1
|
Mustafa MI, Mohammed A. Developing recombinant antibodies by phage display technology to neutralize viral infectious diseases. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100140. [PMID: 38182043 DOI: 10.1016/j.slasd.2024.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
The use of recombinant antibodies developed through phage display technology offers a promising approach for combating viral infectious diseases. By specifically targeting antigens on viral surfaces, these antibodies have the potential to reduce the severity of infections or even prevent them altogether. With the emergence of new and more virulent strains of viruses, it is crucial to develop innovative methods to counteract them. Phage display technology has proven successful in generating recombinant antibodies capable of targeting specific viral antigens, thereby providing a powerful tool to fight viral infections. In this mini-review article, we examine the development of these antibodies using phage display technology, and discuss the associated challenges and opportunities in developing novel treatments for viral infectious diseases. Furthermore, we provide an overview of phage display technology. As these methods continue to evolve and improve, novel and sophisticated tools based on phage display and peptide display systems are constantly emerging, offering exciting prospects for solving scientific, medical, and technological problems related to viral infectious diseases in the near future.
Collapse
Affiliation(s)
- Mujahed I Mustafa
- Department of Biotechnology, College of Applied and Industrial Sciences, University of Bahri, Khartoum, Sudan.
| | - Ahmed Mohammed
- Department of Biotechnology, School of Life Sciences and Technology, Omdurman Islamic university, Omdurman, Sudan
| |
Collapse
|
2
|
Schlotheuber LJ, Lüchtefeld I, Eyer K. Antibodies, repertoires and microdevices in antibody discovery and characterization. LAB ON A CHIP 2024; 24:1207-1225. [PMID: 38165819 PMCID: PMC10898418 DOI: 10.1039/d3lc00887h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/04/2024]
Abstract
Therapeutic antibodies are paramount in treating a wide range of diseases, particularly in auto-immunity, inflammation and cancer, and novel antibody candidates recognizing a vast array of novel antigens are needed to expand the usefulness and applications of these powerful molecules. Microdevices play an essential role in this challenging endeavor at various stages since many general requirements of the overall process overlap nicely with the general advantages of microfluidics. Therefore, microfluidic devices are rapidly taking over various steps in the process of new candidate isolation, such as antibody characterization and discovery workflows. Such technologies can allow for vast improvements in time-lines and incorporate conservative antibody stability and characterization assays, but most prominently screenings and functional characterization within integrated workflows due to high throughput and standardized workflows. First, we aim to provide an overview of the challenges of developing new therapeutic candidates, their repertoires and requirements. Afterward, this review focuses on the discovery of antibodies using microfluidic systems, technological aspects of micro devices and small-scale antibody protein characterization and selection, as well as their integration and implementation into antibody discovery workflows. We close with future developments in microfluidic detection and antibody isolation principles and the field in general.
Collapse
Affiliation(s)
- Luca Johannes Schlotheuber
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
| | - Ines Lüchtefeld
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
- ETH Laboratory for Tumor and Stem Cell Dynamics, Institute of Molecular Health Sciences, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
| |
Collapse
|
3
|
Huang CY, Lok YY, Lin CH, Lai SL, Wu YY, Hu CY, Liao CB, Ho CH, Chou YP, Hsu YH, Lo YH, Chern E. Highly reliable GIGA-sized synthetic human therapeutic antibody library construction. Front Immunol 2023; 14:1089395. [PMID: 37180155 PMCID: PMC10174300 DOI: 10.3389/fimmu.2023.1089395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/12/2023] [Indexed: 05/15/2023] Open
Abstract
Background Monoclonal antibodies (mAbs) and their derivatives are the fastest expanding category of pharmaceuticals. Efficient screening and generation of appropriate therapeutic human antibodies are important and urgent issues in the field of medicine. The successful in vitro biopanning method for antibody screening largely depends on the highly diverse, reliable and humanized CDR library. To rapidly obtain potent human antibodies, we designed and constructed a highly diverse synthetic human single-chain variable fragment (scFv) antibody library greater than a giga in size by phage display. Herein, the novel TIM-3-neutralizing antibodies with immunomodulatory functions derived from this library serve as an example to demonstrate the library's potential for biomedical applications. Methods The library was designed with high stability scaffolds and six complementarity determining regions (CDRs) tailored to mimic human composition. The engineered antibody sequences were optimized for codon usage and subjected to synthesis. The six CDRs with variable length CDR-H3s were individually subjected to β-lactamase selection and then recombined for library construction. Five therapeutic target antigens were used for human antibody generation via phage library biopanning. TIM-3 antibody activity was verified by immunoactivity assays. Results We have designed and constructed a highly diverse synthetic human scFv library named DSyn-1 (DCB Synthetic-1) containing 2.5 × 1010 phage clones. Three selected TIM-3-recognizing antibodies DCBT3-4, DCBT3-19, and DCBT3-22 showed significant inhibition activity by TIM-3 reporter assays at nanomolar ranges and binding affinities in sub-nanomolar ranges. Furthermore, clone DCBT3-22 was exceptionally superior with good physicochemical property and a purity of more than 98% without aggregation. Conclusion The promising results illustrate not only the potential of the DSyn-1 library for biomedical research applications, but also the therapeutic potential of the three novel fully human TIM-3-neutralizing antibodies.
Collapse
Affiliation(s)
- Chao-Yang Huang
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Ying-Yung Lok
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Chia-Hui Lin
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Szu-Liang Lai
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Yen-Yu Wu
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Chih-Yung Hu
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Chu-Bin Liao
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Chen-Hsuan Ho
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Yu-Ping Chou
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Yi-Hsuan Hsu
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Yu-Hsun Lo
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Edward Chern
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- *Correspondence: Edward Chern,
| |
Collapse
|
4
|
Peissert F, Plüss L, Giudice AM, Ongaro T, Villa A, Elsayed A, Nadal L, Dakhel Plaza S, Scietti L, Puca E, De Luca R, Forneris F, Neri D. Selection of a PD-1 blocking antibody from a novel fully human phage display library. Protein Sci 2022; 31:e4486. [PMID: 36317676 PMCID: PMC9667898 DOI: 10.1002/pro.4486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Programmed cell death protein 1 (PD-1) is an immunoregulatory target which is recognized by different monoclonal antibodies, approved for the therapy of multiple types of cancer. Different anti-PD-1 antibodies display different therapeutic properties and there is a pharmaceutical interest to generate and characterize novel anti-PD-1 antibodies. We screened multiple human antibody phage display libraries to target novel epitopes on the PD-1 surface and we discovered a unique and previously undescribed binding specificity (termed D12) from a new antibody library (termed AMG). The library featured antibody fragments in single-chain fragment variable (scFv) format, based on the IGHV3-23*03 (VH ) and IGKV1-39*01 (Vκ) genes. The D12 antibody was characterized by surface plasmon resonance (SPR), cross-reacted with the Cynomolgus monkey antigen and bound to primary human T cells, as shown by flow cytometry. The antibody blocked the PD-1/PD-L1 interaction in vitro with an EC50 value which was comparable to the one of nivolumab, a clinically approved antibody. The fine details of the interaction between D12 and PD-1 were elucidated by x-ray crystallography of the complex at a 3.5 Å resolution, revealing an unprecedented conformational change at the N-terminus of PD-1 following D12 binding, as well as partial overlap with the binding site for the cognate PD-L1 and PD-L2 ligands which prevents their binding. The results of the study suggest that the expansion of antibody library repertoires may facilitate the discovery of novel binding specificities with unique properties that hold promises for the modulation of PD-1 activity in vitro and in vivo.
Collapse
Affiliation(s)
- Frederik Peissert
- Philochem AGOtelfingenSwitzerland
- Biomolecular Sciences and BiotechnologyUniversity School for Advanced Studies IUSS PaviaPaviaItaly
| | - Louis Plüss
- Philochem AGOtelfingenSwitzerland
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich)ZürichSwitzerland
| | | | - Tiziano Ongaro
- The Armenise‐Harvard Laboratory of Structural Biology, Department of Biology and BiotechnologyUniversity of PaviaPaviaItaly
| | | | - Abdullah Elsayed
- Philochem AGOtelfingenSwitzerland
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich)ZürichSwitzerland
| | | | | | - Luigi Scietti
- The Armenise‐Harvard Laboratory of Structural Biology, Department of Biology and BiotechnologyUniversity of PaviaPaviaItaly
| | | | | | - Federico Forneris
- The Armenise‐Harvard Laboratory of Structural Biology, Department of Biology and BiotechnologyUniversity of PaviaPaviaItaly
| | - Dario Neri
- Philochem AGOtelfingenSwitzerland
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich)ZürichSwitzerland
- Philogen SpASovicille (SI)Italy
| |
Collapse
|
5
|
André AS, Moutinho I, Dias JNR, Aires-da-Silva F. In vivo Phage Display: A promising selection strategy for the improvement of antibody targeting and drug delivery properties. Front Microbiol 2022; 13:962124. [PMID: 36225354 PMCID: PMC9549074 DOI: 10.3389/fmicb.2022.962124] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
The discovery of hybridoma technology, described by Kohler and Milstein in 1975, and the resulting ability to generate monoclonal antibodies (mAbs) initiated a new era in antibody research and clinical development. However, limitations of the hybridoma technology as a routine antibody generation method in conjunction with high immunogenicity responses have led to the development of alternative approaches for the streamlined identification of most effective antibodies. Within this context, display selection technologies such as phage display, ribosome display, yeast display, bacterial display, and mammalian cell surface display have been widely promoted over the past three decades as ideal alternatives to traditional hybridoma methods. The display of antibodies on phages is probably the most widespread and powerful of these methods and, since its invention in late 1980s, significant technological advancements in the design, construction, and selection of antibody libraries have been made, and several fully human antibodies generated by phage display are currently approved or in various clinical development stages. With evolving novel disease targets and the emerging of a new generation of therapeutic antibodies, such as bispecific antibodies, antibody drug conjugates (ADCs), and chimeric antigen receptor T (CAR-T) cell therapies, it is clear that phage display is expected to continue to play a central role in antibody development. Nevertheless, for non-standard and more demanding cases aiming to generate best-in-class therapeutic antibodies against challenging targets and unmet medical needs, in vivo phage display selections by which phage libraries are directly injected into animals or humans for isolating and identifying the phages bound to specific tissues offer an advantage over conventional in vitro phage display screening procedures. Thus, in the present review, we will first summarize a general overview of the antibody therapeutic market, the different types of antibody fragments, and novel engineered variants that have already been explored. Then, we will discuss the state-of-the-art of in vivo phage display methodologies as a promising emerging selection strategy for improvement antibody targeting and drug delivery properties.
Collapse
Affiliation(s)
- Ana S. André
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisbon, Portugal
| | - Isa Moutinho
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisbon, Portugal
| | - Joana N. R. Dias
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisbon, Portugal
| | - Frederico Aires-da-Silva
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisbon, Portugal
| |
Collapse
|
6
|
Zambrano N, Froechlich G, Lazarevic D, Passariello M, Nicosia A, De Lorenzo C, Morelli MJ, Sasso E. High-Throughput Monoclonal Antibody Discovery from Phage Libraries: Challenging the Current Preclinical Pipeline to Keep the Pace with the Increasing mAb Demand. Cancers (Basel) 2022; 14:cancers14051325. [PMID: 35267633 PMCID: PMC8909429 DOI: 10.3390/cancers14051325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Monoclonal antibodies are increasingly used for a broad range of diseases. Rising demand must face with time time-consuming and laborious processes to isolate novel monoclonal antibodies. Next-generation sequencing coupled to phage display provides timely and sustainable high throughput selection strategy to rapidly access novel target. Here, we describe the current NGS-guided strategies to identify potential binders from enriched sub-libraires by applying a user-friendly informatic pipeline to identify and discard false positive clones. Rescue step and strategies to boost mAb yield are also discussed to improve the limiting selection and screening steps. Abstract Monoclonal antibodies are among the most powerful therapeutics in modern medicine. Since the approval of the first therapeutic antibody in 1986, monoclonal antibodies keep holding great expectations for application in a range of clinical indications, highlighting the need to provide timely and sustainable access to powerful screening options. However, their application in the past has been limited by time-consuming and expensive steps of discovery and production. The screening of antibody repertoires is a laborious step; however, the implementation of next-generation sequencing-guided screening of single-chain antibody fragments has now largely overcome this issue. This review provides a detailed overview of the current strategies for the identification of monoclonal antibodies from phage display-based libraries. We also discuss the challenges and the possible solutions to improve the limiting selection and screening steps, in order to keep pace with the increasing demand for monoclonal antibodies.
Collapse
Affiliation(s)
- Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
- Correspondence: (N.Z.); (E.S.)
| | - Guendalina Froechlich
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences Ospedale San Raffaele, Via Olgettina 58, 20132 Milano, Italy; (D.L.); (M.J.M.)
| | - Margherita Passariello
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Alfredo Nicosia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Claudia De Lorenzo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Marco J. Morelli
- Center for Omics Sciences Ospedale San Raffaele, Via Olgettina 58, 20132 Milano, Italy; (D.L.); (M.J.M.)
| | - Emanuele Sasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
- Correspondence: (N.Z.); (E.S.)
| |
Collapse
|
7
|
A Simple Whole-Plasmid PCR Method to Construct High-Diversity Synthetic Phage Display Libraries. Mol Biotechnol 2022; 64:791-803. [PMID: 35107752 PMCID: PMC9217769 DOI: 10.1007/s12033-021-00442-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 12/17/2021] [Indexed: 11/03/2022]
Abstract
Phage display technology utilises peptide and antibody libraries with very high diversities to select ligands with specific binding properties. The production of such libraries can be labour intensive and technically challenging and whilst there are commercial sources of libraries, the exploitation of the resulting binders is constrained by ownership of the libraries. Here, a peptide library of ~ 1 × 109 variants for display on gene VIII was produced alongside three VHH antibody libraries with similar diversity, where 12mer, 16mer or 21mer CDR3s were introduced into the highly stable cAbBCII10 scaffold displayed on gene III. The cloning strategy used a simple whole-plasmid PCR method and type IIS restriction enzyme assembly that facilitate the seamless insertion of diversity into any suitable phage coat protein or antibody scaffold. This method reproducibly produced 1 × 109 variants from just 10 transformations and the four libraries had relatively low bias with 82 to 86% of all sequences present as single copies. The functionality of both peptide and antibody libraries were demonstrated by selection of ligands with specific binding properties by biopanning. The peptide library was used to epitope map a monoclonal antibody. The VHH libraries were pooled and used to select an antibody to recombinant human collagen type 1.
Collapse
|
8
|
Bolzati C, Spolaore B. Enzymatic Methods for the Site-Specific Radiolabeling of Targeting Proteins. Molecules 2021; 26:3492. [PMID: 34201280 PMCID: PMC8229434 DOI: 10.3390/molecules26123492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022] Open
Abstract
Site-specific conjugation of proteins is currently required to produce homogenous derivatives for medicine applications. Proteins derivatized at specific positions of the polypeptide chain can actually show higher stability, superior pharmacokinetics, and activity in vivo, as compared with conjugates modified at heterogeneous sites. Moreover, they can be better characterized regarding the composition of the derivatization sites as well as the conformational and activity properties. To this aim, several site-specific derivatization approaches have been developed. Among these, enzymes are powerful tools that efficiently allow the generation of homogenous protein-drug conjugates under physiological conditions, thus preserving their native structure and activity. This review will summarize the progress made over the last decade on the use of enzymatic-based methodologies for the production of site-specific labeled immunoconjugates of interest for nuclear medicine. Enzymes used in this field, including microbial transglutaminase, sortase, galactosyltransferase, and lipoic acid ligase, will be overviewed and their recent applications in the radiopharmaceutical field will be described. Since nuclear medicine can benefit greatly from the production of homogenous derivatives, we hope that this review will aid the use of enzymes for the development of better radio-conjugates for diagnostic and therapeutic purposes.
Collapse
Affiliation(s)
- Cristina Bolzati
- Institute of Condensed Matter Chemistry and Technologies for Energy ICMATE-CNR, Corso Stati Uniti, 4, I-35127 Padova, Italy
| | - Barbara Spolaore
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via Marzolo, 5, I-35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padua, Viale G. Colombo, 3, I-35131 Padova, Italy
| |
Collapse
|
9
|
Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
Collapse
Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| |
Collapse
|
10
|
Azevedo Reis Teixeira A, Erasmus MF, D’Angelo S, Naranjo L, Ferrara F, Leal-Lopes C, Durrant O, Galmiche C, Morelli A, Scott-Tucker A, Bradbury ARM. Drug-like antibodies with high affinity, diversity and developability directly from next-generation antibody libraries. MAbs 2021; 13:1980942. [PMID: 34850665 PMCID: PMC8654478 DOI: 10.1080/19420862.2021.1980942] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/09/2022] Open
Abstract
Therapeutic antibodies must have "drug-like" properties. These include high affinity and specificity for the intended target, biological activity, and additional characteristics now known as "developability properties": long-term stability and resistance to aggregation when in solution, thermodynamic stability to prevent unfolding, high expression yields to facilitate manufacturing, low self-interaction, among others. Sequence-based liabilities may affect one or more of these characteristics. Improving the stability and developability of a lead antibody is typically achieved by modifying its sequence, a time-consuming process that often results in reduced affinity. Here we present a new antibody library format that yields high-affinity binders with drug-like developability properties directly from initial selections, reducing the need for further engineering or affinity maturation. The innovative semi-synthetic design involves grafting natural complementarity-determining regions (CDRs) from human antibodies into scaffolds based on well-behaved clinical antibodies. HCDR3s were amplified directly from B cells, while the remaining CDRs, from which all sequence liabilities had been purged, were replicated from a large next-generation sequencing dataset. By combining two in vitro display techniques, phage and yeast display, we were able to routinely recover a large number of unique, highly developable antibodies against clinically relevant targets with affinities in the subnanomolar to low nanomolar range. We anticipate that the designs and approaches presented here will accelerate the drug development process by reducing the failure rate of leads due to poor antibody affinities and developability.Abbreviations: AC-SINS: affinity-capture self-interaction nanoparticle spectroscopy; CDR: complementarity-determining region; CQA: critical quality attribute; ELISA: enzyme-linked immunoassay; FACS: fluorescence-activated cell sorting; Fv: fragment variable; GM-CSF: granulocyte-macrophage colony-stimulating factor; HCDR3: heavy chain CDR3; IFN2a: interferon α-2; IL6: interleukin-6; MACS: magnetic-activated cell sorting; NGS: next generation sequencing; PCR: polymerase chain reaction; SEC: size-exclusion chromatography; SPR: surface plasmon resonance; TGFβ-R2: transforming growth factor β-R2; VH: variable heavy; VK: variable kappa; VL: variable light; Vl: variable lambda.
Collapse
|
11
|
Nadal L, Corbellari R, Villa A, Weiss T, Weller M, Neri D, De Luca R. Novel human monoclonal antibodies specific to the alternatively spliced domain D of Tenascin C efficiently target tumors in vivo. MAbs 2020; 12:1836713. [PMID: 33136526 PMCID: PMC7646483 DOI: 10.1080/19420862.2020.1836713] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibody-based delivery of bioactive molecules represents a promising strategy for the improvement of cancer immunotherapy. Here, we describe the generation and characterization of R6N, a novel fully human antibody specific to the alternatively spliced domain D of Tenascin C, which is highly expressed in the stroma of primary tumors and metastasis. The R6N antibody recognized its cognate tumor-associated antigen with identical specificity in mouse and human specimens. Moreover, the antibody was able to selectively localize to solid tumors in vivo as evidenced by immunofluorescence-based biodistribution analysis. Encouraged by these results, we developed a novel fusion protein (termed mIL12-R6N) consisting of the murine interleukin 12 fused to the R6N antibody in homodimeric tandem single-chain variable fragment arrangement. mIL12-R6N exhibited potent antitumor activity in immunodeficient mice bearing SKRC52 renal cell carcinoma, as well as in immunocompetent mice bearing SMA-497 glioma. The experiments presented in this work provide a rationale for possible future applications for the R6N antibody for the treatment of cancer patients.
Collapse
Affiliation(s)
- Lisa Nadal
- Biology department, Philochem AG , Otelfingen, Switzerland.,CiBIO (Department of Cellular, Computational and Integrative Biology, University of Trento, Italy , Trento, Italy
| | - Riccardo Corbellari
- Biology department, Philochem AG , Otelfingen, Switzerland.,CiBIO (Department of Cellular, Computational and Integrative Biology, University of Trento, Italy , Trento, Italy
| | | | - Tobias Weiss
- Department of Neurology and Brain Tumor Center, University Hospital Zurich and University of Zurich , Zurich, Switzerland
| | - Michael Weller
- Department of Neurology and Brain Tumor Center, University Hospital Zurich and University of Zurich , Zurich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich) , Zurich, Switzerland
| | | |
Collapse
|
12
|
Oncolytic Adenoviruses: Strategies for Improved Targeting and Specificity. Cancers (Basel) 2020; 12:cancers12061504. [PMID: 32526919 PMCID: PMC7352392 DOI: 10.3390/cancers12061504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is a major health problem. Most of the treatments exhibit systemic toxicity, as they are not targeted or specific to cancerous cells and tumors. Adenoviruses are very promising gene delivery vectors and have immense potential to deliver targeted therapy. Here, we review a wide range of strategies that have been tried, tested, and demonstrated to enhance the specificity of oncolytic viruses towards specific cancer cells. A combination of these strategies and other conventional therapies may be more effective than any of those strategies alone.
Collapse
|
13
|
Abstract
Phage display antibody libraries have proven an invaluable resource for the isolation of diagnostic and potentially therapeutic antibodies, the latter usually being antibody fragments converted into IgG formats. Recent advances in the production of highly diverse and functional antibody libraries are considered here, including for Fabs, scFvs and nanobodies. These advances include codon optimisation during generation of CDR diversity, improved display levels using novel signal sequences, molecular chaperones and isomerases and the use of highly stable scaffolds with relatively high expression levels. In addition, novel strategies for the batch reformatting of scFv and Fab phagemid libraries, derived from phage panning, into IgG formats are described. These strategies allow the screening of antibodies in the end-use format, facilitating more efficient selection of potential therapeutics.
Collapse
|
14
|
Lu RM, Hwang YC, Liu IJ, Lee CC, Tsai HZ, Li HJ, Wu HC. Development of therapeutic antibodies for the treatment of diseases. J Biomed Sci 2020; 27:1. [PMID: 31894001 PMCID: PMC6939334 DOI: 10.1186/s12929-019-0592-z] [Citation(s) in RCA: 1082] [Impact Index Per Article: 270.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
It has been more than three decades since the first monoclonal antibody was approved by the United States Food and Drug Administration (US FDA) in 1986, and during this time, antibody engineering has dramatically evolved. Current antibody drugs have increasingly fewer adverse effects due to their high specificity. As a result, therapeutic antibodies have become the predominant class of new drugs developed in recent years. Over the past five years, antibodies have become the best-selling drugs in the pharmaceutical market, and in 2018, eight of the top ten bestselling drugs worldwide were biologics. The global therapeutic monoclonal antibody market was valued at approximately US$115.2 billion in 2018 and is expected to generate revenue of $150 billion by the end of 2019 and $300 billion by 2025. Thus, the market for therapeutic antibody drugs has experienced explosive growth as new drugs have been approved for treating various human diseases, including many cancers, autoimmune, metabolic and infectious diseases. As of December 2019, 79 therapeutic mAbs have been approved by the US FDA, but there is still significant growth potential. This review summarizes the latest market trends and outlines the preeminent antibody engineering technologies used in the development of therapeutic antibody drugs, such as humanization of monoclonal antibodies, phage display, the human antibody mouse, single B cell antibody technology, and affinity maturation. Finally, future applications and perspectives are also discussed.
Collapse
Affiliation(s)
- Ruei-Min Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Yu-Chyi Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - I-Ju Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Chi-Chiu Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Han-Zen Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Hsin-Jung Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan. .,, 128 Academia Rd., Section 2, Nankang, Taipei, 11529, Taiwan.
| |
Collapse
|
15
|
Almagro JC, Pedraza-Escalona M, Arrieta HI, Pérez-Tapia SM. Phage Display Libraries for Antibody Therapeutic Discovery and Development. Antibodies (Basel) 2019; 8:antib8030044. [PMID: 31544850 PMCID: PMC6784186 DOI: 10.3390/antib8030044] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 01/24/2023] Open
Abstract
Phage display technology has played a key role in the remarkable progress of discovering and optimizing antibodies for diverse applications, particularly antibody-based drugs. This technology was initially developed by George Smith in the mid-1980s and applied by John McCafferty and Gregory Winter to antibody engineering at the beginning of 1990s. Here, we compare nine phage display antibody libraries published in the last decade, which represent the state of the art in the discovery and development of therapeutic antibodies using phage display. We first discuss the quality of the libraries and the diverse types of antibody repertoires used as substrates to build the libraries, i.e., naïve, synthetic, and semisynthetic. Second, we review the performance of the libraries in terms of the number of positive clones per panning, hit rate, affinity, and developability of the selected antibodies. Finally, we highlight current opportunities and challenges pertaining to phage display platforms and related display technologies.
Collapse
Affiliation(s)
- Juan C Almagro
- GlobalBio, Inc., 320, Cambridge, MA 02138, USA.
- UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico.
| | - Martha Pedraza-Escalona
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
| | - Hugo Iván Arrieta
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
| | - Sonia Mayra Pérez-Tapia
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
| |
Collapse
|
16
|
Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
Collapse
Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
| |
Collapse
|
17
|
Akkapeddi P, Fragoso R, Hixon JA, Ramalho AS, Oliveira ML, Carvalho T, Gloger A, Matasci M, Corzana F, Durum SK, Neri D, Bernardes GJL, Barata JT. A fully human anti-IL-7Rα antibody promotes antitumor activity against T-cell acute lymphoblastic leukemia. Leukemia 2019; 33:2155-2168. [PMID: 30850736 PMCID: PMC6733707 DOI: 10.1038/s41375-019-0434-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/17/2019] [Accepted: 02/08/2019] [Indexed: 12/28/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological cancer for which treatment options often result in incomplete therapeutic efficacy and long-term side-effects. Interleukin 7 (IL-7) and its receptor IL-7Rα promote T-ALL development and mutational activation of IL-7Rα associates with very high risk in relapsed disease. Using combinatorial phage-display libraries and antibody reformatting, we generated a fully human IgG1 monoclonal antibody (named B12) against both wild-type and mutant human IL-7Rα, predicted to form a stable complex with IL-7Rα at a different site from IL-7. B12 impairs IL-7/IL-7R-mediated signaling, sensitizes T-ALL cells to treatment with dexamethasone and can induce cell death per se. The antibody also promotes antibody-dependent natural killer-mediated leukemia cytotoxicity in vitro and delays T-cell leukemia development in vivo, reducing tumor burden and promoting mouse survival. B12 is rapidly internalized and traffics to the lysosome, rendering it an attractive vehicle for targeted intracellular delivery of cytotoxic cargo. Consequently, we engineered a B12–MMAE antibody–drug conjugate and provide proof-of-concept evidence that it has increased leukemia cell killing abilities as compared with the naked antibody. Our studies serve as a stepping stone for the development of novel targeted therapies in T-ALL and other diseases where IL-7Rα has a pathological role.
Collapse
Affiliation(s)
- Padma Akkapeddi
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Rita Fragoso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Julie A Hixon
- Cytokines and Immunity Section, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Ana Sofia Ramalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Mariana L Oliveira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Tânia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Andreas Gloger
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain
| | | | | | - Scott K Durum
- Cytokines and Immunity Section, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, Zürich, Switzerland
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal. .,Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - João T Barata
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
| |
Collapse
|
18
|
Dal Ferro M, Rizzo S, Rizzo E, Marano F, Luisi I, Tarasiuk O, Sblattero D. Phage Display Technology for Human Monoclonal Antibodies. Methods Mol Biol 2019; 1904:319-338. [PMID: 30539478 DOI: 10.1007/978-1-4939-8958-4_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During the last 20 years in vitro technologies opened powerful routes to combine the generation of large libraries together with fast selection and screening procedures to identify lead candidates. One of the most successful methods is based on the use of filamentous phages. Functional Antibodies (Abs) fragments can be displayed on the surface of phages by fusing the coding sequence of the antibody variable (V) regions to the phage minor coat protein pIII. By creating large libraries, antibodies with affinities comparable to those obtained using traditional hybridoma technology can be isolated by a series of cycles of selection on the antigen of interest. In this system, antibody genes can be recovered simultaneously with selection and can be easily further engineered, for example by increasing their affinity to levels unobtainable in the immune system, or by modulating their specificity and their effector functions (by recloning into a full-length immunoglobulin scaffold). This chapter describes the basic protocols for antibody library construction and selection of binder with desired specificity.
Collapse
Affiliation(s)
- Marco Dal Ferro
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Serena Rizzo
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Emanuela Rizzo
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Francesca Marano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Immacolata Luisi
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Olga Tarasiuk
- Department of Health Sciences and IRCAD, University of Eastern Piedmont, Novara, Italy
| | | |
Collapse
|
19
|
Colagrossi L, Salpini R, Scutari R, Carioti L, Battisti A, Piermatteo L, Bertoli A, Fabeni L, Minichini C, Trimoulet P, Fleury H, Nebuloso E, De Cristofaro M, Cappiello G, Spanò A, Malagnino V, Mari T, Barlattani A, Iapadre N, Lichtner M, Mastroianni C, Lenci I, Pasquazzi C, De Sanctis GM, Galeota Lanza A, Stanzione M, Stornaiuolo G, Marignani M, Sarmati L, Andreoni M, Angelico M, Ceccherini-Silberstein F, Perno CF, Coppola N, Svicher V. HDV Can Constrain HBV Genetic Evolution in HBsAg: Implications for the Identification of Innovative Pharmacological Targets. Viruses 2018; 10:v10070363. [PMID: 29987240 PMCID: PMC6071122 DOI: 10.3390/v10070363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 02/07/2023] Open
Abstract
Chronic HBV + HDV infection is associated with greater risk of liver fibrosis, earlier hepatic decompensation, and liver cirrhosis hepatocellular carcinoma compared to HBV mono-infection. However, to-date no direct anti-HDV drugs are available in clinical practice. Here, we identified conserved and variable regions in HBsAg and HDAg domains in HBV + HDV infection, a critical finding for the design of innovative therapeutic agents. The extent of amino-acid variability was measured by Shannon-Entropy (Sn) in HBsAg genotype-d sequences from 31 HBV + HDV infected and 62 HBV mono-infected patients (comparable for demographics and virological-parameters), and in 47 HDAg genotype-1 sequences. Positions with Sn = 0 were defined as conserved. The percentage of conserved HBsAg-positions was significantly higher in HBV + HDV infection than HBV mono-infection (p = 0.001). Results were confirmed after stratification for HBeAg-status and patients’ age. A Sn = 0 at specific positions in the C-terminus HBsAg were correlated with higher HDV-RNA, suggesting that conservation of these positions can preserve HDV-fitness. Conversely, HDAg was characterized by a lower percentage of conserved-residues than HBsAg (p < 0.001), indicating higher functional plasticity. Furthermore, specific HDAg-mutations were significantly correlated with higher HDV-RNA, suggesting a role in conferring HDV replicative-advantage. Among HDAg-domains, only the virus-assembly signal exhibited a high genetic conservation (75% of conserved-residues). In conclusion, HDV can constrain HBsAg genetic evolution to preserve its fitness. The identification of conserved regions in HDAg poses the basis for designing innovative targets against HDV-infection.
Collapse
Affiliation(s)
- Luna Colagrossi
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Romina Salpini
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Rossana Scutari
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Luca Carioti
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Arianna Battisti
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Lorenzo Piermatteo
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Lavinia Fabeni
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Carmine Minichini
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania L. Vanvitelli, 81100 Naples, Italy.
| | - Pascale Trimoulet
- Laboratoire de Virologie, Hôpital Pellegrin tripode, 33076 Bordeaux, France.
| | - Hervé Fleury
- Laboratoire de Virologie, Hôpital Pellegrin tripode, 33076 Bordeaux, France.
| | - Elena Nebuloso
- Unit of Microbiology, Sandro Pertini Hospital, 00157 Rome, Italy.
| | | | | | - Alberto Spanò
- Unit of Microbiology, Sandro Pertini Hospital, 00157 Rome, Italy.
| | - Vincenzo Malagnino
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | - Terenzio Mari
- Hepatology Unit, Nuovo Regina Margherita Hospital, 00153 Rome, Italy.
| | - Angelo Barlattani
- Hepatology Unit, Nuovo Regina Margherita Hospital, 00153 Rome, Italy.
| | - Nerio Iapadre
- Infectious Diseases Unit, San Salvatore Hospital, 67100 L'Aquila, Italy.
| | - Miriam Lichtner
- Department of Public Health and Infectious Diseases, Sapienza University, 00185 Rome, Italy.
| | - Claudio Mastroianni
- Department of Public Health and Infectious Diseases, Sapienza University, 00185 Rome, Italy.
| | - Ilaria Lenci
- Hepatology Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | | | | | | | - Maria Stanzione
- Department of Internal Medicine, University of Campania L. Vanvitelli, Viral Unit, 81100 Naples, Italy.
| | - Gianfranca Stornaiuolo
- Department of Internal Medicine, University of Campania L. Vanvitelli, Viral Unit, 81100 Naples, Italy.
| | | | - Loredana Sarmati
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | - Massimo Andreoni
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | - Mario Angelico
- Hepatology Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | | | - Carlo-Federico Perno
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
- Haematology and Oncohematology, University of Milan, 20122 Milan, Italy.
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania L. Vanvitelli, 81100 Naples, Italy.
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| |
Collapse
|
20
|
Madrid R, de la Cruz S, García A, Martín R, González I, García T. Detection of Food Allergens by Phage-Displayed Produced Antibodies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1592:109-128. [PMID: 28315215 DOI: 10.1007/978-1-4939-6925-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Phage display is a powerful tool to produce recombinant antibodies against a given antigen without animal immunization. This technology employs libraries of recombinant bacteriophages that display billions of different functional antibody fragments on their surface. They are selected by panning in vitro against the target antigen in search for specific binders. In this chapter, we describe the selection of single chain variable fragment (scFv) antibodies to be used for detection of allergenic proteins from nuts in food products. The artificial libraries TomLinson I+J (MRC Laboratory of Molecular Biology and MRC Centre for Protein Engineering) were employed that resulted in successful phage-ELISA systems for detection of almond and walnut proteins in commercial food products.
Collapse
Affiliation(s)
- Raquel Madrid
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Silvia de la Cruz
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Aina García
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Rosario Martín
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Isabel González
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain
| | - Teresa García
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Av. Puerta de Hierro a/n, 28040, Madrid, Spain.
| |
Collapse
|
21
|
Pasello M, Mallano A, Flego M, Zamboni S, Giudice AM, Scotlandi K. Construction of Human Naïve Antibody Gene Libraries. Methods Mol Biol 2018; 1827:73-91. [PMID: 30196492 DOI: 10.1007/978-1-4939-8648-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Size and variability often represent an obstacle in generating an effective antibody gene library for the detection of an abundant repertoire of antigens. Therefore, optimizing the construction of a large library is essential for the selection of high-affinity reactive fragments. Here, we report a highly efficient method for the construction of a human naïve antibody gene library for the selection of antibodies as single-chain variable fragments. This protocol is based on many different sets of oligonucleotide primers and multistep electroporation and ligation reactions.This advanced method can be adopted by any molecular biology laboratory to generate a naïve library for use in isolating single-chain fragment variables against specific targets.
Collapse
Affiliation(s)
- Michela Pasello
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab, Rizzoli Orthopedic Institute, Bologna, Italy.
| | - Alessandra Mallano
- National Center For Global Health, The National Institute of Health, Rome, Italy
| | - Michela Flego
- National Center For Global Health, The National Institute of Health, Rome, Italy
| | - Silvia Zamboni
- Department of Neuroscience, The National Institute of Health, Rome, Italy
| | - Anna Maria Giudice
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab, Rizzoli Orthopedic Institute, Bologna, Italy
| | - Katia Scotlandi
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab, Rizzoli Orthopedic Institute, Bologna, Italy
| |
Collapse
|
22
|
Xu L, Carrer A, Zonta F, Qu Z, Ma P, Li S, Ceriani F, Buratto D, Crispino G, Zorzi V, Ziraldo G, Bruno F, Nardin C, Peres C, Mazzarda F, Salvatore AM, Raspa M, Scavizzi F, Chu Y, Xie S, Yang X, Liao J, Liu X, Wang W, Wang S, Yang G, Lerner RA, Mammano F. Design and Characterization of a Human Monoclonal Antibody that Modulates Mutant Connexin 26 Hemichannels Implicated in Deafness and Skin Disorders. Front Mol Neurosci 2017; 10:298. [PMID: 29018324 PMCID: PMC5615210 DOI: 10.3389/fnmol.2017.00298] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/05/2017] [Indexed: 12/21/2022] Open
Abstract
Background: Mutations leading to changes in properties, regulation, or expression of connexin-made channels have been implicated in 28 distinct human hereditary diseases. Eight of these result from variants of connexin 26 (Cx26), a protein critically involved in cell-cell signaling in the inner ear and skin. Lack of non-toxic drugs with defined mechanisms of action poses a serious obstacle to therapeutic interventions for diseases caused by mutant connexins. In particular, molecules that specifically modulate connexin hemichannel function without affecting gap junction channels are considered of primary importance for the study of connexin hemichannel role in physiological as well as pathological conditions. Monoclonal antibodies developed in the last three decades have become the most important class of therapeutic biologicals. Recombinant methods permit rapid selection and improvement of monoclonal antibodies from libraries with large diversity. Methods: By screening a combinatorial library of human single-chain fragment variable (scFv) antibodies expressed in phage, we identified a candidate that binds an extracellular epitope of Cx26. We characterized antibody action using a variety of biochemical and biophysical assays in HeLa cells, organotypic cultures of mouse cochlea and human keratinocyte-derived cells. Results: We determined that the antibody is a remarkably efficient, non-toxic, and completely reversible inhibitor of hemichannels formed by connexin 26 and does not affect direct cell-cell communication via gap junction channels. Importantly, we also demonstrate that the antibody efficiently inhibits hyperative mutant Cx26 hemichannels implicated in autosomal dominant non-syndromic hearing impairment accompanied by keratitis and hystrix-like ichthyosis-deafness (KID/HID) syndrome. We solved the crystal structure of the antibody, identified residues that are critical for binding and used molecular dynamics to uncover its mechanism of action. Conclusions: Although further studies will be necessary to validate the effect of the antibody in vivo, the methodology described here can be extended to select antibodies against hemichannels composed by other connexin isoforms and, consequently, to target other pathologies associated with hyperactive hemichannels. Our study highlights the potential of this approach and identifies connexins as therapeutic targets addressable by screening phage display libraries expressing human randomized antibodies.
Collapse
Affiliation(s)
- Liang Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Andrea Carrer
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China.,CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy
| | - Zhihu Qu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Sheng Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Federico Ceriani
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy
| | - Damiano Buratto
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy
| | - Giulia Crispino
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy.,Venetian Institute of Molecular MedicinePadova, Italy
| | - Veronica Zorzi
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Institute of Otolaryngology, Catholic University School of MedicineRome, Italy
| | - Gaia Ziraldo
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy.,Institute of Otolaryngology, Catholic University School of MedicineRome, Italy
| | - Francesca Bruno
- Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy.,Venetian Institute of Molecular MedicinePadova, Italy
| | - Chiara Nardin
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Science, Roma Tre UniversityRome, Italy
| | - Chiara Peres
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy
| | - Flavia Mazzarda
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Science, Roma Tre UniversityRome, Italy
| | - Anna M Salvatore
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy
| | - Marcello Raspa
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy
| | | | - Youjun Chu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Sichun Xie
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Xuemei Yang
- School of Life Science and Technology, Shanghai Tech UniversityShanghai, China
| | - Jun Liao
- School of Life Science and Technology, Shanghai Tech UniversityShanghai, China
| | - Xiao Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of SciencesShanghai, China.,University of Chinese Academy of SciencesBeijing, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Shanshan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Richard A Lerner
- Department of Cell and Molecular Biology, The Scripps Research InstituteLa Jolla, CA, United States
| | - Fabio Mammano
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China.,CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy.,Venetian Institute of Molecular MedicinePadova, Italy
| |
Collapse
|
23
|
Giudicelli V, Duroux P, Kossida S, Lefranc MP. IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST. BMC Immunol 2017; 18:35. [PMID: 28651553 PMCID: PMC5485737 DOI: 10.1186/s12865-017-0218-8] [Citation(s) in RCA: 14] [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: 04/03/2017] [Accepted: 06/16/2017] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND IMGT®, the international ImMunoGeneTics information system® ( http://www.imgt.org ), was created in 1989 in Montpellier, France (CNRS and Montpellier University) to manage the huge and complex diversity of the antigen receptors, and is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. Immunoglobulins (IG) or antibodies and T cell receptors (TR) are managed and described in the IMGT® databases and tools at the level of receptor, chain and domain. The analysis of the IG and TR variable (V) domain rearranged nucleotide sequences is performed by IMGT/V-QUEST (online since 1997, 50 sequences per batch) and, for next generation sequencing (NGS), by IMGT/HighV-QUEST, the high throughput version of IMGT/V-QUEST (portal begun in 2010, 500,000 sequences per batch). In vitro combinatorial libraries of engineered antibody single chain Fragment variable (scFv) which mimic the in vivo natural diversity of the immune adaptive responses are extensively screened for the discovery of novel antigen binding specificities. However the analysis of NGS full length scFv (~850 bp) represents a challenge as they contain two V domains connected by a linker and there is no tool for the analysis of two V domains in a single chain. METHODS The functionality "Analyis of single chain Fragment variable (scFv)" has been implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST for the analysis of the two V domains of IG and TR scFv. It proceeds in five steps: search for a first closest V-REGION, full characterization of the first V-(D)-J-REGION, then search for a second V-REGION and full characterization of the second V-(D)-J-REGION, and finally linker delimitation. RESULTS For each sequence or NGS read, positions of the 5'V-DOMAIN, linker and 3'V-DOMAIN in the scFv are provided in the 'V-orientated' sense. Each V-DOMAIN is fully characterized (gene identification, sequence description, junction analysis, characterization of mutations and amino changes). The functionality is generic and can analyse any IG or TR single chain nucleotide sequence containing two V domains, provided that the corresponding species IMGT reference directory is available. CONCLUSION The "Analysis of single chain Fragment variable (scFv)" implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST provides the identification and full characterization of the two V domains of full-length scFv (~850 bp) nucleotide sequences from combinatorial libraries. The analysis can also be performed on concatenated paired chains of expressed antigen receptor IG or TR repertoires.
Collapse
Affiliation(s)
- Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Patrice Duroux
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Sofia Kossida
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| |
Collapse
|
24
|
Li Y, Zimmermann G, Scheuermann J, Neri D. Quantitative PCR is a Valuable Tool to Monitor the Performance of DNA-Encoded Chemical Library Selections. Chembiochem 2017; 18:848-852. [PMID: 28220596 PMCID: PMC5606288 DOI: 10.1002/cbic.201600626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Indexed: 01/25/2023]
Abstract
Phage-display libraries and DNA-encoded chemical libraries (DECLs) represent useful tools for the isolation of specific binding molecules from large combinatorial sets of compounds. With both methods, specific binders are recovered at the end of affinity capture procedures by using target proteins of interest immobilized on a solid support. However, although the efficiency of phage-display selections is routinely quantified by counting the phage titer before and after the affinity capture step, no similar quantification procedures have been reported for the characterization of DECL selections. In this article, we describe the potential and limitations of quantitative PCR (qPCR) methods for the evaluation of selection efficiency by using a combinatorial chemical library with more than 35 million compounds. In the experimental conditions chosen for the selections, a quantification of DNA input/recovery over five orders of magnitude could be performed, revealing a successful enrichment of abundant binders, which could be confirmed by DNA sequencing. qPCR provided rapid information about the performance of selections, thus facilitating the optimization of experimental conditions.
Collapse
Affiliation(s)
- Yizhou Li
- Department of Chemistry and Applied Biosciences Swiss Federal
Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3, CH-8093
Zürich (Switzerland)
| | - Gunther Zimmermann
- Department of Chemistry and Applied Biosciences Swiss Federal
Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3, CH-8093
Zürich (Switzerland)
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences Swiss Federal
Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3, CH-8093
Zürich (Switzerland)
| | - Dario Neri
- Department of Chemistry and Applied Biosciences Swiss Federal
Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3, CH-8093
Zürich (Switzerland)
| |
Collapse
|
25
|
Satz AL, Hochstrasser R, Petersen AC. Analysis of Current DNA Encoded Library Screening Data Indicates Higher False Negative Rates for Numerically Larger Libraries. ACS COMBINATORIAL SCIENCE 2017; 19:234-238. [PMID: 28287689 DOI: 10.1021/acscombsci.7b00023] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To optimize future DNA-encoded library design, we have attempted to quantify the library size at which the signal becomes undetectable. To accomplish this we (i) have calculated that percent yields of individual library members following a screen range from 0.002 to 1%, (ii) extrapolated that ∼1 million copies per library member are required at the outset of a screen, and (iii) from this extrapolation predict that false negative rates will begin to outweigh the benefit of increased diversity at library sizes >108. The above analysis is based upon a large internal data set comprising multiple screens, targets, and libraries; we also augmented our internal data with all currently available literature data. In theory, high false negative rates may be overcome by employing larger amounts of library; however, we argue that using more than currently reported amounts of library (≫10 nmoles) is impractical. The above conclusions may be generally applicable to other DNA encoded library platforms, particularly those platforms that do not allow for library amplification.
Collapse
Affiliation(s)
- Alexander L. Satz
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
| | - Remo Hochstrasser
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
| | - Ann C. Petersen
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
| |
Collapse
|
26
|
Comor L, Dolinska S, Bhide K, Pulzova L, Jiménez-Munguía I, Bencurova E, Flachbartova Z, Potocnakova L, Kanova E, Bhide M. Joining the in vitro immunization of alpaca lymphocytes and phage display: rapid and cost effective pipeline for sdAb synthesis. Microb Cell Fact 2017; 16:13. [PMID: 28114943 PMCID: PMC5259998 DOI: 10.1186/s12934-017-0630-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
Background Camelids possess unique functional heavy chain antibodies, which can be produced and modified in vitro as a single domain antibody (sdAb or nanobody) with full antigen binding ability. Production of sdAb in conventional manner requires active immunization of Camelidae animal, which is laborious, time consuming, costly and in many cases not feasible (e.g. in case of highly toxic or infectious antigens). Results In this study, we describe an alternative pipeline that includes in vitro stimulation of naïve alpaca B-lymphocytes by antigen of interest (in this case endothelial cell binding domain of OspA of Borrelia) in the presence of recombinant alpaca interleukins 2 and 4, construction of sdAb phage library, selection of antigen specific sdAb expressed on phages (biopanning) and confirmation of binding ability of sdAb to the antigen. By joining the in vitro immunization and the phage display ten unique phage clones carrying sdAb were selected. Out of ten, seven sdAb showed strong antigen binding ability in phage ELISA. Furthermore, two soluble forms of sdAb were produced and their differential antigen binding affinity was measured with bio-layer interferometry. Conclusion A proposed pipeline has potential to reduce the cost substantially required for maintenance of camelid herd for active immunization. Furthermore, in vitro immunization can be achieved within a week to enrich mRNA copies encoding antigen-specific sdAbs in B cell. This rapid and cost effective pipeline can help researchers to develop efficiently sdAb for diagnostic and therapeutic purposes.
Collapse
Affiliation(s)
- Lubos Comor
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Saskia Dolinska
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Katarina Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Lucia Pulzova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Irene Jiménez-Munguía
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Elena Bencurova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Zuzana Flachbartova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Lenka Potocnakova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Evelina Kanova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia. .,Institute of Neuroimunnology, Slovak Academy of Sciences, Bratislava, Slovakia.
| |
Collapse
|
27
|
Ha KD, Bidlingmaier SM, Su Y, Lee NK, Liu B. Identification of Novel Macropinocytosing Human Antibodies by Phage Display and High-Content Analysis. Methods Enzymol 2017; 585:91-110. [PMID: 28109445 PMCID: PMC8671048 DOI: 10.1016/bs.mie.2016.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Internalizing antibodies have great potential for the development of targeted therapeutics. Antibodies that internalize via the macropinocytosis pathway are particularly promising since macropinocytosis is capable of mediating rapid, bulk uptake and is selectively upregulated in many cancers. We hereby describe a method for identifying antibodies that internalize via macropinocytosis by screening phage-displayed single-chain antibody selection outputs with an automated fluorescent microscopy-based high-content analysis platform. Furthermore, this method can be similarly applied to other endocytic pathways if other fluorescent, pathway-specific, soluble markers are available.
Collapse
Affiliation(s)
| | | | | | | | - Bin Liu
- Corresponding author Department of Anesthesia, University of California at San Francisco, 1001 Potrero Ave., Box 1305, San Francisco, CA 94110-1305,
| |
Collapse
|
28
|
Sterner A, Zehetmeier C. High-Throughput IgG Conversion of Phage Displayed Fab Antibody Fragments by AmplYFast. Methods Mol Biol 2017; 1575:121-143. [PMID: 28255877 DOI: 10.1007/978-1-4939-6857-2_7] [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: 06/06/2023]
Abstract
Phage display of antibody libraries is an invaluable strategy in antibody discovery. Many synthetic antibody library formats utilize monovalent antibody binding fragments (Fab), displayed on filamentous phage and expressed in Escherichia coli for selection and screening procedures, respectively. For most therapeutic applications, however, the final antibody candidate favors a bivalent immunoglobulin G (IgG) format, due to its particular effector function, half-life, and avidity.Here, we present an optimized subcloning method, termed AmplYFast, for the fast and convenient conversion of phage-displayed monovalent Fab fragments into full-length IgG or immunoglobulins of any other isotype. By using biotinylated primers, unique mammalian expression vectors, and multi-well plates, AmplYFast combines the rapid amplification, digestion, and ligation of recombinant Ig heavy and light chain sequences in an easy-to-operate high-throughput manner. Thus, AmplYFast improves quality and efficiency in DNA cloning and significantly minimizes timelines to antibody lead identification.
Collapse
Affiliation(s)
- Andrea Sterner
- MorphoSys AG, Semmelweisstrasse 7, 82152, Planegg, Germany.
| | | |
Collapse
|
29
|
Pasello M, Zamboni S, Mallano A, Flego M, Picci P, Cianfriglia M, Scotlandi K. Design and construction of a new human naïve single-chain fragment variable antibody library, IORISS1. J Biotechnol 2016; 224:1-11. [PMID: 26945728 DOI: 10.1016/j.jbiotec.2016.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/20/2016] [Accepted: 02/24/2016] [Indexed: 12/11/2022]
Abstract
Human monoclonal antibodies are a powerful tool with increasingly successful exploitations and the single chain fragment variable format can be considered the building block for the implementation of more complex and effective antibody-based constructs. Phage display is one of the best and most efficient methods to isolate human antibodies selected from an efficient and variable phage display library. We report a method for the construction of a human naïve single-chain variable fragment library, termed IORISS1. Many different sets of oligonucleotide primers as well as optimized electroporation and ligation reactions were used to generate this library of 1.2×10(9) individual clones. The key difference is the diversity of variable gene templates, which was derived from only 15 non-immunized human donors. The method described here, was used to make a new human naïve single-chain fragment variable phage display library that represents a valuable source of diverse antibodies that can be used as research reagents or as a starting point for the development of therapeutics. Using biopanning, we determined the ability of IORISS1 to yield antibodies. The results we obtained suggest that, by using an optimized protocol, an efficient phage antibody library can be generated.
Collapse
Affiliation(s)
- Michela Pasello
- CRS Development of Biomolecular Therapies, Experimental Oncology Laboratory, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy; PROMETEO Laboratory, STB, RIT Department, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy.
| | - Silvia Zamboni
- PROMETEO Laboratory, STB, RIT Department, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy; Section of Pharmacogenetics, Drug Resistance and Experimental Therapeutics, Department of Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Alessandra Mallano
- Section of Pharmacogenetics, Drug Resistance and Experimental Therapeutics, Department of Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Michela Flego
- Section of Pharmacogenetics, Drug Resistance and Experimental Therapeutics, Department of Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Piero Picci
- CRS Development of Biomolecular Therapies, Experimental Oncology Laboratory, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy; PROMETEO Laboratory, STB, RIT Department, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy
| | - Maurizio Cianfriglia
- Section of Pharmacogenetics, Drug Resistance and Experimental Therapeutics, Department of Drug Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Katia Scotlandi
- CRS Development of Biomolecular Therapies, Experimental Oncology Laboratory, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy; PROMETEO Laboratory, STB, RIT Department, Rizzoli Orthopaedic Institute, 40136 Bologna, Italy.
| |
Collapse
|
30
|
Ossysek K, Uchański T, Kulesza M, Bzowska M, Klaus T, Woś K, Madej M, Bereta J. A new expression vector facilitating production and functional analysis of scFv antibody fragments selected from Tomlinson I + J phagemid libraries. Immunol Lett 2015. [DOI: 10.1016/j.imlet.2015.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
31
|
Hortigüela MJ, Aumailley L, Srivastava A, Cunningham C, Anandakumar S, Robin S, Pandit A, Hu X, Wall JG. Engineering recombinant antibodies for polymer biofunctionalization. POLYM ADVAN TECHNOL 2015. [DOI: 10.1002/pat.3619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- María J. Hortigüela
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| | - Lucie Aumailley
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
- Faculty of Medicine; Laval University and CHU de Quebec Research Center; Quebec Canada
| | - Akshay Srivastava
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| | - Claire Cunningham
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
- Alimentary Glycoscience Research Cluster; National University of Ireland; Galway Ireland
| | - Soshee Anandakumar
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| | - Sylvain Robin
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
- Transgene; Boulevard Gonthier d'Andernach; Parc d'Innovation 67405 Illkirch Graffenstaden France
| | - Abhay Pandit
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| | - Xuejun Hu
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
- Medical College; Dalian University; Xuefu Avenue No.10, Dalian Economical and Technological Development Zone Liaoning 116622 China
| | - J. Gerard Wall
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| |
Collapse
|
32
|
Bujak E, Pretto F, Neri D. Generation and tumor recognition properties of two human monoclonal antibodies specific to cell surface anionic phospholipids. Invest New Drugs 2015; 33:791-800. [PMID: 25983040 DOI: 10.1007/s10637-015-0248-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/29/2015] [Indexed: 11/28/2022]
Abstract
Phosphatidylserine (PS) and other anionic phospholipids, which become exposed on the surface of proliferating endothelial cells, tumor cells and certain leukocytes, have been used as targets for the development of clinical-stage biopharmaceuticals. One of these products (bavituximab) is currently being investigated in Phase 3 clinical trials. There are conflicting reports on the ability of bavituximab and other antibodies to recognize PS directly or through beta-2 glycoprotein 1, a serum protein that is not highly conserved across species. Here, we report on the generation and characterization of two fully human antibodies directed against phosphatidylserine. One of these antibodies (PS72) bound specifically to phosphatidylserine and to phosphatidic acid, but did not recognize other closely related phospholipids, while the other antibody (PS41) also bound to cardiolipin. Both PS72 and PS41 stained 8/9 experimental tumor models in vitro, but both antibodies failed to exhibit a preferential tumor accumulation in vivo, as revealed by quantitative biodistribution analysis. Our findings indicate that anionic phospholipids are exposed and accessible in most tumor types, but cast doubts about the possibility of efficiently targeting tumors in vivo with PS-specific reagents.
Collapse
Affiliation(s)
- Emil Bujak
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland
| | | | | |
Collapse
|
33
|
A Monoclonal Antibody to Human DLK1 Reveals Differential Expression in Cancer and Absence in Healthy Tissues. Antibodies (Basel) 2015. [DOI: 10.3390/antib4020071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
34
|
Kügler J, Wilke S, Meier D, Tomszak F, Frenzel A, Schirrmann T, Dübel S, Garritsen H, Hock B, Toleikis L, Schütte M, Hust M. Generation and analysis of the improved human HAL9/10 antibody phage display libraries. BMC Biotechnol 2015; 15:10. [PMID: 25888378 PMCID: PMC4352240 DOI: 10.1186/s12896-015-0125-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/09/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Antibody phage display is a proven key technology that allows the generation of human antibodies for diagnostics and therapy. From naive antibody gene libraries - in theory - antibodies against any target can be selected. Here we describe the design, construction and characterization of an optimized antibody phage display library. RESULTS The naive antibody gene libraries HAL9 and HAL10, with a combined theoretical diversity of 1.5×10(10) independent clones, were constructed from 98 healthy donors using improved phage display vectors. In detail, most common phagemids employed for antibody phage display are using a combined His/Myc tag for detection and purification. We show that changing the tag order to Myc/His improved the production of soluble antibodies, but did not affect antibody phage display. For several published antibody libraries, the selected number of kappa scFvs were lower compared to lambda scFvs, probably due to a lower kappa scFv or Fab expression rate. Deletion of a phenylalanine at the end of the CL linker sequence in our new phagemid design increased scFv production rate and frequency of selected kappa antibodies significantly. The HAL libraries and 834 antibodies selected against 121 targets were analyzed regarding the used germline V-genes, used V-gene combinations and CDR-H3/-L3 length and composition. The amino acid diversity and distribution in the CDR-H3 of the initial library was retrieved in the CDR-H3 of selected antibodies showing that all CDR-H3 amino acids occurring in the human antibody repertoire can be functionally used and is not biased by E. coli expression or phage selection. Further, the data underline the importance of CDR length variations. CONCLUSION The highly diverse universal antibody gene libraries HAL9/10 were constructed using an optimized scFv phagemid vector design. Analysis of selected antibodies revealed that the complete amino acid diversity in the CDR-H3 was also found in selected scFvs showing the functionality of the naive CDR-H3 diversity.
Collapse
Affiliation(s)
- Jonas Kügler
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany. .,mAb-factory GmbH, Gelsenkirchenstr. 5, 38108, Braunschweig, Germany.
| | - Sonja Wilke
- mAb-factory GmbH, Gelsenkirchenstr. 5, 38108, Braunschweig, Germany.
| | - Doris Meier
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany.
| | - Florian Tomszak
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany.
| | - André Frenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany. .,YUMAB GmbH, Rebenring 33, 38106, Braunschweig, Germany.
| | - Thomas Schirrmann
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany. .,YUMAB GmbH, Rebenring 33, 38106, Braunschweig, Germany.
| | - Stefan Dübel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany.
| | - Henk Garritsen
- Klinikum Braunschweig g GmbH, Institut für Klinische Transfusionsmedizin, Celler Str. 38, 38114, Braunschweig, Germany. .,Department Vaccinology, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124, Braunschweig, Germany.
| | | | | | | | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany.
| |
Collapse
|
35
|
Dennler P, Bailey LK, Spycher PR, Schibli R, Fischer E. Microbial transglutaminase and c-myc-tag: a strong couple for the functionalization of antibody-like protein scaffolds from discovery platforms. Chembiochem 2015; 16:861-7. [PMID: 25688874 DOI: 10.1002/cbic.201500009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 12/30/2022]
Abstract
Antibody-like proteins selected from discovery platforms are preferentially functionalized by site-specific modification as this approach preserves the binding abilities and allows a side-by-side comparison of multiple conjugates. Here we present an enzymatic bioconjugation platform that targets the c-myc-tag peptide sequence (EQKLISEEDL) as a handle for the site-specific modification of antibody-like proteins. Microbial transglutaminase (MTGase) was exploited to form a stable isopeptide bond between the glutamine on the c-myc-tag and various primary-amine-functionalized substrates. We attached eight different functionalities to a c-myc-tagged antibody fragment and used these bioconjugates for downstream applications such as protein multimerization, immobilization on surfaces, fluorescence microscopy, fluorescence-activated cell sorting, and in vivo nuclear imaging. The results demonstrate the versatility of our conjugation strategy for transforming a c-myc-tagged protein into any desired probe.
Collapse
Affiliation(s)
- Patrick Dennler
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, OIPA10A, 5232 Villigen PSI, (Switzerland)
| | | | | | | | | |
Collapse
|