1
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Istomina PV, Gorchakov AA, Paoin C, Yamabhai M. Phage display for discovery of anticancer antibodies. N Biotechnol 2024; 83:205-218. [PMID: 39186973 DOI: 10.1016/j.nbt.2024.08.506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
Antibodies and antibody-based immunotherapeutics are the mainstays of cancer immunotherapy. Expanding the repertoire of cancer-specific and cancer-associated epitopes targetable with antibodies represents an important area of research. Phage display is a powerful approach allowing the use of diverse antibody libraries to be screened for binding to a wide range of targets. In this review, we summarize the basics of phage display technology and highlight the advances in anticancer antibody identification and modification via phage display platform. Finally, we describe phage display-derived anticancer monoclonal antibodies that have been approved to date or are in clinical development.
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Affiliation(s)
- Polina V Istomina
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Suranaree, Muang, 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Andrey A Gorchakov
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8/2, Novosibirsk 630090, Russia
| | - Chatchanok Paoin
- Medical Oncology Division, Institute of Medicine, Suranaree University of Technology, Suranaree, Muang, 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Suranaree, Muang, 111 University Avenue, Nakhon Ratchasima 30000, Thailand.
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2
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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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Van Deuren V, Plessers S, Lavigne R, Robben J. Application of Deep Sequencing in Phage Display. Methods Mol Biol 2024; 2738:333-345. [PMID: 37966608 DOI: 10.1007/978-1-0716-3549-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
This chapter describes the workflow to implement deep sequencing into standard phage display experiments on protein libraries. By harvesting the power of high throughput of these techniques, it allows for comprehensive analysis of the naïve library and library evolution in response to selection by ligand binding. The mutagenized target region of the protein variants encoded by the phage pool is analyzed by Illumina paired-end sequencing. Sequence data are processed to extract selection-enriched amino acid motifs. In addition, a complementary long-read sequencing approach is proposed enabling the monitoring of display vector stability.
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Affiliation(s)
- Vincent Van Deuren
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Sander Plessers
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Animal and Human Health Engineering (A2H), Leuven (Arenberg), KU Leuven, Leuven, Belgium
| | - Johan Robben
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium.
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4
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Nakada-Masuta T, Takeda H, Uchida K. Novel Approach for Obtaining Variable Domain of New Antigen Receptor with Different Physicochemical Properties from Japanese Topeshark ( Hemitriakis japanica). Mar Drugs 2023; 21:550. [PMID: 37999374 PMCID: PMC10672104 DOI: 10.3390/md21110550] [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: 09/30/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
Diverse candidate antibodies are needed to successfully identify therapeutic and diagnostic applications. The variable domain of IgNAR (VNAR), a shark single-domain antibody, has attracted attention owing to its favorable physicochemical properties. The phage display method used to screen for optimal VNARs loses sequence diversity because of the bias caused by the differential ease of protein expression in Escherichia coli. Here, we investigated a VNAR selection method that combined panning with various selection pressures and next-generation sequencing (NGS) analyses to obtain additional candidates. Drawing inspiration from the physiological conditions of sharks and the physicochemical properties of VNARs, we examined the effects of NaCl and urea concentrations, low temperature, and preheating at the binding step of panning. VNAR phage libraries generated from Japanese topeshark (Hemitriakis japanica) were enriched under these conditions. We then performed NGS analysis and attempted to select clones that were specifically enriched under each panning condition. The identified VNARs exhibited higher reactivity than those obtained by panning without selection pressure. Additionally, they possess physicochemical properties that reflect their respective selection pressures. These results can greatly enhance our understanding of VNAR properties and offer guidance for the screening of high-quality VNAR clones that are present at low frequencies.
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Affiliation(s)
- Tomofumi Nakada-Masuta
- Graduate School of Science, Technology and Innovation, Kobe University, 7-1-49 Minatojimaminamimachi Chuo-ku, Kobe 650-0047, Japan;
- Bio-Diagnostic Reagent Technology Center, Sysmex Corporation, 4-3-2 Nishi-ku Takatsukadai, Kobe 651-2271, Japan
| | - Hiroyuki Takeda
- Division of Proteo-Drug-Discovery Sciences, Ehime University Proteo-Science Center, Bunkyocho 3, Matsuyama 790-8577, Japan;
| | - Kazuhisa Uchida
- Graduate School of Science, Technology and Innovation, Kobe University, 7-1-49 Minatojimaminamimachi Chuo-ku, Kobe 650-0047, Japan;
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5
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Martinez BI, Stabenfeldt SE. In Vivo Phage Display as a Biomarker Discovery Tool for the Complex Neural Injury Microenvironment. Curr Protoc 2021; 1:e67. [PMID: 33625787 DOI: 10.1002/cpz1.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The heterogeneous injury pathophysiology of traumatic brain injury (TBI) is a barrier to developing highly sensitive and specific diagnostic tools. Phage display, a protein-protein screening technique routinely used in drug development, has the potential to be a powerful biomarker discovery tool for TBI. However, analysis of these large and diverse phage libraries is a bottleneck to moving through the discovery pipeline in a timely and efficient manner. This article describes a unique discovery pipeline involving domain antibody (dAb) phage in vivo biopanning and next-generation sequencing (NGS) analysis to identify targeting motifs that recognize distinct aspects of TBI pathology. To demonstrate this process, we conduct in vivo biopanning on the controlled cortical impact mouse model of experimental TBI at 1 and 7 days postinjury. Phage accumulation in target tissues is quantified via titers before NGS preparation and analysis. This phage display biomarker discovery pipeline for TBI successfully achieves discovery of temporally specific TBI targeting motifs and may further TBI biomarker research for other characteristics of injury. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Phage production and purification Support Protocol: Controlled cortical impact model Basic Protocol 2: Injection and elution of phage Basic Protocol 3: Amplicon sequencing and sequence analysis.
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Affiliation(s)
- Briana I Martinez
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona.,School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Sarah E Stabenfeldt
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona
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6
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Banerjee S, Singh A, Rawat J, Bansal N, Maan S. Dataset of next-generation sequence reads of nanobody clones in phage display library derived from Indian desert camel ( Camelus dromedarius L.). Data Brief 2021; 34:106663. [PMID: 33385028 PMCID: PMC7770539 DOI: 10.1016/j.dib.2020.106663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
Next-generation sequences (NGS) dataset of nanobody (Nb) clones in a phage display library (PDL) is of immense value as it serves in many different ways, such as: i). estimating the library size, ii). improving selection and identification of Nbs, iii). informing about frequency of V gene families, diversity and length of CDRs, iv). high resolution analysis of natural and synthetic libraries, etc. [1], [2], [3]. We used a fraction of our previously constructed PDL of Nbs derived from an E. coli lipopolysaccharide-immunized Indian desert camel in order to obtain the dataset of NGS reads of Nbs. The cryo-preserved transformants library was revived to extract the Nb-encoding VHH (inserts)-pHEN4 (vector) DNA pool. The DNA sample was used for amplifying VHH pool by PCR [6]. The VHH amplicons band was gel-purified and subjected to NGS using Illumina MiSeqTM platform. 'Nextra XT micro V2 Index' kit was used for the Nb library DNA sample sequencing, with the adaptors: 'i7' (N706: TAGGCATG) and 'i5' (S517: GCGTAAGA). The raw data comprised of a total read count of 182146 (matched= 179591; unmatched=2555), with average read length of 130.33 bases and a total of 23.74 Mb. Of 179591 matched reads, 142004 were paired reads and 37587 broken paired reads. The raw data of NGS reads was submitted to NCBI Sequence Reads Archive accessible at URL: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516512 (dataset ref. [7]), and after analysis deposited in Mendeley Datasets repository, which is accessible at URL: [https://data.mendeley.com/datasets/4rsz3snvk5/3] (dataset ref. [8]). The sequence reads were analyzed by bioinformatics tools [9], [10], [11], [12]. The assembled consensus contigs revealed Nb orthologs of diverse Ag-specificities, including those isolated by conventional panning and Sanger-sequenced functional Nbs. Contig 1 CDR1-3 matched to those of anti-Trypanosoma evansi RoTat1.2 variant surface glycoprotein (VSG), while Contig 2 CDR1-3 matched to those of anti-LPS Nb clones isolated from the library. Contig 3 was however incomplete and lacked CDR3. Despite lacking the depth, the NGS data is a useful guide for selection of antigen-specific Nbs from the library, as demonstrated by anti-T. evansi VSG Nbs, and provides templates for Nb-based diagnostic reagents and therapeutic agents.
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Affiliation(s)
- Somesh Banerjee
- Immunology Section, Department of Veterinary Microbiology, India
| | - Ajit Singh
- Immunology Section, Department of Veterinary Microbiology, India
| | - Jagveer Rawat
- Immunology Section, Department of Veterinary Microbiology, India
| | - Nitish Bansal
- Department of Veterinary Public Helth & Epidemiology, India
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Sushila Maan
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
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7
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Phage Display for Imaging Agent Development. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00062-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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8
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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: 10] [Impact Index Per Article: 3.3] [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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9
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Tu Z, Huang X, Fu J, Hu N, Zheng W, Li Y, Zhang Y. Landscape of variable domain of heavy-chain-only antibody repertoire from alpaca. Immunology 2020; 161:53-65. [PMID: 32506493 DOI: 10.1111/imm.13224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/05/2023] Open
Abstract
Heavy-chain-only antibodies (HCAbs), which are devoid of light chains, have been found naturally occurring in various species including camelids and cartilaginous fish. Because of their high thermostability, refoldability and capacity for cell permeation, the variable regions of the heavy chain of HCAbs (VHHs) have been widely used in diagnosis, bio-imaging, food safety and therapeutics. Most immunogenetic and functional studies of HCAbs are based on case studies or a limited number of low-throughput sequencing data. A complete picture derived from more abundant high-throughput sequencing (HTS) data can help us gain deeper insights. We cloned and sequenced the full-length coding region of VHHs in Alpaca (Vicugna pacos) via HTS in this study. A new pipeline was developed to conduct an in-depth analysis of the HCAb repertoires. Various critical features, including the length distribution of complementarity-determining region 3 (CDR3), V(D)J usage, VJ pairing, germline-specific mutation rate and germline-specific scoring profiles (GSSPs), were systematically characterized. The quantitative data show that V(D)J usage and VHH recombination are highly biased. Interestingly, we found that the average CDR3 length of classical VHHs is longer than that of non-classical ones, whereas the mutation rates are similar in both kinds of VHHs. Finally, GSSPs were built to quantitatively describe and compare sequences that originate from each VJ pair. Overall, this study presents a comprehensive landscape of the HCAb repertoire, which can provide useful guidance for the modeling of somatic hypermutation and the design of novel functional VHHs or VHH repertoires via evolutionary profiles.
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Affiliation(s)
- Zhui Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jinheng Fu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, China
| | - Na Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China.,Maternal and Child Medical Research Institute, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yanping Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China.,Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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10
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Lin J, Gu Y, Xu Y, Yu J, Tang J, Wu L, Zhou Z, Chen C, Liu M, Chun X, Liu H, Nian R, Song H, Zhang J. Characterization and applications of nanobodies against Pseudomonas aeruginosa Exotoxin A selected from single alpaca B cells. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1817782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Jingtao Lin
- Unit of Clinical Laboratory, Dalang Hospital of Dongguan, Dalang, Dongguan, Guangdong, PR China
| | - Yi Gu
- Shenzhen Innova Nanobodi Co., Ltd, Shenzhen, Guangdong, PR China
| | - Yanru Xu
- Unit of Clinical Laboratory, Dalang Hospital of Dongguan, Dalang, Dongguan, Guangdong, PR China
| | - Jianli Yu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, PR China
| | - Jinsong Tang
- Unit of Clinical Laboratory, Dalang Hospital of Dongguan, Dalang, Dongguan, Guangdong, PR China
| | - Lili Wu
- Unit of Clinical Laboratory, Dalang Hospital of Dongguan, Dalang, Dongguan, Guangdong, PR China
| | - Zhengwei Zhou
- Unit of Clinical Laboratory, Dalang Hospital of Dongguan, Dalang, Dongguan, Guangdong, PR China
| | - Cailing Chen
- Unit of Clinical Laboratory, Dalang Hospital of Dongguan, Dalang, Dongguan, Guangdong, PR China
| | - Minjuan Liu
- Unit of Clinical Laboratory, Dalang Hospital of Dongguan, Dalang, Dongguan, Guangdong, PR China
| | - Xuan Chun
- Unit of Clinical Laboratory, Dalang Hospital of Dongguan, Dalang, Dongguan, Guangdong, PR China
| | - Hongling Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, PR China
| | - Rui Nian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, PR China
| | - Haipeng Song
- Shenzhen Innova Nanobodi Co., Ltd, Shenzhen, Guangdong, PR China
| | - Jing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, PR China
- Laboratory of Biomedical Engineering and Technology, Department of Biochemistry, Qilu Medical University, Zibo, Shandong, PR China
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11
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Canassa-DeLeo T, Campo VL, Rodrigues LC, Marchiori MF, Fuzo C, Brigido MM, Sandomenico A, Ruvo M, Maranhão AQ, Dias-Baruffi M. Multifaceted antibodies development against synthetic α-dystroglycan mucin glycopeptide as promising tools for dystroglycanopathies diagnostic. Glycoconj J 2019; 37:77-93. [PMID: 31823246 DOI: 10.1007/s10719-019-09893-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 01/19/2023]
Abstract
Dystroglycanopathies are diseases characterized by progressive muscular degeneration and impairment of patient's quality of life. They are associated with altered glycosylation of the dystrophin-glycoprotein (DGC) complex components, such as α-dystroglycan (α-DG), fundamental in the structural and functional stability of the muscle fiber. The diagnosis of dystroglycanopathies is currently based on the observation of clinical manifestations, muscle biopsies and enzymatic measures, and the available monoclonal antibodies are not specific for the dystrophic hypoglycosylated muscle condition. Thus, modified α-DG mucins have been considered potential targets for the development of new diagnostic strategies toward these diseases. In this context, this work describes the synthesis of the hypoglycosylated α-DG mimetic glycopeptide NHAc-Gly-Pro-Thr-Val-Thr[αMan]-Ile-Arg-Gly-BSA (1) as a potential tool for the development of novel antibodies applicable to dystroglycanopathies diagnosis. Glycopeptide 1 was used for the development of polyclonal antibodies and recombinant monoclonal antibodies by Phage Display technology. Accordingly, polyclonal antibodies were reactive to glycopeptide 1, which enables the application of anti-glycopeptide 1 antibodies in immune reactive assays targeting hypoglycosylated α-DG. Regarding monoclonal antibodies, for the first time variable heavy (VH) and variable light (VL) immunoglobulin domains were selected by Phage Display, identified by NGS and described by in silico analysis. The best-characterized VH and VL domains were cloned, expressed in E. coli Shuffle T7 cells, and used to construct a single chain fragment variable that recognized the Glycopeptide 1 (GpαDG1 scFv). Molecular modelling of glycopeptide 1 and GpαDG1 scFv suggested that their interaction occurs through hydrogen bonds and hydrophobic contacts involving amino acids from scFv (I51, Y33, S229, Y235, and P233) and R8 and α-mannose from Glycopeptide 1.
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Affiliation(s)
- Thais Canassa-DeLeo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Vanessa Leiria Campo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil.,Centro Universitário Barão de Mauá, Rua Ramos de Azevedo 423, Jardim Paulista, CEP, Ribeirão Preto, 14090-180, SP, Brazil
| | - Lílian Cataldi Rodrigues
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marcelo Fiori Marchiori
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Carlos Fuzo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marcelo Macedo Brigido
- Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, DF, CEP 70910-900, Brazil
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Andrea Queiroz Maranhão
- Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, DF, CEP 70910-900, Brazil
| | - Marcelo Dias-Baruffi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil.
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12
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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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13
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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14
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Martinez BI, Stabenfeldt SE. Current trends in biomarker discovery and analysis tools for traumatic brain injury. J Biol Eng 2019; 13:16. [PMID: 30828380 PMCID: PMC6381710 DOI: 10.1186/s13036-019-0145-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/06/2019] [Indexed: 12/13/2022] Open
Abstract
Traumatic brain injury (TBI) affects 1.7 million people in the United States each year, causing lifelong functional deficits in cognition and behavior. The complex pathophysiology of neural injury is a primary barrier to developing sensitive and specific diagnostic tools, which consequentially has a detrimental effect on treatment regimens. Biomarkers of other diseases (e.g. cancer) have provided critical insight into disease emergence and progression that lend to developing powerful clinical tools for intervention. Therefore, the biomarker discovery field has recently focused on TBI and made substantial advancements to characterize markers with promise of transforming TBI patient diagnostics and care. This review focuses on these key advances in neural injury biomarkers discovery, including novel approaches spanning from omics-based approaches to imaging and machine learning as well as the evolution of established techniques.
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Affiliation(s)
- Briana I. Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- School of Biological and Health Systems Engineering, Ira A. Fulton School of Engineering, Arizona State University, PO Box 879709, Tempe, AZ 85287-9709 USA
| | - Sarah E. Stabenfeldt
- School of Biological and Health Systems Engineering, Ira A. Fulton School of Engineering, Arizona State University, PO Box 879709, Tempe, AZ 85287-9709 USA
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15
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Shriver-Lake LC, Liu JL, Zabetakis D, Sugiharto VA, Lee CR, Defang GN, Wu SJL, Anderson GP, Goldman ER. Selection and Characterization of Anti-Dengue NS1 Single Domain Antibodies. Sci Rep 2018; 8:18086. [PMID: 30591706 PMCID: PMC6308234 DOI: 10.1038/s41598-018-35923-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
Reliable detection and diagnosis of dengue virus (DENV) is important for both patient care and epidemiological control. Starting with a llama immunized with a mixture of recombinant nonstructural protein 1 (NS1) antigen from the four DENV serotypes, a phage display immune library of single domain antibodies was constructed and binders selected which exhibited specificity and affinity for DENV NS1. Each of these single domain antibodies was evaluated for its binding affinity to NS1 from the four serotypes, and incorporated into a sandwich format for NS1 detection. An optimal pair was chosen that provided the best combination of sensitivity for all four DENV NS1 antigens spiked into 50% human serum while showing no cross reactivity to NS1 from Zika virus, yellow fever virus, tick-borne encephalitis virus, and minimal binding to NS1 from Japanese encephalitis virus and West Nile virus. These rugged and robust recombinant binding molecules offer attractive alternatives to conventional antibodies for implementation into immunoassays destined for resource limited locals.
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Affiliation(s)
- Lisa C Shriver-Lake
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Jinny L Liu
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Dan Zabetakis
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Victor A Sugiharto
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Cheng-Rei Lee
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Gabriel N Defang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Shuenn-Jue L Wu
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - George P Anderson
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Ellen R Goldman
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA.
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16
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Challenges in the Structural-Functional Characterization of Multidomain, Partially Disordered Proteins CBP and p300: Preparing Native Proteins and Developing Nanobody Tools. Methods Enzymol 2018; 611:607-675. [PMID: 30471702 DOI: 10.1016/bs.mie.2018.09.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structural and functional characterization of large multidomain signaling proteins containing long disordered linker regions represents special methodological and conceptual challenges. These proteins show extreme structural heterogeneity and have complex posttranslational modification patterns, due to which traditional structural biology techniques provide results that are often difficult to interpret. As demonstrated through the example of two such multidomain proteins, CREB-binding protein (CBP) and its paralogue, p300, even the expression and purification of such proteins are compromised by their extreme proteolytic sensitivity and structural heterogeneity. In this chapter, we describe the effective expression of CBP and p300 in a eukaryotic host, Sf9 insect cells, followed by their tandem affinity purification based on two terminal tags to ensure their structural integrity. The major focus of this chapter is on the development of novel accessory tools, single-domain camelid antibodies (nanobodies), for structural-functional characterization. Specific nanobodies against full-length CBP and p300 can specifically target their different regions and can be used for their marking, labeling, and structural stabilization in a broad range of in vitro and in vivo studies. Here, we describe four high-affinity nanobodies binding to the KIX and the HAT domains, either mimicking known interacting partners or revealing new functionally relevant conformations. As immunization of llamas results in nanobody libraries with a great sequence variation, deep sequencing and interaction analysis with different regions of the proteins provide a novel approach toward developing a panel of specific nanobodies.
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17
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Anti-Drug Antibodies: Emerging Approaches to Predict, Reduce or Reverse Biotherapeutic Immunogenicity. Antibodies (Basel) 2018; 7:antib7020019. [PMID: 31544871 PMCID: PMC6698869 DOI: 10.3390/antib7020019] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
The development of anti-drug antibodies (ADAs) following administration of biotherapeutics to patients is a vexing problem that is attracting increasing attention from pharmaceutical and biotechnology companies. This serious clinical problem is also spawning creative research into novel approaches to predict, avoid, and in some cases even reverse such deleterious immune responses. CD4+ T cells are essential players in the development of most ADAs, while memory B-cell and long-lived plasma cells amplify and maintain these responses. This review summarizes methods to predict and experimentally identify T-cell and B-cell epitopes in therapeutic proteins, with a particular focus on blood coagulation factor VIII (FVIII), whose immunogenicity is clinically significant and is the subject of intensive current research. Methods to phenotype ADA responses in humans are described, including T-cell stimulation assays, and both established and novel approaches to determine the titers, epitopes and isotypes of the ADAs themselves. Although rational protein engineering can reduce the immunogenicity of many biotherapeutics, complementary, novel approaches to induce specific tolerance, especially during initial exposures, are expected to play significant roles in future efforts to reduce or reverse these unwanted immune responses.
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18
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Manjunath GP, Ramanujam PL, Galande S. Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling. J Biosci 2018; 43:155-171. [PMID: 29485124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein scaffolds as essential backbones for organization of supramolecular signalling complexes are a recurrent theme in several model systems. Scaffold proteins preferentially employ linear peptide binding motifs for recruiting their interaction partners. PDZ domains are one of the more commonly encountered peptide binding domains in several proteins including those involved in scaffolding functions. This domain is known for its promiscuity both in terms of ligand selection, mode of interaction with its ligands as well as its association with other protein interaction domains. PDZ domains are subject to several means of regulations by virtue of their functional diversity. Additionally, the PDZ domains are refractive to the effect of mutations and maintain their three-dimensional architecture under extreme mutational load. The biochemical and biophysical basis for this selectivity as well as promiscuity has been investigated and reviewed extensively. The present review focuses on the plasticity inherent in PDZ domains and its implications for modular organization as well as evolution of cellular signalling pathways in higher eukaryotes.
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Affiliation(s)
- G P Manjunath
- Indian Institute of Science Education and Research, Pune 411 008, India
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19
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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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20
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Jara-Acevedo R, Díez P, González-González M, Dégano RM, Ibarrola N, Góngora R, Orfao A, Fuentes M. Screening Phage-Display Antibody Libraries Using Protein Arrays. Methods Mol Biol 2018; 1701:365-380. [PMID: 29116516 DOI: 10.1007/978-1-4939-7447-4_20] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phage-display technology constitutes a powerful tool for the generation of specific antibodies against a predefined antigen. The main advantages of phage-display technology in comparison to conventional hybridoma-based techniques are: (1) rapid generation time and (2) antibody selection against an unlimited number of molecules (biological or not). However, the main bottleneck with phage-display technology is the validation strategies employed to confirm the greatest number of antibody fragments. The development of new high-throughput (HT) techniques has helped overcome this great limitation. Here, we describe a new method based on an array technology that allows the deposition of hundreds to thousands of phages by micro-contact on a unique nitrocellulose surface. This setup comes in combination with bioinformatic approaches that enables simultaneous affinity screening in a HT format of antibody-displaying phages.
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Affiliation(s)
- Ricardo Jara-Acevedo
- ImmunoStep SL. Edificio Centro de Investigación del Cáncer. Avda. Coimbra s/n, 37007, Salamanca, Spain
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - María González-González
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Rosa María Dégano
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain.
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain.
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21
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Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling. J Biosci 2017. [DOI: 10.1007/s12038-017-9727-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Liu JL, Shriver-Lake LC, Anderson GP, Zabetakis D, Goldman ER. Selection, characterization, and thermal stabilization of llama single domain antibodies towards Ebola virus glycoprotein. Microb Cell Fact 2017; 16:223. [PMID: 29233140 PMCID: PMC5726015 DOI: 10.1186/s12934-017-0837-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/28/2017] [Indexed: 12/26/2022] Open
Abstract
Background A key advantage of recombinant antibody technology is the ability to optimize and tailor reagents. Single domain antibodies (sdAbs), the recombinantly produced variable domains derived from camelid and shark heavy chain antibodies, provide advantages of stability and solubility and can be further engineered to enhance their properties. In this study, we generated sdAbs specific for Ebola virus envelope glycoprotein (GP) and increased their stability to expand their utility for use in austere locals. Ebola virus is extremely virulent and causes fatal hemorrhagic fever in ~ 50 percent of the cases. The viral GP binds to host cell receptors to facilitate viral entry and thus plays a critical role in pathogenicity. Results An immune phage display library containing more than 107 unique clones was developed from a llama immunized with a combination of killed Ebola virus and recombinantly produced GP. We panned the library to obtain GP binding sdAbs and isolated sdAbs from 5 distinct sequence families. Three GP binders with dissociation constants ranging from ~ 2 to 20 nM, and melting temperatures from ~ 57 to 72 °C were selected for protein engineering in order to increase their stability through a combination of consensus sequence mutagenesis and the addition of a non-canonical disulfide bond. These changes served to increase the melting temperatures of the sdAbs by 15–17 °C. In addition, fusion of a short positively charged tail to the C-terminus which provided ideal sites for the chemical modification of these sdAbs resulted in improved limits of detection of GP and Ebola virus like particles while serving as tracer antibodies. Conclusions SdAbs specific for Ebola GP were selected and their stability and functionality were improved utilizing protein engineering. Thermal stability of antibody reagents may be of particular importance when operating in austere locations that lack reliable refrigeration. Future efforts can evaluate the potential of these isolated sdAbs as candidates for diagnostic or therapeutic applications for Ebola. Electronic supplementary material The online version of this article (10.1186/s12934-017-0837-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinny L Liu
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Lisa C Shriver-Lake
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - George P Anderson
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Dan Zabetakis
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Ellen R Goldman
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA.
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23
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Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology 2017; 153:31-41. [PMID: 28898398 DOI: 10.1111/imm.12838] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high-throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high-throughput sequencing has made it possible to obtain large-scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high-throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high-throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Life Science Zurich Graduate School, Systems Biology, ETH Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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24
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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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25
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Strategies to Obtain Diverse and Specific Human Monoclonal Antibodies From Transgenic Animals. Transplantation 2017; 101:1770-1776. [DOI: 10.1097/tp.0000000000001702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Deschaght P, Vintém AP, Logghe M, Conde M, Felix D, Mensink R, Gonçalves J, Audiens J, Bruynooghe Y, Figueiredo R, Ramos D, Tanghe R, Teixeira D, Van de Ven L, Stortelers C, Dombrecht B. Large Diversity of Functional Nanobodies from a Camelid Immune Library Revealed by an Alternative Analysis of Next-Generation Sequencing Data. Front Immunol 2017; 8:420. [PMID: 28443097 PMCID: PMC5385344 DOI: 10.3389/fimmu.2017.00420] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/24/2017] [Indexed: 12/21/2022] Open
Abstract
Next-generation sequencing (NGS) has been applied successfully to the field of therapeutic antibody discovery, often outperforming conventional screening campaigns which tend to identify only the more abundant selective antibody sequences. We used NGS to mine the functional nanobody repertoire from a phage-displayed camelid immune library directed to the recepteur d’origine nantais (RON) receptor kinase. Challenges to this application of NGS include accurate removal of read errors, correct identification of related sequences, and establishing meaningful inclusion criteria for sequences-of-interest. To this end, a sequence identity threshold was defined to separate unrelated full-length sequence clusters by exploring a large diverse set of publicly available nanobody sequences. When combined with majority-rule consensus building, applying this elegant clustering approach to the NGS data set revealed a wealth of >5,000-enriched candidate RON binders. The huge binding potential predicted by the NGS approach was explored through a set of randomly selected candidates: 90% were confirmed as RON binders, 50% of which functionally blocked RON in an ERK phosphorylation assay. Additional validation came from the correct prediction of all 35 RON binding nanobodies which were identified by a conventional screening campaign of the same immune library. More detailed characterization of a subset of RON binders revealed excellent functional potencies and a promising epitope diversity. In summary, our approach exposes the functional diversity and quality of the outbred camelid heavy chain-only immune response and confirms the power of NGS to identify large numbers of promising nanobodies.
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27
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Yang W, Yoon A, Lee S, Kim S, Han J, Chung J. Next-generation sequencing enables the discovery of more diverse positive clones from a phage-displayed antibody library. Exp Mol Med 2017; 49:e308. [PMID: 28336957 PMCID: PMC5382563 DOI: 10.1038/emm.2017.22] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 12/19/2022] Open
Abstract
Phage display technology provides a powerful tool to screen a library for a binding molecule via an enrichment process. It has been adopted as a critical technology in the development of therapeutic antibodies. However, a major drawback of phage display technology is that because the degree of the enrichment cannot be controlled during the bio-panning process, it frequently results in a limited number of clones. In this study, we applied next-generation sequencing (NGS) to screen clones from a library and determine whether a greater number of clones can be identified using NGS than using conventional methods. Three chicken immune single-chain variable fragment (scFv) libraries were subjected to bio-panning on prostate-specific antigen (PSA). Phagemid DNA prepared from the original libraries as well as from the Escherichia coli pool after each round of bio-panning was analyzed using NGS, and the heavy chain complementarity-determining region 3 (HCDR3) sequences of the scFv clones were determined. Subsequently, through two-step linker PCR and cloning, the entire scFv gene was retrieved and analyzed for its reactivity to PSA in a phage enzyme immunoassay. After four rounds of bio-panning, the conventional colony screening method was performed for comparison. The scFv clones retrieved from NGS analysis included all clones identified by the conventional colony screening method as well as many additional clones. The enrichment of the HCDR3 sequence throughout the bio-panning process was a positive predictive factor for the selection of PSA-reactive scFv clones.
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Affiliation(s)
- Wonjun Yang
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea.,Department of Cancer Biology, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Aerin Yoon
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sanghoon Lee
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Soohyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea.,Department of Cancer Biology, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Jungwon Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea.,Department of Cancer Biology, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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Lopez T, Nam DH, Kaihara E, Mustafa Z, Ge X. Identification of highly selective MMP-14 inhibitory Fabs by deep sequencing. Biotechnol Bioeng 2017; 114:1140-1150. [PMID: 28090632 DOI: 10.1002/bit.26248] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/02/2017] [Accepted: 01/08/2017] [Indexed: 02/01/2023]
Abstract
Matrix metalloproteinase (MMP)-14 is an important target for cancer treatment due to its critical roles in tumor invasion and metastasis. Previous failures of all compound-based broad-spectrum MMP inhibitors in clinical trials suggest that selectivity is the key for a successful therapy. With inherent high specificity, monoclonal antibodies (mAbs) therefore arise as attractive inhibitors able to target the particular MMP of interest. As a routine screening method, enzyme-linked immunosorbent assays (ELISA) have been applied to panned phage libraries for the isolation of mAbs inhibiting MMP-14. However, because of suboptimal growth conditions and insufficient antibody expression associated with monoclonal ELISA, a considerable number of potentially inhibitory clones might not be identified. Taking advantage of next-generation sequencing (NGS), we monitored enrichment profiles of millions of antibody clones along three rounds of phage panning, and identified 20 Fab inhibitors of MMP-14 with inhibition IC50 values of 10-4,000 nM. Among these inhibitory Fabs, 15 were not found by monoclonal phage ELISA. Particularly, Fab R2C7 exhibited an inhibition potency of 100 nM with an excellent selectivity to MMP-14 over MMP-9. Inhibition kinetics and epitope mapping suggested that as a competitive inhibitor, R2C7 directly bound to the vicinity of the MMP-14 catalytic site. This study demonstrates that deep sequencing is a powerful tool to facilitate the systematic discovery of mAbs with protease inhibition functions. Biotechnol. Bioeng. 2017;114: 1140-1150. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Tyler Lopez
- Department of Chemical and Environmental Engineering, University of California, 900 University Ave, Riverside, California 92521
| | - Dong Hyun Nam
- Department of Chemical and Environmental Engineering, University of California, 900 University Ave, Riverside, California 92521
| | - Evan Kaihara
- Department of Chemical and Environmental Engineering, University of California, 900 University Ave, Riverside, California 92521
| | - Zahid Mustafa
- Department of Chemical and Environmental Engineering, University of California, 900 University Ave, Riverside, California 92521
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California, 900 University Ave, Riverside, California 92521
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