1
|
Verma S, Dufort MJ, Olsen TM, Kimmel S, Labuda JC, Scharffenberger S, McGuire AT, Harrison OJ. Antigen-level resolution of commensal-specific B cell responses can be enabled by phage display screening coupled with B cell tetramers. Immunity 2024; 57:1428-1441.e8. [PMID: 38723638 PMCID: PMC11168869 DOI: 10.1016/j.immuni.2024.04.014] [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: 10/12/2023] [Revised: 02/07/2024] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
Induction of commensal-specific immunity contributes to tissue homeostasis, yet the mechanisms underlying induction of commensal-specific B cells remain poorly understood in part due to a lack of tools to identify these cells. Using phage display, we identified segmented filamentous bacteria (SFB) antigens targeted by serum and intestinal antibodies and generated B cell tetramers to track SFB-specific B cells in gut-associated lymphoid tissues. We revealed a compartmentalized response in SFB-specific B cell activation, with a gradient of immunoglobulin A (IgA), IgG1, and IgG2b isotype production along Peyer's patches contrasted by selective production of IgG2b within mesenteric lymph nodes. V(D)J sequencing and monoclonal antibody generation identified somatic hypermutation driven affinity maturation to SFB antigens under homeostatic conditions. Combining phage display and B cell tetramers will enable investigation of the ontogeny and function of commensal-specific B cell responses in tissue immunity, inflammation, and repair.
Collapse
Affiliation(s)
- Sheenam Verma
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Matthew J Dufort
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Tayla M Olsen
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Samantha Kimmel
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Jasmine C Labuda
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Sam Scharffenberger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Oliver J Harrison
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Immunology, University of Washington, Seattle, WA, USA.
| |
Collapse
|
2
|
Steinke S, Roth KDR, Englick R, Langreder N, Ballmann R, Fühner V, Zilkens KJK, Moreira GMSG, Koch A, Azzali F, Russo G, Schubert M, Bertoglio F, Heine PA, Hust M. Mapping Epitopes by Phage Display. Methods Mol Biol 2023; 2702:563-585. [PMID: 37679639 DOI: 10.1007/978-1-0716-3381-6_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Monoclonal antibodies (mAbs) are valuable biological molecules, serving for many applications. Therefore, it is advantageous to know the interaction pattern between antibodies and their antigens. Regions on the antigen which are recognized by the antibodies are called epitopes, and the respective molecular counterpart of the epitope on the mAbs is called paratope. These epitopes can have many different compositions and/or structures. Knowing the epitope is a valuable information for the development or improvement of biological products, e.g., diagnostic assays, therapeutic mAbs, and vaccines, as well as for the elucidation of immune responses. Most of the techniques for epitope mapping rely on the presentation of the target, or parts of it, in a way that it can interact with a certain mAb. Among the techniques used for epitope mapping, phage display is a versatile technology that allows the display of a library of oligopeptides or fragments from a single gene product on the phage surface, which then can interact with several antibodies to define epitopes. In this chapter, a protocol for the construction of a single-target oligopeptide phage library, as well as for the panning procedure for epitope mapping using phage display is given.
Collapse
Affiliation(s)
- Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ruben Englick
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Gustavo Marçal Schmidt Garcia Moreira
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Sector for Antibody and Protein Biochemistry, Tacalyx GmbH, Berlin, Germany
| | - Allan Koch
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Innovationszentrum Niedersachsen GmbH, startup.niedersachsen, Hannover, Germany
| | - Filippo Azzali
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
| |
Collapse
|
3
|
Heine PA, Ballmann R, Thevarajah P, Russo G, Moreira GMSG, Hust M. Biomarker Discovery by ORFeome Phage Display. Methods Mol Biol 2023; 2702:543-561. [PMID: 37679638 DOI: 10.1007/978-1-0716-3381-6_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Phage display is an efficient and robust method for protein-protein interaction studies. Although it is mostly used for antibody generation, it can be also utilized for the discovery of immunogenic proteins that could be used as biomarkers. Through this technique, a genome or metagenome is fragmented and cloned into a phagemid vector. The resulting protein fragments from this genetic material are displayed on M13 phage surface, while the corresponding gene fragments are packaged. This packaging process uses the pIII deficient helperphage, called Hyperphage (M13KO7 ΔpIII), so open reading frames (ORFs) are enriched in these libraries, giving the name to this method: ORFeome phage display. After conducting a selection procedure, called "bio-panning," relevant immunogenic peptides or protein fragments are selected using purified antibodies or serum samples, and can be used as potential biomarkers. As ORFeome phage display is an in vitro method, only the DNA or cDNA of the species of interest is needed. Therefore, this approach is also suitable for organisms that are hard to cultivate, or metagenomic samples, for example. An additional advantage is that the biomarker discovery is not limited to surface proteins due to the presentation of virtually every kind of peptide or protein fragment encoded by the ORFeome on the phage surface. At last, the selected biomarkers can be the start for the development of diagnostic assays, vaccines, or protein interaction studies.
Collapse
Affiliation(s)
- Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Praveen Thevarajah
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Gustavo Marçal Schmidt Garcia Moreira
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Tacalyx GmbH, Sector for Antibody and Protein Biochemistry, Berlin, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
| |
Collapse
|
4
|
Ballmann R, Hotop SK, Bertoglio F, Steinke S, Heine PA, Chaudhry MZ, Jahn D, Pucker B, Baldanti F, Piralla A, Schubert M, Čičin-Šain L, Brönstrup M, Hust M, Dübel S. ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein. Viruses 2022; 14:1326. [PMID: 35746797 PMCID: PMC9229677 DOI: 10.3390/v14061326] [Citation(s) in RCA: 4] [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: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of the spike, and therefore lose neutralization efficacy against emerging SARS-CoV-2 variants, which frequently mutate in the RBD region. Previously, phage display has been used to identify epitopes of antibody responses against several diseases. Such epitopes have been applied to design vaccines or neutralize antibodies. Here, we constructed an ORFeome phage display library for the SARS-CoV-2 genome. Open reading frames (ORFs) representing the SARS-CoV-2 genome were displayed on the surface of phage particles in order to identify enriched immunogenic epitopes from COVID-19 patients. Library quality was assessed by both NGS and epitope mapping of a monoclonal antibody with a known binding site. The most prominent epitope captured represented parts of the fusion peptide (FP) of the spike. It is associated with the cell entry mechanism of SARS-CoV-2 into the host cell; the serine protease TMPRSS2 cleaves the spike within this sequence. Blocking this mechanism could be a potential target for non-RBD binding therapeutic anti-SARS-CoV-2 antibodies. As mutations within the FP amino acid sequence have been rather rare among SARS-CoV-2 variants so far, this may provide an advantage in the fight against future virus variants.
Collapse
Affiliation(s)
- Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Sven-Kevin Hotop
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - M. Zeeshan Chaudhry
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany;
| | - Boas Pucker
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstr 1, 38106 Braunschweig, Germany;
| | - Fausto Baldanti
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy;
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Fondazione Policlinico, 27100 Pavia, Italy;
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Fondazione Policlinico, 27100 Pavia, Italy;
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Luka Čičin-Šain
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| |
Collapse
|
5
|
Puccio S, Grillo G, Consiglio A, Soluri MF, Sblattero D, Cotella D, Santoro C, Liuni S, Bellis GD, Lugli E, Peano C, Licciulli F. InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data. Nucleic Acids Res 2020; 48:W200-W207. [PMID: 32402076 PMCID: PMC7319578 DOI: 10.1093/nar/gkaa363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 01/03/2023] Open
Abstract
High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the 'interactome sequencing' approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains ('domainome') or epitopes ('epitome') from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https://InteractomeSeq.ba.itb.cnr.it/.
Collapse
Affiliation(s)
- Simone Puccio
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan), 20089, Italy
| | - Giorgio Grillo
- Institute for Biomedical Technologies, National Research Council, Bari 70100, Italy
| | - Arianna Consiglio
- Institute for Biomedical Technologies, National Research Council, Bari 70100, Italy
| | - Maria Felicia Soluri
- Department of Health Sciences & Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara 28100, Italy
| | - Daniele Sblattero
- Department of Life Sciences, University of Trieste, Trieste 34100, Italy
| | - Diego Cotella
- Department of Health Sciences & Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara 28100, Italy
| | - Claudio Santoro
- Department of Health Sciences & Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara 28100, Italy
| | - Sabino Liuni
- Institute for Biomedical Technologies, National Research Council, Bari 70100, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, Segrate (Milan) 20090, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan), 20089, Italy.,Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan) 20089, Italy
| | - Clelia Peano
- Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano (Milan) 20089, Italy.,Genomic Unit, Humanitas Clinical and Research Center, IRCCS,Rozzano (Milan) 20089, Italy
| | - Flavio Licciulli
- Institute for Biomedical Technologies, National Research Council, Bari 70100, Italy
| |
Collapse
|
6
|
Pyruvate dehydrogenase complex-enzyme 2, a new target for Listeria spp. detection identified using combined phage display technologies. Sci Rep 2020; 10:15267. [PMID: 32943681 PMCID: PMC7498459 DOI: 10.1038/s41598-020-72159-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
The genus Listeria comprises ubiquitous bacteria, commonly present in foods and food production facilities. In this study, three different phage display technologies were employed to discover targets, and to generate and characterize novel antibodies against Listeria: antibody display for biomarker discovery and antibody generation; ORFeome display for target identification; and single-gene display for epitope characterization. With this approach, pyruvate dehydrogenase complex—enzyme 2 (PDC-E2) was defined as a new detection target for Listeria, as confirmed by immunomagnetic separation-mass spectrometry (IMS-MS). Immunoblot and fluorescence microscopy showed that this protein is accessible on the bacterial cell surface of living cells. Recombinant PDC-E2 was produced in E. coli and used to generate 16 additional antibodies. The resulting set of 20 monoclonal scFv-Fc was tested in indirect ELISA against 17 Listeria and 16 non-Listeria species. Two of them provided 100% sensitivity (CI 82.35–100.0%) and specificity (CI 78.20–100.0%), confirming PDC-E2 as a suitable target for the detection of Listeria. The binding region of 18 of these antibodies was analyzed, revealing that ≈ 90% (16/18) bind to the lipoyl domains (LD) of the target. The novel target PDC-E2 and highly specific antibodies against it offer new opportunities to improve the detection of Listeria.
Collapse
|
7
|
Verma V, Joshi G, Gupta A, Chaudhary VK. An efficient ORF selection system for DNA fragment libraries based on split beta-lactamase complementation. PLoS One 2020; 15:e0235853. [PMID: 32701967 PMCID: PMC7377443 DOI: 10.1371/journal.pone.0235853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/23/2020] [Indexed: 11/29/2022] Open
Abstract
PCR-based amplification of annotated genes has allowed construction of expression clones at genome-scale using classical and recombination-based cloning technologies. However, genome-scale expression and purification of proteins for down-stream applications is often limited by challenges such as poor expression, low solubility, large size of multi-domain proteins, etc. Alternatively, DNA fragment libraries in expression vectors can serve as the source of protein fragments with each fragment encompassing a function of its whole protein counterpart. However, the random DNA fragmentation and cloning result in only 1 out of 18 clones being in the correct open-reading frame (ORF), thus, reducing the overall efficiency of the system. This necessitates the selection of correct ORF before expressing the protein fragments. This paper describes a highly efficient ORF selection system for DNA fragment libraries, which is based on split beta-lactamase protein fragment complementation. The system has been designed to allow seamless transfer of selected DNA fragment libraries into any downstream vector systems using a restriction enzyme-free cloning strategy. The strategy has been applied for the selection of ORF using model constructs to show near 100% selection of the clone encoding correct ORF. The system has been further validated by construction of an ORF-selected DNA fragment library of 30 genes of M. tuberculosis. Further, we have successfully demonstrated the cytosolic expression of ORF-selected protein fragments in E. coli.
Collapse
Affiliation(s)
- Vaishali Verma
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Gopal Joshi
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Amita Gupta
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Vijay K. Chaudhary
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- * E-mail:
| |
Collapse
|
8
|
Kopertekh L, Meyer T, Freyer C, Hust M. Transient plant production of Salmonella Typhimurium diagnostic antibodies. ACTA ACUST UNITED AC 2019; 21:e00314. [PMID: 30847285 PMCID: PMC6389800 DOI: 10.1016/j.btre.2019.e00314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 12/16/2022]
Abstract
Salmonella Typhimurium is one of the most important zoonotic pathogens worldwide and a major cause of economic losses in the pig production chain. The emergence of multi-drug resistant strains over the past years has led to considerations about an enhanced surveillance of bacterial food contamination. Currently, ELISA is the method of choice for high throughput identification of S. Typhimurium. The sensitivity and specificity of this assay might be improved by application of new diagnostic antibodies. We focused on plant-based expression of candidate diagnostic TM43-E10 antibodies discovered using as antigen the S. Typhimurium OmpD protein. The scFv-TM43-E10 and scFv-Fc-TM43-E10 antibody derivatives have been successfully produced in N. benthamiana using a deconstructed movement-deficient PVX vector supplemented with the γb silencing suppressor from Poa semilatent virus. The plant-made antibodies showed the same antigen-binding specificity as that of the microbial/mammalian cell-produced counterparts and could recognize the OmpD antigen in S. Typhimurium infected plant samples.
Collapse
Affiliation(s)
- Lilya Kopertekh
- Julius Kühn-Institut, Bundesforschungsinstitut für Kulturpflanzen, Institut für die Sicherheit biotechnologischer Verfahren bei Pflanzen, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
- Corresponding author.
| | - Torsten Meyer
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Cornelia Freyer
- Julius Kühn-Institut, Bundesforschungsinstitut für Kulturpflanzen, Institut für die Sicherheit biotechnologischer Verfahren bei Pflanzen, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr. 7, 38106, Braunschweig, Germany
| |
Collapse
|
9
|
Ramli SR, Moreira GMSG, Zantow J, Goris MGA, Nguyen VK, Novoselova N, Pessler F, Hust M. Discovery of Leptospira spp. seroreactive peptides using ORFeome phage display. PLoS Negl Trop Dis 2019; 13:e0007131. [PMID: 30677033 PMCID: PMC6363232 DOI: 10.1371/journal.pntd.0007131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/05/2019] [Accepted: 01/05/2019] [Indexed: 12/12/2022] Open
Abstract
Background Leptospirosis is the most common zoonotic disease worldwide. The diagnostic performance of a serological test for human leptospirosis is mainly influenced by the antigen used in the test assay. An ideal serological test should cover all serovars of pathogenic leptospires with high sensitivity and specificity and use reagents that are relatively inexpensive to produce and can be used in tropical climates. Peptide-based tests fulfil at least the latter two requirements, and ORFeome phage display has been successfully used to identify immunogenic peptides from other pathogens. Methodology/Principal findings Two ORFeome phage display libraries of the entire Leptospira spp. genomes from five local strains isolated in Malaysia and seven WHO reference strains were constructed. Subsequently, 18 unique Leptospira peptides were identified in a screen using a pool of sera from patients with acute leptospirosis. Five of these were validated by titration ELISA using different pools of patient or control sera. The diagnostic performance of these five peptides was then assessed against 16 individual sera from patients with acute leptospirosis and 16 healthy donors and was compared to that of two recombinant reference proteins from L. interrogans. This analysis revealed two peptides (SIR16-D1 and SIR16-H1) from the local isolates with good accuracy for the detection of acute leptospirosis (area under the ROC curve: 0.86 and 0.78, respectively; sensitivity: 0.88 and 0.94; specificity: 0.81 and 0.69), which was close to that of the reference proteins LipL32 and Loa22 (area under the ROC curve: 0.91 and 0.80; sensitivity: 0.94 and 0.81; specificity: 0.75 and 0.75). Conclusions/Significance This analysis lends further support for using ORFeome phage display to identify pathogen-associated immunogenic peptides, and it suggests that this technique holds promise for the development of peptide-based diagnostics for leptospirosis and, possibly, of vaccines against this pathogen. Leptospirosis is an infectious disease that is transmitted from animals to humans. It is associated with a broad range of clinical presentations, and diagnostic tests with high diagnostic accuracy are required in order to enable accurate diagnosis. Leptospirosis is diagnosed by detecting DNA of the pathogen or antibodies against it in patients’ blood; the latter are preferred in resource limited regions, and diagnostics based on peptides (small fragments of proteins) are advantageous because they are inexpensive to produce and more stable in hot climates than full-length proteins. We used a technique called open reading frame phage display to identify peptides from Leptospira spp. that could be used to detect antibodies against them in human blood. In this method, the pathogen’s genome is fragmented, the corresponding peptides displayed on the surfaces of phages (viruses that infect bacteria), and the peptides that bind most strongly to the patients’ antibodies are then selected by screening. Using this method, we identified 2 leptospiral peptides that accurately identified antibodies against Leptospira spp. in sera from patients with leptospirosis. These results are encouraging because they demonstrate that ORFeome phage display may be a powerful tool to develop better diagnostics for leptospirosis for use in less developed areas.
Collapse
Affiliation(s)
- Siti Roszilawati Ramli
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Braunschweig University of Technology, Braunschweig, Germany
- Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Gustavo M. S. G. Moreira
- Institute for Biochemistry, Biotechnology and Bioinformatics, Braunschweig University of Technology, Braunschweig, Germany
| | - Jonas Zantow
- Institute for Biochemistry, Biotechnology and Bioinformatics, Braunschweig University of Technology, Braunschweig, Germany
| | - Marga G. A. Goris
- OIE and National Collaborating Centre for Reference and Research on Leptospirosis Academic Medical Center, Department of Medical Microbiology, University of Amsterdam, Amsterdam, the Netherlands
| | - Van Kinh Nguyen
- Research Group Biomarkers for Infectious Diseases, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany
| | - Natalia Novoselova
- Research Group Biomarkers for Infectious Diseases, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Frank Pessler
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany
- * E-mail: (FP); (MH)
| | - Michael Hust
- Institute for Biochemistry, Biotechnology and Bioinformatics, Braunschweig University of Technology, Braunschweig, Germany
- * E-mail: (FP); (MH)
| |
Collapse
|
10
|
Fühner V, Heine PA, Zilkens KJC, Meier D, Roth KDR, Moreira GMSG, Hust M, Russo G. Epitope Mapping via Phage Display from Single-Gene Libraries. Methods Mol Biol 2019; 1904:353-375. [PMID: 30539480 DOI: 10.1007/978-1-4939-8958-4_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Antibodies are widely used in a large variety of research applications, for diagnostics and therapy of numerous diseases, primarily cancer and autoimmune diseases. Antibodies are binding specifically to target structures (antigens). The antigen-binding properties are not only dependent on the antibody sequence, but also on the discrete antigen region recognized by the antibody (epitope). Knowing the epitope is valuable information for the improvement of diagnostic assays or therapeutic antibodies, as well as to understand the immune response of a vaccine. While huge progress has been made in the pipelines for the generation and functional characterization of antibodies, the available technologies for epitope mapping are still lacking effectiveness in terms of time and effort. Also, no technique available offers the absolute guarantee of succeeding. Thus, research to develop and improve epitope mapping techniques is still an active field. Phage display from random peptide libraries or single-gene libraries are currently among the most exploited methods for epitope mapping. The first is based on the generation of mimotopes and it is fastened to the need of high-throughput sequencing and complex bioinformatic analysis. The second provides original epitope sequences without requiring complex analysis or expensive techniques, but depends on further investigation to define the functional amino acids within the epitope. In this book chapter, we describe how to perform epitope mapping by antigen fragment phage display from single-gene antigen libraries and how to construct these types of libraries. Thus, we also provide figures and analysis to demonstrate the actual potential of this technique and to prove the necessity of certain procedural steps.
Collapse
Affiliation(s)
- Viola Fühner
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Philip Alexander Heine
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Doris Meier
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany.
| | - Giulio Russo
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
11
|
Abstract
Among the molecules of the immune system, antibodies, particularly monoclonal antibodies (mAbs), have been shown to be interesting for many biological applications. Due to their ability to recognize only a unique part of their target, mAbs are usually very specific. These targets can have many different compositions, but the most common ones are proteins or peptides that are usually from outside the host, although self-proteins can also be targeted in autoimmune diseases, or in some types of cancer. The parts of a mAb that interact with its target compose the paratope, while the recognized parts of the target compose the epitope. Knowing the epitope is valuable for the improvement of a biological product, e.g., a diagnostic assay, a therapeutic mAb, or a vaccine, as well as for the elucidation of immune responses. The current techniques for epitope mapping rely on the presentation of the target, or parts of it, in a way that it can interact with a certain mAb. Even though there are several techniques available, each has its pros and cons. Thus, the choice for one of them is usually dependent on the preference and availability of the researcher, opening possibility for improvement, or development of alternative techniques. Phage display, for example, is a versatile technology, which allows the presentation of many different oligopeptides that can be tested against different antibodies, fitting the need for an epitope mapping approach. In this chapter, a protocol for the construction of a single-target oligopeptide phage library, as well as for the panning procedure for epitope mapping using phage display is given.
Collapse
Affiliation(s)
| | - Viola Fühner
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany.
| |
Collapse
|
12
|
Abstract
ORFeome phage display allows the efficient functional screening of entire proteomes or even metaproteomes to identify immunogenic proteins. For this purpose, randomly fragmented, whole genomes or metagenomes are cloned into a phage-display vector allowing positive selection for open reading frames (ORF) to improve the library quality. These libraries display all possible proteins encoded by a pathogen or a microbiome on the phage surface. Consequently, immunogenic proteins can be selected from these libraries using disease-related immunoglobulins from patient serum. ORFeome phage display in particular allows the identification of immunogenic proteins that are only expressed in the host-pathogen interaction but not in cultivation, as well as the detection of very low expressed and very small immunogens and immunogenic proteins of non-cultivable organisms. The identified immunogenic proteins are potential biomarkers for the development of diagnostic assays or vaccines. These articles will give an introduction to ORFeome phage-display technology and give detailed protocols to identify immunogenic proteins by phage display.
Collapse
Affiliation(s)
- Jonas Zantow
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | | | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany.
| |
Collapse
|
13
|
Høydahl LS, Nilssen NR, Gunnarsen KS, Pré MFD, Iversen R, Roos N, Chen X, Michaelsen TE, Sollid LM, Sandlie I, Løset GÅ. Multivalent pIX phage display selects for distinct and improved antibody properties. Sci Rep 2016; 6:39066. [PMID: 27966617 PMCID: PMC5155289 DOI: 10.1038/srep39066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022] Open
Abstract
Phage display screening readily allows for the identification of a multitude of antibody specificities, but to identify optimal lead candidates remains a challenge. Here, we direct the antibody-capsid fusion away from the signal sequence-dependent secretory SEC pathway in E. coli by utilizing the intrinsic signal sequence-independent property of pIX to obtain virion integration. This approach was combined with the use of an engineered helper phage known to improve antibody pIX display and retrieval. By direct comparison with pIII display, we demonstrate that antibody display using this pIX system translates into substantially improved retrieval of desired specificities with favorable biophysical properties in de novo selection. We show that the effect was due to less E. coli host toxicity during phage propagation conferred by the lack of a signal sequence. This pIX combinatorial display platform provides a generic alternative route for obtaining good binders with high stability and may thus find broad applicability.
Collapse
Affiliation(s)
- Lene S Høydahl
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway.,Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Nicolay R Nilssen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway.,Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Kristin S Gunnarsen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - M Fleur du Pré
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Rasmus Iversen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Norbert Roos
- Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Xi Chen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Terje E Michaelsen
- Department of Immunology, Norwegian Institute of Public Health, N-0403 Oslo, Norway.,School of Pharmacy, University of Oslo, N-0316 Oslo, Norway
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre and Department of Immunology, University of Oslo, N-0372 Oslo, Norway
| | - Inger Sandlie
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway.,Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Geir Å Løset
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway.,Department of Biosciences, University of Oslo, N-0316 Oslo, Norway.,Nextera AS, N-0349 Oslo, Norway
| |
Collapse
|
14
|
Zantow J, Just S, Lagkouvardos I, Kisling S, Dübel S, Lepage P, Clavel T, Hust M. Mining gut microbiome oligopeptides by functional metaproteome display. Sci Rep 2016; 6:34337. [PMID: 27703179 PMCID: PMC5050496 DOI: 10.1038/srep34337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/12/2016] [Indexed: 12/25/2022] Open
Abstract
Pathogen infections, autoimmune diseases, and chronic inflammatory disorders are associated with systemic antibody responses from the host immune system. Disease-specific antibodies can be important serum biomarkers, but the identification of antigens associated with specific immune reactions is challenging, in particular if complex communities of microorganisms are involved in the disease progression. Despite promising new diagnostic opportunities, the discovery of these serological markers becomes more difficult with increasing complexity of microbial communities. In the present work, we used a metagenomic M13 phage display approach to select immunogenic oligopeptides from the gut microbiome of transgenic mice suffering from chronic ileitis. We constructed three individual metaproteome phage display libraries with a library size of approximately 107 clones each. Using serum antibodies, we selected and validated three oligopeptides that induced specific antibody responses in the mouse model. This proof-of-concept study provides the first successful application of functional metaproteome display for the study of protein-protein interactions and the discovery of potential disease biomarkers.
Collapse
Affiliation(s)
- Jonas Zantow
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics - Department for Biotechnology, Germany
| | - Sarah Just
- Technische Universität München, ZIEL Institute for Food and Health, Freising, Germany
| | - Ilias Lagkouvardos
- Technische Universität München, ZIEL Institute for Food and Health, Freising, Germany
| | - Sigrid Kisling
- Technische Universität München, ZIEL Institute for Food and Health, Freising, Germany
| | - Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics - Department for Biotechnology, Germany
| | - Patricia Lepage
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Thomas Clavel
- Technische Universität München, ZIEL Institute for Food and Health, Freising, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics - Department for Biotechnology, Germany
| |
Collapse
|
15
|
Vandormael P, Verschueren P, De Winter L, Somers V. cDNA phage display for the discovery of theranostic autoantibodies in rheumatoid arthritis. Immunol Res 2016; 65:307-325. [DOI: 10.1007/s12026-016-8839-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
16
|
Fructose 1,6-Bisphosphate Aldolase, a Novel Immunogenic Surface Protein on Listeria Species. PLoS One 2016; 11:e0160544. [PMID: 27489951 PMCID: PMC4973958 DOI: 10.1371/journal.pone.0160544] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 07/21/2016] [Indexed: 12/12/2022] Open
Abstract
Listeria monocytogenes is a ubiquitous food-borne pathogen, and its presence in food or production facilities highlights the importance of surveillance. Increased understanding of the surface exposed antigens on Listeria would provide potential diagnostic and therapeutic targets. In the present work, using mass spectrometry and genetic cloning, we show that fructose-1,6-bisphosphate aldolase (FBA) class II in Listeria species is the antigen target of the previously described mAb-3F8. Western and dot blot assays confirmed that the mAb-3F8 could distinguish all tested Listeria species from close-related bacteria. Localization studies indicated that FBA is present in every fraction of Listeria cells, including supernatant and the cell wall, setting Listeria spp. as one of the few bacteria described to have this protein on their cell surface. Epitope mapping using ORFeome display and a peptide membrane revealed a 14-amino acid peptide as the potential mAb-3F8 epitope. The target epitope in FBA allowed distinguishing Listeria spp. from closely-related bacteria, and was identified as part of the active site in the dimeric enzyme. However, its function in cell surface seems not to be host cell adhesion-related. Western and dot blot assays further demonstrated that mAb-3F8 together with anti-InlA mAb-2D12 could differentiate pathogenic from non-pathogenic Listeria isolated from artificially contaminated cheese. In summary, we report FBA as a novel immunogenic surface target useful for the detection of Listeria genus.
Collapse
|
17
|
Connor DO, Zantow J, Hust M, Bier FF, von Nickisch-Rosenegk M. Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display. PLoS One 2016; 11:e0148986. [PMID: 26859666 PMCID: PMC4747489 DOI: 10.1371/journal.pone.0148986] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/26/2016] [Indexed: 12/14/2022] Open
Abstract
Neisseria gonorrhoeae is one of the most prevalent sexually transmitted diseases worldwide with more than 100 million new infections per year. A lack of intense research over the last decades and increasing resistances to the recommended antibiotics call for a better understanding of gonococcal infection, fast diagnostics and therapeutic measures against N. gonorrhoeae. Therefore, the aim of this work was to identify novel immunogenic proteins as a first step to advance those unresolved problems. For the identification of immunogenic proteins, pHORF oligopeptide phage display libraries of the entire N. gonorrhoeae genome were constructed. Several immunogenic oligopeptides were identified using polyclonal rabbit antibodies against N. gonorrhoeae. Corresponding full-length proteins of the identified oligopeptides were expressed and their immunogenic character was verified by ELISA. The immunogenic character of six proteins was identified for the first time. Additional 13 proteins were verified as immunogenic proteins in N. gonorrhoeae.
Collapse
Affiliation(s)
- Daniel O. Connor
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Jonas Zantow
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Markus von Nickisch-Rosenegk
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| |
Collapse
|
18
|
Becker M, Felsberger A, Frenzel A, Shattuck WMC, Dyer M, Kügler J, Zantow J, Mather TN, Hust M. Application of M13 phage display for identifying immunogenic proteins from tick (Ixodes scapularis) saliva. BMC Biotechnol 2015; 15:43. [PMID: 26024663 PMCID: PMC4449557 DOI: 10.1186/s12896-015-0167-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/15/2015] [Indexed: 12/11/2022] Open
Abstract
Background Ticks act as vectors for a large number of different pathogens, perhaps most notably Borrelia burgdorferi, the causative agent of Lyme disease. The most prominent tick vector in the United States is the blacklegged tick, Ixodes scapularis. Tick bites are of special public health concern since there are no vaccines available against most tick-transmitted pathogens. Based on the observation that certain non-natural host animals such as guinea pigs or humans can develop adaptive immune responses to tick bites, anti-tick vaccination is a potential approach to tackle health risks associated with tick bites. Results The aim of this study was to use an oligopeptide phage display strategy to identify immunogenic salivary gland proteins from I. scapularis that are recognized by human immune sera. Oligopeptide libraries were generated from salivary gland mRNA of 18 h fed nymphal I. scapularis. Eight immunogenic oligopeptides were selected using human immune sera. Three selected immunogenic oligopeptides were cloned and produced as recombinant proteins. The immunogenic character of an identified metalloprotease (MP1) was validated with human sera. This enzyme has been described previously and was hypothesized as immunogenic which was confirmed in this study. Interestingly, it also has close homologs in other Ixodes species. Conclusion An immunogenic protein of I. scapularis was identified by oligopeptide phage display. MP1 is a potential candidate for vaccine development.
Collapse
Affiliation(s)
- Martin Becker
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr.7, 38106, Braunschweig, Germany. .,University of Rhode Island, URI Center for Vector-Borne Disease, 231 Woodward Hall, 9 East Alumni Avenue, Suite 7, 02881, Kingston, RI, USA. .,Present Address: Max-Planck-Institute for Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
| | - André Felsberger
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr.7, 38106, Braunschweig, Germany. .,Present Address: YUMAB GmbH, Rebenring 33, 38106, Braunschweig, Germany.
| | - André Frenzel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr.7, 38106, Braunschweig, Germany.
| | - Wendy M C Shattuck
- University of Rhode Island, URI Center for Vector-Borne Disease, 231 Woodward Hall, 9 East Alumni Avenue, Suite 7, 02881, Kingston, RI, USA.
| | - Megan Dyer
- University of Rhode Island, URI Center for Vector-Borne Disease, 231 Woodward Hall, 9 East Alumni Avenue, Suite 7, 02881, Kingston, RI, USA.
| | - Jonas Kügler
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr.7, 38106, Braunschweig, Germany.
| | - Jonas Zantow
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr.7, 38106, Braunschweig, Germany.
| | - Thomas N Mather
- University of Rhode Island, URI Center for Vector-Borne Disease, 231 Woodward Hall, 9 East Alumni Avenue, Suite 7, 02881, Kingston, RI, USA.
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr.7, 38106, Braunschweig, Germany.
| |
Collapse
|
19
|
Interaction analysis through proteomic phage display. BIOMED RESEARCH INTERNATIONAL 2014; 2014:176172. [PMID: 25295249 PMCID: PMC4177731 DOI: 10.1155/2014/176172] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/11/2014] [Accepted: 08/19/2014] [Indexed: 11/29/2022]
Abstract
Phage display is a powerful technique for profiling specificities of peptide binding domains. The method is suited for the identification of high-affinity ligands with inhibitor potential when using highly diverse combinatorial peptide phage libraries. Such experiments further provide consensus motifs for genome-wide scanning of ligands of potential biological relevance. A complementary but considerably less explored approach is to display expression products of genomic DNA, cDNA, open reading frames (ORFs), or oligonucleotide libraries designed to encode defined regions of a target proteome on phage particles. One of the main applications of such proteomic libraries has been the elucidation of antibody epitopes. This review is focused on the use of proteomic phage display to uncover protein-protein interactions of potential relevance for cellular function. The method is particularly suited for the discovery of interactions between peptide binding domains and their targets. We discuss the largely unexplored potential of this method in the discovery of domain-motif interactions of potential biological relevance.
Collapse
|
20
|
Oligopeptide m13 phage display in pathogen research. Viruses 2013; 5:2531-45. [PMID: 24136040 PMCID: PMC3814601 DOI: 10.3390/v5102531] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 12/19/2022] Open
Abstract
Phage display has become an established, widely used method for selection of peptides, antibodies or alternative scaffolds. The use of phage display for the selection of antigens from genomic or cDNA libraries of pathogens which is an alternative to the classical way of identifying immunogenic proteins is not well-known. In recent years several new applications for oligopeptide phage display in disease related fields have been developed which has led to the identification of various new antigens. These novel identified immunogenic proteins provide new insights into host pathogen interactions and can be used for the development of new diagnostic tests and vaccines. In this review we focus on the M13 oligopeptide phage display system for pathogen research but will also give examples for lambda phage display and for applications in other disease related fields. In addition, a detailed technical work flow for the identification of immunogenic oligopeptides using the pHORF system is given. The described identification of immunogenic proteins of pathogens using oligopeptide phage display can be linked to antibody phage display resulting in a vaccine pipeline.
Collapse
|
21
|
Gupta A, Shrivastava N, Grover P, Singh A, Mathur K, Verma V, Kaur C, Chaudhary VK. A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries. PLoS One 2013; 8:e75212. [PMID: 24086469 PMCID: PMC3785514 DOI: 10.1371/journal.pone.0075212] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/08/2013] [Indexed: 11/19/2022] Open
Abstract
Phagemid-based expression of cloned genes fused to the gIIIP coding sequence and rescue using helper phages, such as VCSM13, has been used extensively for constructing large antibody phage display libraries. However, for randomly primed cDNA and gene fragment libraries, this system encounters reading frame problems wherein only one of 18 phages display the translated foreign peptide/protein fused to phagemid-encoded gIIIP. The elimination of phages carrying out-of-frame inserts is vital in order to improve the quality of phage display libraries. In this study, we designed a novel helper phage, AGM13, which carries trypsin-sensitive sites within the linker regions of gIIIP. This renders the phage highly sensitive to trypsin digestion, which abolishes its infectivity. For open reading frame (ORF) selection, the phagemid-borne phages are rescued using AGM13, so that clones with in-frame inserts express fusion proteins with phagemid-encoded trypsin-resistant gIIIP, which becomes incorporated into the phages along with a few copies of AGM13-encoded trypsin-sensitive gIIIP. In contrast, clones with out-of-frame inserts produce phages carrying only AGM13-encoded trypsin-sensitive gIIIP. Trypsin treatment of the phage population renders the phages with out-of-frame inserts non-infectious, whereas phages carrying in-frame inserts remain fully infectious and can hence be enriched by infection. This strategy was applied efficiently at a genome scale to generate an ORF-enriched whole genome fragment library from Mycobacterium tuberculosis, in which nearly 100% of the clones carried in-frame inserts after selection. The ORF-enriched libraries were successfully used for identification of linear and conformational epitopes for monoclonal antibodies specific to mycobacterial proteins.
Collapse
Affiliation(s)
- Amita Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
- * E-mail: (AG); (VKC)
| | - Nimisha Shrivastava
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Payal Grover
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Ajay Singh
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Kapil Mathur
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Vaishali Verma
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Charanpreet Kaur
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Vijay K. Chaudhary
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
- * E-mail: (AG); (VKC)
| |
Collapse
|
22
|
Meyer T, Schirrmann T, Frenzel A, Miethe S, Stratmann-Selke J, Gerlach GF, Strutzberg-Minder K, Dübel S, Hust M. Identification of immunogenic proteins and generation of antibodies against Salmonella Typhimurium using phage display. BMC Biotechnol 2012; 12:29. [PMID: 22703709 PMCID: PMC3423037 DOI: 10.1186/1472-6750-12-29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 05/25/2012] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Solely in Europoe, Salmonella Typhimurium causes more than 100,000 infections per year. Improved detection of livestock colonised with S. Typhimurium is necessary to prevent foodborne diseases. Currently, commercially available ELISA assays are based on a mixture of O-antigens (LPS) or total cell lysate of Salmonella and are hampered by cross-reaction. The identification of novel immunogenic proteins would be useful to develop ELISA based diagnostic assays with a higher specificity. RESULTS A phage display library of the entire Salmonella Typhimurium genome was constructed and 47 immunogenic oligopeptides were identified using a pool of convalescent sera from pigs infected with Salmonella Typhimurium. The corresponding complete genes of seven of the identified oligopeptids were cloned. Five of them were produced in E. coli. The immunogenic character of these antigens was validated with sera from pigs infeced with S. Tyhimurium and control sera from non-infected animals. Finally, human antibody fragments (scFv) against these five antigens were selected using antibody phage display and characterised. CONCLUSION In this work, we identified novel immunogenic proteins of Salmonella Typhimurium and generated antibody fragments against these antigens completely based on phage display. Five immunogenic proteins were validated using a panel of positive and negative sera for prospective applications in diagnostics of Salmonela Typhimurium.
Collapse
Affiliation(s)
- Torsten Meyer
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr.7, 38106 Braunschweig, Germany
| | - Thomas Schirrmann
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr.7, 38106 Braunschweig, Germany
| | - André Frenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr.7, 38106 Braunschweig, Germany
| | - Sebastian Miethe
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr.7, 38106 Braunschweig, Germany
| | - Janin Stratmann-Selke
- IVD GmbH Heisterbergallee 12, 30453 Hannover, Germany
- Present address: vaxxinova GmbH diagnostics, Johann-Krane-Weg 42, 48149 Münster, Germany
| | | | | | - Stefan Dübel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr.7, 38106 Braunschweig, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstr.7, 38106 Braunschweig, Germany
| |
Collapse
|
23
|
Nilssen NR, Frigstad T, Pollmann S, Roos N, Bogen B, Sandlie I, Løset GÅ. DeltaPhage--a novel helper phage for high-valence pIX phagemid display. Nucleic Acids Res 2012; 40:e120. [PMID: 22539265 PMCID: PMC3439877 DOI: 10.1093/nar/gks341] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phage display has been instrumental in discovery of novel binding peptides and folded domains for the past two decades. We recently reported a novel pIX phagemid display system that is characterized by a strong preference for phagemid packaging combined with low display levels, two key features that support highly efficient affinity selection. However, high diversity in selected repertoires are intimately coupled to high display levels during initial selection rounds. To incorporate this additional feature into the pIX display system, we have developed a novel helper phage termed DeltaPhage that allows for high-valence display on pIX. This was obtained by inserting two amber mutations close to the pIX start codon, but after the pVII translational stop, conditionally inactivating the helper phage encoded pIX. Until now, the general notion has been that display on pIX is dependent on wild-type complementation, making high-valence display unachievable. However, we found that DeltaPhage does facilitate high-valence pIX display when used with a non-suppressor host. Here, we report a side-by-side comparison with pIII display, and we find that this novel helper phage complements existing pIX phagemid display systems to allow both low and high-valence display, making pIX display a complete and efficient alternative to existing pIII phagemid display systems.
Collapse
Affiliation(s)
- Nicolay R Nilssen
- Centre for Immune Regulation, Oslo University Hospital, N-0027, Oslo, Norway
| | | | | | | | | | | | | |
Collapse
|
24
|
Georgieva Y, Konthur Z. Design and screening of M13 phage display cDNA libraries. Molecules 2011; 16:1667-81. [PMID: 21330956 PMCID: PMC6259656 DOI: 10.3390/molecules16021667] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/14/2011] [Accepted: 02/15/2011] [Indexed: 12/17/2022] Open
Abstract
The last decade has seen a steady increase in screening of cDNA expression product libraries displayed on the surface of filamentous bacteriophage. At the same time, the range of applications extended from the identification of novel allergens over disease markers to protein-protein interaction studies. However, the generation and selection of cDNA phage display libraries is subjected to intrinsic biological limitations due to their complex nature and heterogeneity, as well as technical difficulties regarding protein presentation on the phage surface. Here, we review the latest developments in this field, discuss a number of strategies and improvements anticipated to overcome these challenges making cDNA and open reading frame (ORF) libraries more readily accessible for phage display. Furthermore, future trends combining phage display with next generation sequencing (NGS) will be presented.
Collapse
Affiliation(s)
- Yuliya Georgieva
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | | |
Collapse
|
25
|
Fitting J, Killian D, Junghanss C, Willenbrock S, Murua Escobar H, Lange S, Nolte I, Barth S, Tur MK. Generation of recombinant antibody fragments that target canine dendritic cells by phage display technology. Vet Comp Oncol 2010; 9:183-95. [PMID: 21848621 DOI: 10.1111/j.1476-5829.2010.00246.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
One of the main goals in cancer immunotherapy is the efficient activation of the host immune system against tumour cells. Dendritic cells (DCs) can induce specific anti-tumour immune responses in both experimental animal models and humans. However, most preclinical studies using small animal models show only limited correlation with studies carried out in clinical settings, whereas laboratory dogs naturally develop tumours that are biologically and histopathologically similar to their human counterparts. Here, we describe the generation and characterization of recombinant antibodies against canine DCs, isolated using the Tomlinson phage display system. We successfully isolated highly specific single-chain variable fragment (scFv) antibodies in a sequential three-step panning strategy involving depletion on canine peripheral blood mononuclear cells followed by positive selection on native canine DCs. This provides the basis for an antibody-based method for the immunological detection and manipulation of DCs and for monitoring antigen-specific immune responses.
Collapse
Affiliation(s)
- J Fitting
- Experimental Medicine and Immunotherapy, Department of Applied Medical Engineering, Helmholtz Institute for Biomedical Engineering, University Hospital RWTH Aachen, Aachen, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Hust M, Meyer T, Voedisch B, Rülker T, Thie H, El-Ghezal A, Kirsch MI, Schütte M, Helmsing S, Meier D, Schirrmann T, Dübel S. A human scFv antibody generation pipeline for proteome research. J Biotechnol 2010; 152:159-70. [PMID: 20883731 DOI: 10.1016/j.jbiotec.2010.09.945] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 09/13/2010] [Accepted: 09/16/2010] [Indexed: 01/28/2023]
Abstract
The functional decryption of the human proteome is the challenge which follows the sequencing of the human genome. Specific binders to every human protein are key reagents for this purpose. In vitro antibody selection using phage display offers one possible solution that can meet the demand for 25,000 or more antibodies, but needs substantial standardisation and minimalisation. To evaluate this potential, three human, naive antibody gene libraries (HAL4/7/8) were constructed and a standardised antibody selection pipeline was set up. The quality of the libraries and the selection pipeline was validated with 110 antigens, including human, other mammalian, fungal or bacterial proteins, viruses or haptens. Furthermore, the abundance of VH, kappa and lambda subfamilies during library cloning and the E. coli based phage display system on library packaging and the selection of scFvs was evaluated from the analysis of 435 individual antibodies, resulting in the first comprehensive comparison of V gene subfamily use for all steps of an antibody phage display pipeline. Further, a compatible cassette vector set for E. coli and mammalian expression of antibody fragments is described, allowing in vivo biotinylation, enzyme fusion and Fc fusion.
Collapse
Affiliation(s)
- Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie und Biotechnologie, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Meyer T, Stratmann-Selke J, Meens J, Schirrmann T, Gerlach GF, Frank R, Dübel S, Strutzberg-Minder K, Hust M. Isolation of scFv fragments specific to OmpD of Salmonella Typhimurium. Vet Microbiol 2010; 147:162-9. [PMID: 20708859 DOI: 10.1016/j.vetmic.2010.06.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 05/26/2010] [Accepted: 06/23/2010] [Indexed: 10/19/2022]
Abstract
Pork meat is one of the major sources for human infections with Salmonella enterica subspecies enterica serovars. Further, zoonoses caused by S. enterica subspecies enterica serovars are responsible for substantial economical losses in industrial countries. Quick and reliable detection of this infection is urgently needed to improve consumer security. Due to its capability to identify infections independent of the species, a competitive ELISA is the preferable method for the detection of anti-Salmonella antibodies in serum. Recombinant antibody fragments (scFvs) were isolated from the naive human antibody gene library HAL7 by phage display. Recombinant produced outer membrane protein D (OmpD) of Salmonella Typhimurium was used as antigen. The characterization of the isolated single chain Fv (scFv) antibodies was done by enzyme-linked immunosorbent assay (ELISA), immunoblot, sequencing, epitope mapping and size exclusion chromatography (SEC). The detection of anti-OmpD IgGs in swine sera by competitive ELISA was shown in a proof of principle concept. Furthermore, the developed competitive ELISA would be compatible to a recently published DIVA vaccine, allow to distinguish between infected and vaccinated pigs.
Collapse
Affiliation(s)
- Torsten Meyer
- Technische Universität Braunschweig, Institut für Biochemie und Biotechnologie, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Di Niro R, Sulic AM, Mignone F, D'Angelo S, Bordoni R, Iacono M, Marzari R, Gaiotto T, Lavric M, Bradbury ARM, Biancone L, Zevin-Sonkin D, De Bellis G, Santoro C, Sblattero D. Rapid interactome profiling by massive sequencing. Nucleic Acids Res 2010; 38:e110. [PMID: 20144949 PMCID: PMC2875021 DOI: 10.1093/nar/gkq052] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We have developed a high-throughput protein expression and interaction analysis platform that combines cDNA phage display library selection and massive gene sequencing using the 454 platform. A phage display library of open reading frame (ORF) fragments was created from mRNA derived from different tissues. This was used to study the interaction network of the enzyme transglutaminase 2 (TG2), a multifunctional enzyme involved in the regulation of cell growth, differentiation and apoptosis, associated with many different pathologies. After two rounds of panning with TG2 we assayed the frequency of ORFs within the selected phage population using 454 sequencing. Ranking and analysis of more than 120 000 sequences allowed us to identify several potential interactors, which were subsequently confirmed in functional assays. Within the identified clones, three had been previously described as interacting proteins (fibronectin, SMOC1 and GSTO2), while all the others were new. When compared with standard systems, such as microtiter enzyme-linked immunosorbant assay, the method described here is dramatically faster and yields far more information about the interaction under study, allowing better characterization of complex systems. For example, in the case of fibronectin, it was possible to identify the specific domains involved in the interaction.
Collapse
Affiliation(s)
- Roberto Di Niro
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Schirrmann T, Hust M. Construction of human antibody gene libraries and selection of antibodies by phage display. Methods Mol Biol 2010; 651:177-209. [PMID: 20686967 DOI: 10.1007/978-1-60761-786-0_11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recombinant antibodies as therapeutics offer new opportunities for the treatment of many tumor diseases. To date, 18 antibody-based drugs are approved for cancer treatment and hundreds of anti-tumor antibodies are under development. The first clinically approved antibodies were of murine origin or human-mouse chimeric. However, since murine antibody domains are immunogenic in human patients and could result in human anti-mouse antibody (HAMA) responses, currently mainly humanized and fully human antibodies are developed for therapeutic applications.Here, in vitro antibody selection technologies directly allow the selection of human antibodies and the corresponding genes from human antibody gene libraries. Antibody phage display is the most common way to generate human antibodies and has already yielded thousands of recombinant antibodies for research, diagnostics and therapy. Here, we describe methods for the construction of human scFv gene libraries and the antibody selection.
Collapse
Affiliation(s)
- Thomas Schirrmann
- Department of Biotechnology, Institute of Biochemistry and Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | |
Collapse
|
30
|
Naseem S, Meens J, Jores J, Heller M, Dübel S, Hust M, Gerlach GF. Phage display-based identification and potential diagnostic application of novel antigens from Mycoplasma mycoides subsp. mycoides small colony type. Vet Microbiol 2009; 142:285-92. [PMID: 19900769 DOI: 10.1016/j.vetmic.2009.09.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Revised: 09/26/2009] [Accepted: 09/29/2009] [Indexed: 11/28/2022]
Abstract
Contagious Bovine Pleuropneumonia caused by Mycoplasma mycoides subsp. mycoides small colony type is a respiratory disease of considerable economic importance in sub-Saharan Africa; control of the disease in Africa is hampered by diagnostic tests which are suited for herd-level but not for individual animal diagnostics. In the work presented we identified 22 potential immunogenic antigens of the Kenyan outbreak strain B237 by using phage display technology. We determined the relative strength of immunogenicity, the discriminatory capacity between bovine positive and negative sera, and the cross-reactivity with rabbit hyperimmune sera directed against 15 different mycoplasmal species. The three best-performing antigens, a conserved hypothetical protein (MSC_0636), a glycosyl transferase (MSC_0108), and an acyl carrier protein phosphodiesterase (MSC_0029) were considered candidate diagnostic proteins. They were expressed as GST-fusion proteins in Escherichia coli, purified, and used in an ELISA as solid phase antigens. The diagnostic potential of the recombinant antigens was tested using the sera of ten experimentally infected animals and six control animals. This prototype test resulted in 100% diagnostic sensitivity and specificity. In comparison, the complement fixation test and the competitive ELISA performed with a diagnostic sensitivity of 70% and 60%, respectively.
Collapse
Affiliation(s)
- Shamoon Naseem
- Stiftung Tierärztliche Hochschule Hannover, Institut für Mikrobiologie, Zentrum für Infektionsmedizin, Hannover, Germany
| | | | | | | | | | | | | |
Collapse
|
31
|
New perspective for phage display as an efficient and versatile technology of functional proteomics. Appl Microbiol Biotechnol 2009; 85:909-19. [PMID: 19885657 DOI: 10.1007/s00253-009-2277-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 09/23/2009] [Accepted: 09/23/2009] [Indexed: 10/20/2022]
Abstract
Phage display with antibody libraries has been widely used with versatile applications. However, phage display with cDNA libraries is rare and inefficient. Because of uncontrollable reading frames and stop codons in cDNA repertoires, high percentage of phage clones identified from conventional cDNA libraries are non-open reading frames (non-ORFs) encoding unnatural short peptides with minimal implications in protein networks. Consequently, phage display has not been used as a technology of functional proteomics to elucidate protein-protein interactions like yeast two-hybrid system and mass spectrometry-based technologies. Several strategies, including C-terminal display and ORF cDNA libraries, have been explored to circumvent the technical problem. The accumulative endeavors eventually led to the efficient elucidation of a large number of tubby- and phosphatidylserine-binding proteins in recent studies by ORF phage display with minimal reading frame issue. ORF phage display inherits all the versatile applications of antibody phage display, but enables efficient identification of real endogenous proteins with efficiency, sensitivity, and accuracy comparable to other technologies of functional proteomics. Its ELISA-like procedure can be conveniently adapted by individual laboratories or fully automated for high-throughput screening. Thus, ORF phage display is an efficient, sensitive, versatile, and convenient technology of functional proteomics for elucidation of global and pathway-specific protein-protein interactions, disease mechanisms, or therapeutic targets.
Collapse
|
32
|
Pelat T, Hust M, Hale M, Lefranc MP, Dübel S, Thullier P. Isolation of a human-like antibody fragment (scFv) that neutralizes ricin biological activity. BMC Biotechnol 2009; 9:60. [PMID: 19563687 PMCID: PMC2716335 DOI: 10.1186/1472-6750-9-60] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 06/30/2009] [Indexed: 11/26/2022] Open
Abstract
Background Ricin is a lethal toxin that inhibits protein synthesis. It is easily extracted from a ubiquitously grown plant, Ricinus communis, and thus readily available for use as a bioweapon (BW). Anti-ricin antibodies provide the only known therapeutic against ricin intoxication. Results In this study, after immunizing a non-human primate (Macaca fascicularis) with the ricin chain A (RTA), a phage-displayed immune library was built (2 × 108 clones), that included the λ light chain fragment. The library was screened against ricin, and specific binders were sequenced and further analyzed. The best clone, 43RCA, was isolated using a new, stringent neutralization test. 43RCA had a high, picomolar affinity (41 pM) and neutralized ricin efficiently (IC50 = 23 ± 3 ng/ml, corresponding to a [scFv]/[ricin] molar ratio of 4). The neutralization capacity of 43RCA compared favourably with that of polyclonal anti-deglycosylated A chain (anti-dgRCA) IgGs, obtained from hyperimmune mouse serum, which were more efficient than any monoclonal at our disposal. The 43RCA sequence is very similar to that for human IgG germline genes, with 162 of 180 identical amino acids for the VH and VL (90% sequence identity). Conclusion Results of the characterization studies, and the high degree of identity with human germline genes, altogether make this anti-ricin scFv, or an IgG derived from it, a likely candidate for use in humans to minimize effects caused by ricin intoxication.
Collapse
Affiliation(s)
- Thibaut Pelat
- Groupe de biotechnologie des anticorps, Département de biologie des agents transmissibles, Centre de Recherche du Service de Santé des Armées, La Tronche, France.
| | | | | | | | | | | |
Collapse
|
33
|
Kirsch MI, Hülseweh B, Nacke C, Rülker T, Schirrmann T, Marschall HJ, Hust M, Dübel S. Development of human antibody fragments using antibody phage display for the detection and diagnosis of Venezuelan equine encephalitis virus (VEEV). BMC Biotechnol 2008; 8:66. [PMID: 18764933 PMCID: PMC2543005 DOI: 10.1186/1472-6750-8-66] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2007] [Accepted: 09/02/2008] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Venezuelan equine encephalitis virus (VEEV) belongs to the Alphavirus group. Several species of this family are also pathogenic to humans and are recognized as potential agents of biological warfare and terrorism. The objective of this work was the generation of recombinant antibodies for the detection of VEEV after a potential bioterrorism assault or an natural outbreak of VEEV. RESULTS In this work, human anti-VEEV single chain Fragments variable (scFv) were isolated for the first time from a human naïve antibody gene library using optimized selection processes. In total eleven different scFvs were identified and their immunological specificity was assessed. The specific detection of the VEEV strains TC83, H12/93 and 230 by the selected antibody fragments was proved. Active as well as formalin inactivated virus particles were recognized by the selected antibody fragments which could be also used for Western blot analysis of VEEV proteins and immunohistochemistry of VEEV infected cells. The anti-VEEV scFv phage clones did not show any cross-reactivity with Alphavirus species of the Western equine encephalitis virus (WEEV) and Eastern equine encephalitis virus (EEEV) antigenic complex, nor did they react with Chikungunya virus (CHIKV), if they were used as detection reagent. CONCLUSION For the first time, this study describes the selection of antibodies against a human pathogenic virus from a human naïve scFv antibody gene library using complete, active virus particles as antigen. The broad and sensitive applicability of scFv-presenting phage for the immunological detection and diagnosis of Alphavirus species was demonstrated. The selected antibody fragments will improve the fast identification of VEEV in case of a biological warfare or terroristic attack or a natural outbreak.
Collapse
Affiliation(s)
- Martina Inga Kirsch
- Abteilung Biotechnologie, Institut für Biochemie und Biotechnologie, Technische Universität Braunschweig, Spielmannstraβe 7, 38106, Braunschweig, Germany
| | - Birgit Hülseweh
- Armed Forces Scientific Institute for Protection Technologies – NBC Protection (WIS), Humboldtstraße 1, 29633, Munster, Germany
| | - Christoph Nacke
- Abteilung Biotechnologie, Institut für Biochemie und Biotechnologie, Technische Universität Braunschweig, Spielmannstraβe 7, 38106, Braunschweig, Germany
| | - Torsten Rülker
- Abteilung Biotechnologie, Institut für Biochemie und Biotechnologie, Technische Universität Braunschweig, Spielmannstraβe 7, 38106, Braunschweig, Germany
| | - Thomas Schirrmann
- Abteilung Biotechnologie, Institut für Biochemie und Biotechnologie, Technische Universität Braunschweig, Spielmannstraβe 7, 38106, Braunschweig, Germany
| | - Hans-Jürgen Marschall
- Armed Forces Scientific Institute for Protection Technologies – NBC Protection (WIS), Humboldtstraße 1, 29633, Munster, Germany
| | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie und Biotechnologie, Technische Universität Braunschweig, Spielmannstraβe 7, 38106, Braunschweig, Germany
| | - Stefan Dübel
- Abteilung Biotechnologie, Institut für Biochemie und Biotechnologie, Technische Universität Braunschweig, Spielmannstraβe 7, 38106, Braunschweig, Germany
| |
Collapse
|
34
|
Kügler J, Nieswandt S, Gerlach GF, Meens J, Schirrmann T, Hust M. Identification of immunogenic polypeptides from a Mycoplasma hyopneumoniae genome library by phage display. Appl Microbiol Biotechnol 2008; 80:447-58. [PMID: 18636254 DOI: 10.1007/s00253-008-1576-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 06/11/2008] [Accepted: 06/11/2008] [Indexed: 10/21/2022]
Abstract
The identification of immunogenic polypeptides of pathogens is helpful for the development of diagnostic assays and therapeutic applications like vaccines. Routinely, these proteins are identified by two-dimensional polyacrylamide gel electrophoresis and Western blot using convalescent serum, followed by mass spectrometry. This technology, however, is limited, because low or differentially expressed proteins, e.g. dependent on pathogen-host interaction, cannot be identified. In this work, we developed and improved a M13 genomic phage display-based method for the selection of immunogenic polypeptides of Mycoplasma hyopneumoniae, a pathogen causing porcine enzootic pneumonia. The fragmented genome of M. hyopneumoniae was cloned into a phage display vector, and the genomic library was packaged using the helperphage Hyperphage to enrich open reading frames (ORFs). Afterwards, the phage display library was screened by panning using convalescent serum. The analysis of individual phage clones resulted in the identification of five genes encoding immunogenic proteins, only two of which had been previously identified and described as immunogenic. This M13 genomic phage display, directly combining ORF enrichment and the presentation of the corresponding polypeptide on the phage surface, complements proteome-based methods for the identification of immunogenic polypeptides and is particularly well suited for the use in mycoplasma species.
Collapse
Affiliation(s)
- Jonas Kügler
- Abteilung Biotechnologie, Institut für Biochemie und Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | | | | | | | | |
Collapse
|
35
|
Thie H, Schirrmann T, Paschke M, Dübel S, Hust M. SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli. N Biotechnol 2008; 25:49-54. [DOI: 10.1016/j.nbt.2008.01.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 01/04/2008] [Accepted: 01/13/2008] [Indexed: 10/22/2022]
|
36
|
Abstract
This review focusses on the isolation of proteins from genomic or cDNA expression products libraries displayed on phage. The use of phage display is highlighted for the characterization of binding proteins with diverse biological functions. Phage display is compared with another strategy, the yeast two-hybrid method. The combination of both strategies is especially powerful to eliminate false positives and to get information on the biochemical functions of proteins.
Collapse
Affiliation(s)
- Jean-Luc Jestin
- URA CNRS 2128, Département de Biologie Structurale et Chimie, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris 15, France.
| |
Collapse
|
37
|
Hust M, Dübel S, Schirrmann T. Selection of recombinant antibodies from antibody gene libraries. Methods Mol Biol 2008; 408:243-55. [PMID: 18314587 DOI: 10.1007/978-1-59745-547-3_14] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
After the sequencing of the human genome is completed, the research focus shifts toward the analysis of gene products. The human genome encodes more than 30,000 genes. Owing to alternative mRNA splicing and posttranslational modifications, for example, glycosylation, phoshorylation, and so on, the number of different proteins of human proteome is supposed to easily exceed 90,000. Antibodies are key detection reagents for the "postgenomic" analysis of these proteins. Any systematic investigation of the human proteome requires high throughput methods for antibody generation. In vitro selection systems utilizing recombinant antibody repertoires offer this capability and capacity. The most commonly used contemporary in vitro selection system is antibody phage display, which has already yielded thousands of useful antibodies for therapy, research, and diagnostics. Herein, methods are described for the selection of recombinant antibody fragments from naive antibody gene libraries.
Collapse
|
38
|
Pelat T, Hust M, Laffly E, Condemine F, Bottex C, Vidal D, Lefranc MP, Dübel S, Thullier P. High-affinity, human antibody-like antibody fragment (single-chain variable fragment) neutralizing the lethal factor (LF) of Bacillus anthracis by inhibiting protective antigen-LF complex formation. Antimicrob Agents Chemother 2007; 51:2758-64. [PMID: 17517846 PMCID: PMC1932538 DOI: 10.1128/aac.01528-06] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The anthrax lethal toxin (LT) consists of two subunits, the protective antigen (PA) and the lethal factor (LF), and is essential for anthrax pathogenesis. Several recombinant antibodies directed against PA and intended for medical use have been obtained, but none against LF, despite the recommendations of anthrax experts. Here we describe an anti-LF single-chain variable fragment (scFv) that originated from an immunized macaque (Macaca fascicularis) and was obtained by phage display. Panning of the library of 1.8 x 10(8) clones allowed the isolation of 2LF, a high-affinity (equilibrium dissociation constant, 1.02 nM) scFv, which is highly neutralizing in the standardized in vitro assay (50% inhibitory concentration, 1.20 +/- 0.06 nM) and in an in vivo assay. The scFv neutralizes anthrax LT by inhibiting the formation of the LF-PA complex. The genes encoding 2LF are very similar to those of human immunoglobulin germ line genes, sharing substantial (84.2%) identity with their most similar, germinally encoded counterparts; this feature favors medical applications. These results, and others formerly published, demonstrate that our approach can generate antibody fragments suitable for prophylaxis and therapeutics.
Collapse
Affiliation(s)
- Thibaut Pelat
- Groupe de Biotechnologie des Anticorps, Département de Biologie des Agents Transmissibles, La Tronche, France
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
Background The connection of the variable part of the heavy chain (VH) and and the variable part of the light chain (VL) by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv) was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv) fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab) with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. Results Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd) and the light chain (LC), resulting in the formation of a single chain Fab fragment (scFab), can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC) connecting the constant part 1 of the heavy chain (CH1) and the constant part of the light chain (CL) were best suited for phage display and production of soluble antibody fragments. Beside the expression system E. coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies) as well as multimers were characterised. Conclusion A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of common standard sera for detection.
Collapse
|