advantages (stability, tumor penetration) with the first therapeutic approval in 2018 cementing the clinical viability of this format. Structured data and sequence information of nanobodies will enable the accelerated clinical development of nanobody-based therapeutics. Though the nanobody sequence and structure data are deposited in the public domain at an accelerating pace, the heterogeneity of sources and lack of standardization hampers reliable harvesting of nanobody information. We address this issue by creating the Integrated Database of Nanobodies for Immunoinformatics (INDI, http://naturalantibody.com/nanobodies). INDI collates nanobodies from all the major public outlets of biological sequences: patents, GenBank, next-generation sequencing repositories, structures and scientific publications. We equip INDI with powerful nanobody-specific sequence and text search facilitating access to >11 million nanobody sequences. INDI should facilitate development of novel nanobody-specific computational protocols helping to deliver on the therapeutic promise of this drug format.
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Affiliation(s)
| | | | - Adam Volanakis
- Harvard Medical School, 240 Longwood Ave, Boston, MA, USA
| | | | - Natalie Castellana
- Abterra Biosciences Inc. 3030 Bunker Hill Street Suite 218, San Diego, CA 92109, USA
| | - Stefano Bonissone
- Abterra Biosciences Inc. 3030 Bunker Hill Street Suite 218, San Diego, CA 92109, USA
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9
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Wagner TR, Rothbauer U. Nanobodies - Little helpers unravelling intracellular signaling. Free Radic Biol Med 2021; 176:46-61. [PMID: 34536541 DOI: 10.1016/j.freeradbiomed.2021.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022]
Abstract
The identification of diagnostic and therapeutic targets requires a comprehensive understanding of cellular processes, for which advanced technologies in biomedical research are needed. The emergence of nanobodies (Nbs) derived from antibody fragments of camelid heavy chain-only antibodies as intracellular research tools offers new possibilities to study and modulate target antigens in living cells. Here we summarize this rapidly changing field, beginning with a brief introduction of Nbs, followed by an overview of how target-specific Nbs can be generated, and introduce the selection of intrabodies as research tools. Intrabodies, by definition, are intracellular functional Nbs that target ectopic or endogenous intracellular antigens within living cells. Such binders can be applied in various formats, e.g. as chromobodies for live cell microscopy or as biosensors to decipher complex intracellular signaling pathways. In addition, protein knockouts can be achieved by target-specific Nbs, while modulating Nbs have the potential as future therapeutics. The development of fine-tunable and switchable Nb-based systems that simultaneously provide spatial and temporal control has recently taken the application of these binders to the next level.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany.
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10
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Nannini F, Senicar L, Parekh F, Kong KJ, Kinna A, Bughda R, Sillibourne J, Hu X, Ma B, Bai Y, Ferrari M, Pule MA, Onuoha SC. Combining phage display with SMRTbell next-generation sequencing for the rapid discovery of functional scFv fragments. MAbs 2021; 13:1864084. [PMID: 33382949 PMCID: PMC7781620 DOI: 10.1080/19420862.2020.1864084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Phage display technology in combination with next-generation sequencing (NGS) currently is a state-of-the-art method for the enrichment and isolation of monoclonal antibodies from diverse libraries. However, the current NGS methods employed for sequencing phage display libraries are limited by the short contiguous read lengths associated with second-generation sequencing platforms. Consequently, the identification of antibody sequences has conventionally been restricted to individual antibody domains or to the analysis of single domain binding moieties such as camelid VHH or cartilaginous fish IgNAR antibodies. In this study, we report the application of third-generation sequencing to address this limitation. We used single molecule real time (SMRT) sequencing coupled with hairpin adaptor loop ligation to facilitate the accurate interrogation of full-length single-chain Fv (scFv) libraries. Our method facilitated the rapid isolation and testing of scFv antibodies enriched from phage display libraries within days following panning. Two libraries against CD160 and CD123 were panned and monitored by NGS. Analysis of NGS antibody data sets led to the isolation of several functional scFv antibodies that were not identified by conventional panning and screening strategies. Our approach, which combines phage display selection of immune libraries with the full-length interrogation of scFv fragments, is an easy method to discover functional antibodies, with a range of affinities and biophysical characteristics.
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Affiliation(s)
| | | | | | - Khai J. Kong
- Cancer Institute, University College London, London, UK
| | | | | | | | - Xihao Hu
- GV20 Therapeutics LLC, Cambridge, MA, USA
| | - Biao Ma
- Autolus Therapeutics, London, UK
| | | | | | - Martin A. Pule
- Cancer Institute, University College London, London, UK
- Autolus Therapeutics, London, UK
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11
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Abstract
Ever since the discovery of antibodies, they have been generated by complicated multi-step procedures. Typically, these involve sequencing, cloning, and screening after expression of the antibodies in a suitable organism and format. Here, a staphylococcal nanobody display is described that omits many the abovementioned intermediate steps and allows for simultaneous screening of multiple targets without prior knowledge nor expression of the binders. This paper reports a detailed, general step-by-step protocol to achieve nanobodies of high affinity. Apart from its focus on radioactive and fluorescent targets, it gives options for various other target formats and additional applications for the staphylococcal library; including flow cytometry and immunoprecipitation. This provides a system for antibody engineers that can be easily adopted to their specific needs.
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Affiliation(s)
- Marco Cavallari
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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12
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Criscitiello MF, Kraev I, Lange S. Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)-Novel insights into camelid immunity. Mol Immunol 2020; 117:37-53. [PMID: 31733447 PMCID: PMC7112542 DOI: 10.1016/j.molimm.2019.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/05/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Furthermore, PADs have been found to be a phylogenetically conserved regulator for extracellular vesicle (EVs) release. EVs are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins in serum and serum-EVs are described for the first time in camelids, using the llama (Lama glama L. 1758) as a model animal. We report a poly-dispersed population of llama serum EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. In serum, 60 deiminated proteins were identified that were not in EVs, and 25 deiminated proteins were found to be unique to EVs, with 43 shared deiminated protein hits between both serum and EVs. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in llama serum. PAD homologues were identified in llama serum by Western blotting, via cross reaction with human PAD antibodies, and detected at an expected 70 kDa size. This is the first report of deiminated proteins in serum and EVs of a camelid species, highlighting a hitherto unrecognized post-translational modification in key immune and metabolic proteins in camelids, which may be translatable to and inform a range of human metabolic and inflammatory pathologies.
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Affiliation(s)
- Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, 77843, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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13
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Oxford nanopore sequencing enables rapid discovery of single-domain antibodies from phage display libraries. Biotechniques 2019; 65:351-356. [PMID: 30477332 DOI: 10.2144/btn-2018-0123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antibody (Ab) repertoire sequencing using high-throughput massively parallel technologies has contributed substantially to the understanding of Ab responses following infection, vaccination and autoimmunity. Because individual B-cell receptors are recombined and diversified somatically, genomic comparisons are limited, and distinguishing rare variants from sequencing errors is a major challenge. Oxford Nanopore Technologies' MinION is a highly portable and cost-effective third-generation sequencing instrument, but has not been used for Ab repertoire sequencing due to its high error rate (approximately 1/10 bases). Here, we applied nanopore sequencing to single-domain Ab (sdAb) repertoires and phage-displayed sdAb libraries. We show that despite low overall data fidelity, sdAb sequences could be reconstructed above a frequency threshold (∼100 copies); however, distinguishing clonal sdAb variants was not always possible. The data quality was sufficient to enable rapid identification of antigen-specific sdAb sequences enriched during panning of phage display libraries, obviating the need for screening single clones.
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Miura N, Miyamoto K, Ohtani Y, Yaginuma K, Aburaya S, Kitagawa Y, Aoki W, Ueda M. Domain swapping of complementarity-determining region in nanobodies produced by Pichia pastoris. AMB Express 2019; 9:107. [PMID: 31309388 PMCID: PMC6629726 DOI: 10.1186/s13568-019-0833-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
Easy preparation of chimeric nanobodies with various scaffolds is important for customizing abilities of nanobodies toward practical utilization. To accomplish high-throughput production of various nanobodies, utilization of microbes is an attractive option. In the present study, various chimeric nanobodies were prepared using the methylotrophic yeast Pichia pastoris. We designed chimeric nanobodies with complementarity-determining regions (CDRs) against green fluorescent protein (GFP) or cluster of differentiation 4 (CD4) based on the scaffold of GFP-nanobody. FLAG-tagged chimeric nanobodies were prepared by one-step cloning and produced using P. pastoris. Secreted chimeric nanobodies were purified from the culture media of P. pastoris transformants. Relative binding abilities of purified chimeric nanobodies to GFP and CD4 was tested using a BIACORE T-200. P. pastoris successfully produced a high yield of FLAG-tagged chimeric nanobodies. FLAG-tagged GFP- and CD4-nanobodies were shown to specifically bind to GFP and CD4, respectively. Chimeric nanobodies, in which the CDR2 or 3 of GFP-nanobody was replaced with CDRs of CD4-nanobody, acquired the ability to bind to CD4 without binding to GFP. These results demonstrate successful production of functional chimeric nanobodies using P. pastoris. These results also suggest that swapping of CDRs, especially CDRs 2 or 3, potentially enables a novel method of creating nanobodies.
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15
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Lagoutte P, Lugari A, Elie C, Potisopon S, Donnat S, Mignon C, Mariano N, Troesch A, Werle B, Stadthagen G. Combination of ribosome display and next generation sequencing as a powerful method for identification of affibody binders against β-lactamase CTX-M15. N Biotechnol 2019; 50:60-69. [PMID: 30634000 DOI: 10.1016/j.nbt.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/15/2023]
Abstract
CTX-M15 is one of the most widespread, extended spectrum β-lactamases, a major determinant of antibiotic resistance representing urgent public health threats, among enterobacterial strains infecting humans and animals. Here we describe the selection of binders to CTX-M15 from a combinatorial affibody library displayed on ribosomes. Upon three increasingly selective ribosome display iterations, selected variants were identified by next generation sequencing (NGS). Nine affibody variants with high relative abundance bearing QRP and QLH amino acid motifs at residues 9-11 were produced and characterized in terms of stability, affinity and specificity. All affibodies were correctly folded, with affinities ranging from 0.04 to 2 μM towards CTX-M15, and successfully recognized CTX-M15 in bacterial lysates, culture supernatants and on whole bacteria. It was further demonstrated that the binding of affibody molecules to CTX-M15 modulated the enzyme's kinetic parameters. This work provides an approach using ribosome display coupled to NGS for the rapid generation of protein ligands of interest in diagnostic and research applications.
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Affiliation(s)
| | - Adrien Lugari
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Céline Elie
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | | | | | | | | | - Alain Troesch
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Bettina Werle
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France.
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16
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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 PMCID: PMC5961013 DOI: 10.1093/nar/gky077] [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: 08/31/2016] [Revised: 12/25/2017] [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.
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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
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17
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Eden T, Menzel S, Wesolowski J, Bergmann P, Nissen M, Dubberke G, Seyfried F, Albrecht B, Haag F, Koch-Nolte F. A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation. Front Immunol 2018; 8:1989. [PMID: 29410663 PMCID: PMC5787055 DOI: 10.3389/fimmu.2017.01989] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/21/2017] [Indexed: 12/20/2022] Open
Abstract
Nanobodies (Nbs) are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully generated agonistic and antagonistic Nbs against several cell surface ecto-enzymes and ligand-gated ion channels.
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Affiliation(s)
- Thomas Eden
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janusz Wesolowski
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philine Bergmann
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marion Nissen
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gudrun Dubberke
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabienne Seyfried
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Birte Albrecht
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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18
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Gonzalez-Sapienza G, Rossotti MA, Tabares-da Rosa S. Single-Domain Antibodies As Versatile Affinity Reagents for Analytical and Diagnostic Applications. Front Immunol 2017; 8:977. [PMID: 28871254 PMCID: PMC5566570 DOI: 10.3389/fimmu.2017.00977] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/31/2017] [Indexed: 12/23/2022] Open
Abstract
With just three CDRs in their variable domains, the antigen-binding site of camelid heavy-chain-only antibodies (HcAbs) has a more limited structural diversity than that of conventional antibodies. Even so, this does not seem to limit their specificity and high affinity as HcAbs against a broad range of structurally diverse antigens have been reported. The recombinant form of their variable domain [nanobody (Nb)] has outstanding properties that make Nbs, not just an alternative option to conventional antibodies, but in many cases, these properties allow them to reach analytical or diagnostic performances that cannot be accomplished with conventional antibodies. These attributes include comprehensive representation of the immune specificity in display libraries, easy adaptation to high-throughput screening, exceptional stability, minimal size, and versatility as affinity building block. Here, we critically reviewed each of these properties and highlight their relevance with regard to recent developments in different fields of immunosensing applications.
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Affiliation(s)
| | - Martín A Rossotti
- Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, UDELAR, Montevideo, Uruguay
| | - Sofía Tabares-da Rosa
- Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, UDELAR, Montevideo, Uruguay
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