1
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Bates TA, Trank-Greene M, Nguyenla X, Anastas A, Gurmessa SK, Merutka IR, Dixon SD, Shumate A, Groncki AR, Parson MAH, Ingram JR, Barklis E, Burke JE, Shinde U, Ploegh HL, Tafesse FG. ESAT-6 undergoes self-association at phagosomal pH and an ESAT-6-specific nanobody restricts M. tuberculosis growth in macrophages. eLife 2024; 12:RP91930. [PMID: 38805257 PMCID: PMC11132683 DOI: 10.7554/elife.91930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) is known to survive within macrophages by compromising the integrity of the phagosomal compartment in which it resides. This activity primarily relies on the ESX-1 secretion system, predominantly involving the protein duo ESAT-6 and CFP-10. CFP-10 likely acts as a chaperone, while ESAT-6 likely disrupts phagosomal membrane stability via a largely unknown mechanism. we employ a series of biochemical analyses, protein modeling techniques, and a novel ESAT-6-specific nanobody to gain insight into the ESAT-6's mode of action. First, we measure the binding kinetics of the tight 1:1 complex formed by ESAT-6 and CFP-10 at neutral pH. Subsequently, we demonstrate a rapid self-association of ESAT-6 into large complexes under acidic conditions, leading to the identification of a stable tetrameric ESAT-6 species. Using molecular dynamics simulations, we pinpoint the most probable interaction interface. Furthermore, we show that cytoplasmic expression of an anti-ESAT-6 nanobody blocks Mtb replication, thereby underlining the pivotal role of ESAT-6 in intracellular survival. Together, these data suggest that ESAT-6 acts by a pH-dependent mechanism to establish two-way communication between the cytoplasm and the Mtb-containing phagosome.
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Affiliation(s)
- Timothy A Bates
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - Mila Trank-Greene
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - Xammy Nguyenla
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - Aidan Anastas
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - Sintayehu K Gurmessa
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - Ilaria R Merutka
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - Shandee D Dixon
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science UniversityPortlandUnited States
| | - Abigail R Groncki
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - Matthew AH Parson
- Department of Biochemistry and Microbiology, University of VictoriaVictoriaCanada
| | - Jessica R Ingram
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
| | - John E Burke
- Department of Biochemistry and Microbiology, University of VictoriaVictoriaCanada
- Department of Biochemistry and Molecular Biology, The University of British ColumbiaVancouverCanada
| | - Ujwal Shinde
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science UniversityPortlandUnited States
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences UniversityPortlandUnited States
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2
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Aripov VS, Volkova NV, Ilyichev AA, Shcherbakov DN. Problems of creating antibody phage libraries and their solutions. Vavilovskii Zhurnal Genet Selektsii 2024; 28:249-257. [PMID: 38680186 PMCID: PMC11043502 DOI: 10.18699/vjgb-24-29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/18/2024] [Accepted: 01/19/2023] [Indexed: 05/01/2024] Open
Abstract
Phage display has become an efficient, reliable and popular molecular technique for generating libraries encompassing millions or even billions of clones of divergent peptides or proteins. The method is based on the correspondence between phage genotype and phenotype, which ensures the presentation of recombinant proteins of known amino acid composition on the surface of phage particles. The use of affinity selection allows one to choose variants with affinity for different targets from phage libraries. The implementation of the antibody phage display technique has revolutionized the field of clinical immunology, both for developing tools to diagnose infectious diseases and for producing therapeutic agents. It has also become the basis for efficient and relatively inexpensive methods for studying protein-protein interactions, receptor binding sites, as well as epitope and mimotope identification. The antibody phage display technique involves a number of steps, and the final result depends on their successful implementation. The diversity, whether natural or obtained by combinatorial chemistry, is the basis of any library. The choice of molecular techniques is critical to ensure that this diversity is maintained during the phage library preparation step and during the transformation of E. coli cells. After a helper phage is added to the suspension of transformed E. coli cells, a bacteriophage library is formed, which is a working tool for performing the affinity selection procedure and searching for individual molecules. Despite the apparent simplicity of generating phage antibody libraries, a number of subtleties need to be taken into account. First, there are the features of phage vector preparation. Currently, a large number of phagemid vectors have been developed, and their selection is also of great importance. The key step is preparing competent E. coli cells and the technology of their transformation. The choice of a helper phage and the method used to generate it is also important. This article discusses the key challenges faced by researchers in constructing phage antibody libraries.
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Affiliation(s)
- V S Aripov
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - N V Volkova
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - A A Ilyichev
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - D N Shcherbakov
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
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3
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Bates TA, Trank-Greene M, Nguyenla X, Anastas A, Gurmessa SK, Merutka IR, Dixon SD, Shumate A, Groncki AR, Parson MAH, Ingram JR, Barklis E, Burke JE, Shinde U, Ploegh HL, Tafesse FG. ESAT-6 undergoes self-association at phagosomal pH and an ESAT-6 specific nanobody restricts M. tuberculosis growth in macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.16.553641. [PMID: 37645775 PMCID: PMC10462100 DOI: 10.1101/2023.08.16.553641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is known to survive within macrophages by compromising the integrity of the phagosomal compartment in which it resides. This activity primarily relies on the ESX-1 secretion system, predominantly involving the protein duo ESAT-6 and CFP-10. CFP-10 likely acts as a chaperone, while ESAT-6 likely disrupts phagosomal membrane stability via a largely unknown mechanism. we employ a series of biochemical analyses, protein modeling techniques, and a novel ESAT-6-specific nanobody to gain insight into the ESAT-6's mode of action. First, we measure the binding kinetics of the tight 1:1 complex formed by ESAT-6 and CFP-10 at neutral pH. Subsequently, we demonstrate a rapid self-association of ESAT-6 into large complexes under acidic conditions, leading to the identification of a stable tetrameric ESAT-6 species. Using molecular dynamics simulations, we pinpoint the most probable interaction interface. Furthermore, we show that cytoplasmic expression of an anti-ESAT-6 nanobody blocks Mtb replication, thereby underlining the pivotal role of ESAT-6 in intracellular survival. Together, these data suggest that ESAT-6 acts by a pH dependent mechanism to establish two-way communication between the cytoplasm and the Mtb-containing phagosome.
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Affiliation(s)
- Timothy A Bates
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - Mila Trank-Greene
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - Xammy Nguyenla
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - Aidan Anastas
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - Sintayehu K Gurmessa
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - Ilaria R Merutka
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - Shandee D Dixon
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon, United States
| | - Abigail R Groncki
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - Matthew AH Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Jessica R Ingram
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada
| | - Ujwal Shinde
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon, United States
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States
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4
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Najafi A, Valadan R, Asgarian-Omran H, Rafiei A, Tehrani M. Single domain antibodies specific for HER2 dimerization domain effectively disrupts HER2 dimerization. Int Immunopharmacol 2023; 124:110999. [PMID: 37804659 DOI: 10.1016/j.intimp.2023.110999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/09/2023]
Abstract
Dimer-dependent phosphorylation of HER2 receptor is a key event for the signal transduction of HER family of receptors which correlates with tumor invasion and metastasis. New generation of therapies based on dimerization domain inhibition using monoclonal or fragment antibodies was introduced. A potent method for manufacturing antibodies and antibody fragments is the phage display antibody library method. A recombinant phage was generated using the phage display method from synthetic dAb library. Subtractive biopanning was performed on sepharose 4b resin. Evaluation of success of subtractive biopanning was confirmed by the PCR fingerprinting after the fourth round of biopanning. The fourth round of biopanning results in the isolation of several dimerization domain reactive clones based on the polyclonal phage ELISA results. Monoclonal phage cell ELISA was used to select the positive clones with the highest affinity, and they were subsequently employed for functional tests. Cell-ELISA, MTT assay and dimerization inhibition test revealed that the reactivity and specificity of the selected monoclonal phage to dimerization domain of HER2. Further, Annexin V/PI staining and gene expression analysis showed that increased apoptosis rates. Also, in silico binding of the selected clones to conformational structure of HER2 was applied, using protein-protein docking tool of the ICM-Pro software, and showed sdAbs were specifically interacted with dimerization domain of the receptor. In conclusion, we have identified a single domain targeting HER2 dimerization, which represents a promising therapeutic and diagnostic candidate for HER2-positive cancers. Purified sdAb needs to more research to evaluate it both in vivo and in vitro via functional tests to determine if it can be applied for treatment and diagnostics.
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Affiliation(s)
- Ahmad Najafi
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Reza Valadan
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell-Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Hossein Asgarian-Omran
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell-Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Alireza Rafiei
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell-Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mohsen Tehrani
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell-Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
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5
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Peissert F, Pedotti M, Corbellari R, Simonelli L, De Gasparo R, Tamagnini E, Plüss L, Elsayed A, Matasci M, De Luca R, Cassaniti I, Sammartino JC, Piralla A, Baldanti F, Neri D, Varani L. Adapting Neutralizing Antibodies to Viral Variants by Structure-Guided Affinity Maturation Using Phage Display Technology. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2300088. [PMID: 37829677 PMCID: PMC10566804 DOI: 10.1002/gch2.202300088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Indexed: 10/14/2023]
Abstract
Neutralizing monoclonal antibodies have achieved great efficacy and safety for the treatment of numerous infectious diseases. However, their neutralization potency is often rapidly lost when the target antigen mutates. Instead of isolating new antibodies each time a pathogen variant arises, it can be attractive to adapt existing antibodies, making them active against the new variant. Potential benefits of this approach include reduced development time, cost, and regulatory burden. Here a methodology is described to rapidly evolve neutralizing antibodies of proven activity, improving their function against new pathogen variants without losing efficacy against previous ones. The reported procedure is based on structure-guided affinity maturation using combinatorial mutagenesis and phage display technology. Its use against the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is demonstrated, but it is suitable for any other pathogen. As proof of concept, the method is applied to CoV-X2, a human bispecific antibody that binds with high affinity to the early SARS-CoV-2 variants but lost neutralization potency against Delta. Antibodies emerging from the affinity maturation selection exhibit significantly improved neutralization potency against Delta and no loss of efficacy against the other viral sequences tested. These results illustrate the potential application of structure-guided affinity maturation in facilitating the rapid adaptation of neutralizing antibodies to pathogen variants.
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Affiliation(s)
| | - Mattia Pedotti
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | | | - Luca Simonelli
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Raoul De Gasparo
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Elia Tamagnini
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Louis Plüss
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
| | | | | | | | - Irene Cassaniti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Jose’ Camilla Sammartino
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Antonio Piralla
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Fausto Baldanti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
- Department of Clinical Surgical Diagnostic and Pediatric SciencesUniversità degli Studi di PaviaPavia27100Italy
| | - Dario Neri
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
- Philogen SpALocalità Bellaria 35Sovicille (SI)53018Italy
| | - Luca Varani
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
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6
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França RKA, Studart IC, Bezerra MRL, Pontes LQ, Barbosa AMA, Brigido MM, Furtado GP, Maranhão AQ. Progress on Phage Display Technology: Tailoring Antibodies for Cancer Immunotherapy. Viruses 2023; 15:1903. [PMID: 37766309 PMCID: PMC10536222 DOI: 10.3390/v15091903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The search for innovative anti-cancer drugs remains a challenge. Over the past three decades, antibodies have emerged as an essential asset in successful cancer therapy. The major obstacle in developing anti-cancer antibodies is the need for non-immunogenic antibodies against human antigens. This unique requirement highlights a disadvantage to using traditional hybridoma technology and thus demands alternative approaches, such as humanizing murine monoclonal antibodies. To overcome these hurdles, human monoclonal antibodies can be obtained directly from Phage Display libraries, a groundbreaking tool for antibody selection. These libraries consist of genetically engineered viruses, or phages, which can exhibit antibody fragments, such as scFv or Fab on their capsid. This innovation allows the in vitro selection of novel molecules directed towards cancer antigens. As foreseen when Phage Display was first described, nowadays, several Phage Display-derived antibodies have entered clinical settings or are undergoing clinical evaluation. This comprehensive review unveils the remarkable progress in this field and the possibilities of using clever strategies for phage selection and tailoring the refinement of antibodies aimed at increasingly specific targets. Moreover, the use of selected antibodies in cutting-edge formats is discussed, such as CAR (chimeric antigen receptor) in CAR T-cell therapy or ADC (antibody drug conjugate), amplifying the spectrum of potential therapeutic avenues.
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Affiliation(s)
- Renato Kaylan Alves França
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.F.); (M.M.B.)
- Graduate Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Igor Cabral Studart
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza 60440-970, Brazil
| | - Marcus Rafael Lobo Bezerra
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza 60440-970, Brazil
| | - Larissa Queiroz Pontes
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza 60440-970, Brazil
| | - Antonio Marcos Aires Barbosa
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Applied Informatics, University of Fortaleza, Fortaleza 60811-905, Brazil
| | - Marcelo Macedo Brigido
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.F.); (M.M.B.)
| | - Gilvan Pessoa Furtado
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza 60440-970, Brazil
| | - Andréa Queiroz Maranhão
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.F.); (M.M.B.)
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7
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Struijf EM, De la O Becerra KI, Ruyken M, de Haas CJC, van Oosterom F, Siere DY, van Keulen JE, Heesterbeek DAC, Dolk E, Heukers R, Bardoel BW, Gros P, Rooijakkers SHM. Inhibition of cleavage of human complement component C5 and the R885H C5 variant by two distinct high affinity anti-C5 nanobodies. J Biol Chem 2023; 299:104956. [PMID: 37356719 PMCID: PMC10374974 DOI: 10.1016/j.jbc.2023.104956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023] Open
Abstract
The human complement system plays a crucial role in immune defense. However, its erroneous activation contributes to many serious inflammatory diseases. Since most unwanted complement effector functions result from C5 cleavage into C5a and C5b, development of C5 inhibitors, such as clinically approved monoclonal antibody eculizumab, are of great interest. Here, we developed and characterized two anti-C5 nanobodies, UNbC5-1 and UNbC5-2. Using surface plasmon resonance, we determined a binding affinity of 119.9 pM for UNbC5-1 and 7.7 pM for UNbC5-2. Competition experiments determined that the two nanobodies recognize distinct epitopes on C5. Both nanobodies efficiently interfered with C5 cleavage in a human serum environment, as they prevented red blood cell lysis via membrane attack complexes (C5b-9) and the formation of chemoattractant C5a. The cryo-EM structure of UNbC5-1 and UNbC5-2 in complex with C5 (3.6 Å resolution) revealed that the binding interfaces of UNbC5-1 and UNbC5-2 overlap with known complement inhibitors eculizumab and RaCI3, respectively. UNbC5-1 binds to the MG7 domain of C5, facilitated by a hydrophobic core and polar interactions, and UNbC5-2 interacts with the C5d domain mostly by salt bridges and hydrogen bonds. Interestingly, UNbC5-1 potently binds and inhibits C5 R885H, a genetic variant of C5 that is not recognized by eculizumab. Altogether, we identified and characterized two different, high affinity nanobodies against human C5. Both nanobodies could serve as diagnostic and/or research tools to detect C5 or inhibit C5 cleavage. Furthermore, the residues targeted by UNbC5-1 hold important information for therapeutic inhibition of different polymorphic variants of C5.
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Affiliation(s)
- Eva M Struijf
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Karla I De la O Becerra
- Structural Biochemistry Group, Faculty of Science, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Maartje Ruyken
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Carla J C de Haas
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fleur van Oosterom
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Danique Y Siere
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joanne E van Keulen
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dani A C Heesterbeek
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | | | - Bart W Bardoel
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Piet Gros
- Structural Biochemistry Group, Faculty of Science, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Suzan H M Rooijakkers
- Department Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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8
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Alonso Villela SM, Kraïem-Ghezal H, Bouhaouala-Zahar B, Bideaux C, Aceves Lara CA, Fillaudeau L. Production of recombinant scorpion antivenoms in E. coli: current state and perspectives. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12578-1. [PMID: 37199752 DOI: 10.1007/s00253-023-12578-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
Scorpion envenomation is a serious health problem in tropical and subtropical zones. The access to scorpion antivenom is sometimes limited in availability and specificity. The classical production process is cumbersome, from the hyper-immunization of the horses to the IgG digestion and purification of the F(ab)'2 antibody fragments. The production of recombinant antibody fragments in Escherichia coli is a popular trend due to the ability of this microbial host to produce correctly folded proteins. Small recombinant antibody fragments, such as single-chain variable fragments (scFv) and nanobodies (VHH), have been constructed to recognize and neutralize the neurotoxins responsible for the envenomation symptoms in humans. They are the focus of interest of the most recent studies and are proposed as potentially new generation of pharmaceuticals for their use in immunotherapy against scorpion stings of the Buthidae family. This literature review comprises the current status on the scorpion antivenom market and the analyses of cross-reactivity of commercial scorpion anti-serum against non-specific scorpion venoms. Recent studies on the production of new recombinant scFv and nanobodies will be presented, with a focus on the Androctonus and Centruroides scorpion species. Protein engineering-based technology could be the key to obtaining the next generation of therapeutics capable of neutralizing and cross-reacting against several types of scorpion venoms. KEY POINTS: • Commercial antivenoms consist of predominantly purified equine F(ab)'2fragments. • Nanobody-based antivenom can neutralize Androctonus venoms and have a low immunogenicity. • Affinity maturation and directed evolution are used to obtain potent scFv families against Centruroides scorpions.
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Affiliation(s)
| | - Hazar Kraïem-Ghezal
- Laboratoire Des Venins Et Molécules Thérapeutiques, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur BP74, 1002, Tunis, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratoire Des Venins Et Molécules Thérapeutiques, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur BP74, 1002, Tunis, Tunisia.
- Faculté de Médecine de Tunis, Université de Tunis El Manar, Tunis, Tunisia.
| | - Carine Bideaux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Luc Fillaudeau
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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9
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Contreras MA, Serrano-Rivero Y, González-Pose A, Salazar-Uribe J, Rubio-Carrasquilla M, Soares-Alves M, Parra NC, Camacho-Casanova F, Sánchez-Ramos O, Moreno E. Design and Construction of a Synthetic Nanobody Library: Testing Its Potential with a Single Selection Round Strategy. Molecules 2023; 28:molecules28093708. [PMID: 37175117 PMCID: PMC10180287 DOI: 10.3390/molecules28093708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
Nanobodies (Nbs) are single domain antibody fragments derived from heavy-chain antibodies found in members of the Camelidae family. They have become a relevant class of biomolecules for many different applications because of several important advantages such as their small size, high solubility and stability, and low production costs. On the other hand, synthetic Nb libraries are emerging as an attractive alternative to animal immunization for the selection of antigen-specific Nbs. Here, we present the design and construction of a new synthetic nanobody library using the phage display technology, following a structure-based approach in which the three hypervariable loops were subjected to position-specific randomization schemes. The constructed library has a clonal diversity of 108 and an amino acid variability that matches the codon distribution set by design at each randomized position. We have explored the capabilities of the new library by selecting nanobodies specific for three antigens: vascular endothelial growth factor (VEGF), tumor necrosis factor (TNF) and the glycoprotein complex (GnGc) of Andes virus. To test the potential of the library to yield a variety of antigen-specific Nbs, we introduced a biopanning strategy consisting of a single selection round using stringent conditions. Using this approach, we obtained several binders for each of the target antigens. The constructed library represents a promising nanobody source for different applications.
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Affiliation(s)
- María Angélica Contreras
- Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion 4070386, Chile
| | | | - Alaín González-Pose
- Faculty of Basic Sciences, University of Medellin, Medellin 050026, Colombia
| | | | | | - Matheus Soares-Alves
- Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion 4070386, Chile
| | - Natalie C Parra
- Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion 4070386, Chile
| | - Frank Camacho-Casanova
- Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion 4070386, Chile
| | - Oliberto Sánchez-Ramos
- Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion 4070386, Chile
| | - Ernesto Moreno
- Faculty of Basic Sciences, University of Medellin, Medellin 050026, Colombia
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10
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Yang Z, Wu Z, Santich BH, Liu J, Liu C, Cheung NKV. Targeting Intracellular Antigens with pMHC-Binding Antibodies: A Phage Display Approach. Methods Mol Biol 2023; 2702:327-345. [PMID: 37679628 DOI: 10.1007/978-1-0716-3381-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Antibodies that bind peptide-MHC (pMHC) complex in a manner akin to T cell receptor (TCR) have not only helped in understanding the mechanism of TCR-pMHC interactions in the context of T cell biology but also spurred considerable interest in recent years as potential cancer therapeutics. Traditional methods to generate such antibodies using hybridoma and B cell sorting technologies are sometimes inadequate, possibly due to the small contribution of peptide to the overall B cell epitope space on the surface of the pMHC complex (typical peptide MW = 1 kDa versus MHC MW = 45 kDa) and to the multiple efficiency limiting steps inherent in these methods. In this chapter we describe phage display approaches, including a cell panning strategy, for the rapid generation of such antibodies with high specificity and affinity.
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Affiliation(s)
| | - Zhihao Wu
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian H Santich
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | | | - Cheng Liu
- Eureka Therapeutics, Emeryville, CA, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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11
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Abstract
Phage display has been applied successfully for the rapid isolation of monoclonal antibodies against various targets including infectious diseases, autoantigens, cancer markers, and even small molecules. The main component in any phage display experiment is the availability of an antibody library to carry out the selection process of target-specific antibodies through an iterative process termed as biopanning. To generate human antibody libraries, the antibody repertoire can be obtained from human peripheral blood mononuclear cell (PBMC) or directly from cell-sorted B-cell populations. The choice of antibody isotype is dictated by the nature of the library. Naïve libraries would utilize IgM repertoires, whereas the IgG repertoire is commonly used for immune libraries. Antibody genes are amplified through polymerase chain reaction (PCR) and paired in a combinatorial fashion to expand the diversity of the cloned library repertoire. The protocol here describes the use of a two-step cloning method that can be applied for the construction of either a naïve or immune human antibody library in Fab format followed by the subsequent panning.
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Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
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12
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Li X, Jones KS, Acca FE, Chapados CD, Driscoll HA, Fuller EP, Mendez QM, Mirando G, Weiner MP, Ferguson MR. Epivolve: A Protocol for Site-Directed Antibodies. Methods Mol Biol 2023; 2702:587-601. [PMID: 37679640 PMCID: PMC10568616 DOI: 10.1007/978-1-0716-3381-6_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Researchers can often successfully generate antibodies to predicted epitopes. Especially when the epitopes are on the surface of a protein or in a hydrophilic loop. But it is difficult to direct recombinant antibodies to bind either to- or near a specific amino acid on a protein or peptide. We have developed a unique immune-targeting strategy, that we call "Epivolve," that enables us to make site-specific antibodies (Abs). Epivolve technology leverages a highly immunogenic modified amino acid that acts as a "pseudo-hapten" immuno-target and takes advantage of Ab affinity maturation technologies to make high-affinity site-specific antibodies. Epivolve functions by the evolution of an Ab paratope to either synonymous or especially non-synonymous amino acid (aa) binding. Here we describe the use of Epivolve technology in phage display and the protocols for developing site-specific antibodies.
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Affiliation(s)
| | | | | | | | | | - Emily P Fuller
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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13
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Fehrsen J, Wemmer S, van Wyngaardt W. Construction of Chicken and Ostrich Antibody Libraries. Methods Mol Biol 2023; 2702:77-92. [PMID: 37679616 DOI: 10.1007/978-1-0716-3381-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Recombinant antibody libraries based on chicken immunoglobulin genes are potentially valuable sources of phage-displayed scFvs for use in veterinary diagnostics and research. To add diversity to the scFv repertoire, we expanded the library to include genes from the ostrich, indigenous to southern Africa. The libraries described in this chapter are based on the chicken and ostrich variable heavy and light chain immunoglobulin genes joined by a short flexible linker cloned in the phagemid vector pHEN1. The resulting phagemids produce either scFvs displayed on the surface of the fusion phage subsequent to co-infection with helper phage or soluble scFvs following IPTG induction. This chapter provides detailed and proven methods for the construction of such libraries.
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Affiliation(s)
- Jeanni Fehrsen
- ARC-Onderstepoort Veterinary Research, Pretoria, South Africa.
| | - Susan Wemmer
- ARC-Onderstepoort Veterinary Research, Pretoria, South Africa
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Ruschig M, Heine PA, Fühner V, Zilkens KJK, Steinke S, Schubert M, Bertoglio F, Hust M. Construction of Human Immune and Naive scFv Phage Display Libraries. Methods Mol Biol 2023; 2702:15-37. [PMID: 37679613 DOI: 10.1007/978-1-0716-3381-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Antibody phage display is a widely used in vitro selection technology for the generation of human recombinant antibodies and has yielded thousands of useful antibodies for research, diagnostics, and therapy. In order to successfully generate antibodies using phage display, the basis is the construction of high-quality antibody gene libraries. Here, we describe detailed methods for the construction of such high-quality immune and naive scFv gene libraries of human origin. These protocols were used to develop human naive (e.g., HAL9/10) and immune libraries, which resulted in thousands of specific antibodies for all kinds of applications.
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Affiliation(s)
- Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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Muñoz-López P, Ribas-Aparicio RM, Becerra-Báez EI, Fraga-Pérez K, Flores-Martínez LF, Mateos-Chávez AA, Luria-Pérez R. Single-Chain Fragment Variable: Recent Progress in Cancer Diagnosis and Therapy. Cancers (Basel) 2022; 14:cancers14174206. [PMID: 36077739 PMCID: PMC9455005 DOI: 10.3390/cancers14174206] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Recombinant antibody fragments have shown remarkable potential as diagnostic and therapeutic tools in the fight against cancer. The single-chain fragment variable (scFv) that contains the complete antigen-binding domains of a whole antibody, has several advantages such as a high specificity and affinity for antigens, a low immunogenicity, and the proven ability to penetrate tumor tissues and diffuse. This review provides an overview of the current studies on the principle, generation, and applications of scFvs, particularly in the diagnosis and therapy of cancer, and underscores their potential use in clinical trials. Abstract Cancer remains a public health problem worldwide. Although conventional therapies have led to some excellent outcomes, some patients fail to respond to treatment, they have few therapeutic alternatives and a poor survival prognosis. Several strategies have been proposed to overcome this issue. The most recent approach is immunotherapy, particularly the use of recombinant antibodies and their derivatives, such as the single-chain fragment variable (scFv) containing the complete antigen-binding domains of a whole antibody that successfully targets tumor cells. This review describes the recent progress made with scFvs as a cancer diagnostic and therapeutic tool, with an emphasis on preclinical approaches and their potential use in clinical trials.
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Affiliation(s)
- Paola Muñoz-López
- Unit of Investigative Research on Hemato-Oncological Diseases, Hospital Infantil de México Federico Gómez, Doctor Márquez 162, Mexico City 06720, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico
| | - Elayne Irene Becerra-Báez
- Unit of Investigative Research on Hemato-Oncological Diseases, Hospital Infantil de México Federico Gómez, Doctor Márquez 162, Mexico City 06720, Mexico
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico
| | - Karla Fraga-Pérez
- Unit of Investigative Research on Hemato-Oncological Diseases, Hospital Infantil de México Federico Gómez, Doctor Márquez 162, Mexico City 06720, Mexico
| | - Luis Fernando Flores-Martínez
- Unit of Investigative Research on Hemato-Oncological Diseases, Hospital Infantil de México Federico Gómez, Doctor Márquez 162, Mexico City 06720, Mexico
| | - Armando Alfredo Mateos-Chávez
- Unit of Investigative Research on Hemato-Oncological Diseases, Hospital Infantil de México Federico Gómez, Doctor Márquez 162, Mexico City 06720, Mexico
| | - Rosendo Luria-Pérez
- Unit of Investigative Research on Hemato-Oncological Diseases, Hospital Infantil de México Federico Gómez, Doctor Márquez 162, Mexico City 06720, Mexico
- Correspondence: ; Tel.: +52-(55)-5228-9917 (ext. 4401)
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16
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Favorskaya IA, Shcheblyakov DV, Esmagambetov IB, Dolzhikova IV, Alekseeva IA, Korobkova AI, Voronina DV, Ryabova EI, Derkaev AA, Kovyrshina AV, Iliukhina AA, Botikov AG, Voronina OL, Egorova DA, Zubkova OV, Ryzhova NN, Aksenova EI, Kunda MS, Logunov DY, Naroditsky BS, Gintsburg AL. Single-Domain Antibodies Efficiently Neutralize SARS-CoV-2 Variants of Concern. Front Immunol 2022; 13:822159. [PMID: 35281053 PMCID: PMC8907979 DOI: 10.3389/fimmu.2022.822159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/28/2022] [Indexed: 11/21/2022] Open
Abstract
Virus-neutralizing antibodies are one of the few treatment options for COVID-19. The evolution of SARS-CoV-2 virus has led to the emergence of virus variants with reduced sensitivity to some antibody-based therapies. The development of potent antibodies with a broad spectrum of neutralizing activity is urgently needed. Here we isolated a panel of single-domain antibodies that specifically bind to the receptor-binding domain of SARS-CoV-2 S glycoprotein. Three of the selected antibodies exhibiting most robust neutralization potency were used to generate dimeric molecules. We observed that these modifications resulted in up to a 200-fold increase in neutralizing activity. The most potent heterodimeric molecule efficiently neutralized each of SARS-CoV-2 variant of concern, including Alpha, Beta, Gamma, Delta and Omicron variants. This heterodimeric molecule could be a promising drug candidate for a treatment for COVID-19 caused by virus variants of concern.
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Affiliation(s)
- Irina A Favorskaya
- Medical Microbiology Department, Federal State Budget Institution "National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Dmitry V Shcheblyakov
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Ilias B Esmagambetov
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Inna V Dolzhikova
- Department of the National Virus Collection, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Irina A Alekseeva
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasia I Korobkova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Daria V Voronina
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Ekaterina I Ryabova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Artem A Derkaev
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anna V Kovyrshina
- Department of the National Virus Collection, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anna A Iliukhina
- Department of the National Virus Collection, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey G Botikov
- Department of the National Virus Collection, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga L Voronina
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Daria A Egorova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga V Zubkova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Natalia N Ryzhova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Ekaterina I Aksenova
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Marina S Kunda
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Denis Y Logunov
- Medical Microbiology Department, Federal State Budget Institution "National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Boris S Naroditsky
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexandr L Gintsburg
- Department of Genetics and Molecular Biology of Bacteria, Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
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Yue H, Li Y, Yang M, Mao C. T7 Phage as an Emerging Nanobiomaterial with Genetically Tunable Target Specificity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103645. [PMID: 34914854 PMCID: PMC8811829 DOI: 10.1002/advs.202103645] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/27/2021] [Indexed: 05/05/2023]
Abstract
Bacteriophages, also known as phages, are specific antagonists against bacteria. T7 phage has drawn massive attention in precision medicine owing to its distinctive advantages, such as short replication cycle, ease in displaying peptides and proteins, high stability and cloning efficiency, facile manipulation, and convenient storage. By introducing foreign gene into phage DNA, T7 phage can present foreign peptides or proteins site-specifically on its capsid, enabling it to become a nanoparticle that can be genetically engineered to screen and display a peptide or protein capable of recognizing a specific target with high affinity. This review critically introduces the biomedical use of T7 phage, ranging from the detection of serological biomarkers and bacterial pathogens, recognition of cells or tissues with high affinity, design of gene vectors or vaccines, to targeted therapy of different challenging diseases (e.g., bacterial infection, cancer, neurodegenerative disease, inflammatory disease, and foot-mouth disease). It also discusses perspectives and challenges in exploring T7 phage, including the understanding of its interactions with human body, assembly into scaffolds for tissue regeneration, integration with genome editing, and theranostic use in clinics. As a genetically modifiable biological nanoparticle, T7 phage holds promise as biomedical imaging probes, therapeutic agents, drug and gene carriers, and detection tools.
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Affiliation(s)
- Hui Yue
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiang310027P. R. China
| | - Yan Li
- Institute of Applied Bioresource ResearchCollege of Animal ScienceZhejiang UniversityYuhangtang Road 866HangzhouZhejiang310058P. R. China
| | - Mingying Yang
- Institute of Applied Bioresource ResearchCollege of Animal ScienceZhejiang UniversityYuhangtang Road 866HangzhouZhejiang310058P. R. China
| | - Chuanbin Mao
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiang310027P. R. China
- Department of Chemistry and BiochemistryStephenson Life Science Research CenterInstitute for Biomedical Engineering, Science and TechnologyUniversity of Oklahoma101 Stephenson ParkwayNormanOklahoma73019‐5251USA
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18
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Liu B, Yang D. Easily Established and Multifunctional Synthetic Nanobody Libraries as Research Tools. Int J Mol Sci 2022; 23:ijms23031482. [PMID: 35163405 PMCID: PMC8835997 DOI: 10.3390/ijms23031482] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
Nanobodies, or VHHs, refer to the antigen-binding domain of heavy-chain antibodies (HCAbs) from camelids. They have been widely used as research tools for protein purification and structure determination due to their small size, high specificity, and high stability, overcoming limitations with conventional antibody fragments. However, animal immunization and subsequent retrieval of antigen-specific nanobodies are expensive and complicated. Construction of synthetic nanobody libraries using DNA oligonucleotides is a cost-effective alternative for immunization libraries and shows great potential in identifying antigen-specific or even conformation-specific nanobodies. This review summarizes and analyses synthetic nanobody libraries in the current literature, including library design and biopanning methods, and further discusses applications of antigen-specific nanobodies obtained from synthetic libraries to research.
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19
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Ang CS, Sacharz J, Leeming MG, Nie S, Varshney S, Scott NE, Williamson NA. Getting more out of FLAG-Tag co-immunoprecipitation mass spectrometry experiments using FAIMS. J Proteomics 2022; 254:104473. [PMID: 34990820 DOI: 10.1016/j.jprot.2021.104473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
Co-immunoprecipitation of proteins coupled to mass spectrometry is critical for the understanding of protein interaction networks. In instances where a suitable antibody is not available, it is common to graft synthetic tags onto a target protein sequence thereby allowing the use of commercially available antibodies for affinity purification. A common approach is through FLAG-Tag co-immunoprecipitation. To allow the selective elution of protein complexes, competitive displacement using a large molar excess of the tag peptides is often carried out. Yet, this creates downstream challenges for the mass spectrometry analysis due to the presence of large quantities of these peptides. Here, we demonstrate that Field Asymmetric Ion Mobility Spectrometry (FAIMS), a gas phase ion separation device prior to mass spectrometry analysis can be applied to FLAG-Tag co-immunoprecipitation experiments to increase the depth of protein coverage. By excluding these abundant tag peptides, we were able to observe deeper coverage of interacting proteins and as a result, deeper biological insights, without the need for additional sample handling or altering sample preparation protocols. SIGNIFICANCE: We have shown that application of FAIMS separation in the gas phase can increase the proteome coverage of Flag-Tagged co-immunoprecipitation mass spectrometry experiments versus one without FAIMS. We were able to observe deeper coverage of interacting proteins and as a result, deeper biological insights, without additional sample handling, fractionation, machine run time or modifying the sample preparation protocol.
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Affiliation(s)
- Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3052, Australia.
| | - Joanna Sacharz
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Michael G Leeming
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Swati Varshney
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3052, Australia.
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20
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Davydova EK. Protein Engineering: Advances in Phage Display for Basic Science and Medical Research. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S146-S110. [PMID: 35501993 PMCID: PMC8802281 DOI: 10.1134/s0006297922140127] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Functional Protein Engineering became the hallmark in biomolecule manipulation in the new millennium, building on and surpassing the underlying structural DNA manipulation and recombination techniques developed and employed in the last decades of 20th century. Because of their prominence in almost all biological processes, proteins represent extremely important targets for engineering enhanced or altered properties that can lead to improvements exploitable in healthcare, medicine, research, biotechnology, and industry. Synthetic protein structures and functions can now be designed on a computer and/or evolved using molecular display or directed evolution methods in the laboratory. This review will focus on the recent trends in protein engineering and the impact of this technology on recent progress in science, cancer- and immunotherapies, with the emphasis on the current achievements in basic protein research using synthetic antibody (sABs) produced by phage display pipeline in the Kossiakoff laboratory at the University of Chicago (KossLab). Finally, engineering of the highly specific binding modules, such as variants of Streptococcal protein G with ultra-high orthogonal affinity for natural and engineered antibody scaffolds, and their possible applications as a plug-and-play platform for research and immunotherapy will be described.
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Affiliation(s)
- Elena K Davydova
- The University of Chicago, Department of Biochemistry and Molecular Biology, Chicago, IL 60637, USA.
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21
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Dooley H. Generation of VNAR Libraries from Immunized Sharks and Selection of Target-Specific Clones. Methods Mol Biol 2022; 2421:57-72. [PMID: 34870811 DOI: 10.1007/978-1-0716-1944-5_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cartilaginous fishes (sharks, skates, rays, and chimeras) are the most phylogenetically distant lineage relative to mammals in which somatically rearranging immunoglobulins (Igs or antibodies) have also been found. Alongside their conventional (heavy-light chain) isotypes, IgM and IgW, sharks produce the novel isotype, IgNAR, a heavy-chain homodimer. Naturally lacking light chains, antigen binding is mediated by two highly soluble and independently functioning variable domains, or VNARs, each having a molecular weight of approximately 12 kDa. The small size, high affinity for antigen, and extreme structural stability of single-domain VNARs make them an emerging prospect for use in therapeutic, diagnostic, and research applications. In this chapter, we detail the immunization protocol we use to raise an antigen-specific IgNAR response in the nurse shark (Ginglymostoma cirratum), the subsequent cloning of the variable domains from this isotype, and the selection of antigen-specific VNARs by phage display.
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Affiliation(s)
- Helen Dooley
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Institute of Marine & Environmental Technology, Baltimore, MD, USA.
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The B-cell Receptor Autoantigen LRPAP1 Can Replace Variable Antibody Regions to Target Mantle Cell Lymphoma Cells. Hemasphere 2021; 5:e620. [PMID: 34263144 PMCID: PMC8274796 DOI: 10.1097/hs9.0000000000000620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/16/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022] Open
Abstract
Mantle cell lymphoma (MCL) accounts for 5%–10% of all lymphomas. The disease’s genetic hallmark is the t(11; 14)(q13; q32) translocation. In younger patients, the first-line treatment is chemoimmunotherapy followed by autologous stem cell transplantation. Upon disease progression, novel and targeted agents such as the BTK inhibitor ibrutinib, the BCL-2 inhibitor venetoclax, or the combination of both are increasingly used, but even after allogeneic stem cell transplantation or CAR T-cell therapy, MCL remains incurable for most patients. Chronic antigenic stimulation of the B-cell receptor (BCR) is thought to be essential for the pathogenesis of many B-cell lymphomas. LRPAP1 has been identified as the autoantigenic BCR target in about 1/3 of all MCLs. Thus, LRPAP1 could be used to target MCL cells, however, there is currently no optimal therapeutic format to integrate LRPAP1. We have therefore integrated LRPAP1 into a concept termed BAR, for B-cell receptor antigens for reverse targeting. A bispecific BAR body was synthesized consisting of the lymphoma-BCR binding epitope of LRPAP1 and a single chain fragment targeting CD3 or CD16 to recruit/engage T or NK cells. In addition, a BAR body consisting of an IgG1 antibody and the lymphoma-BCR binding epitope of LRPAP1 replacing the variable regions was synthesized. Both BAR bodies mediated highly specific cytotoxic effects against MCL cells in a dose-dependent manner at 1–20 µg/mL. In conclusion, LRPAP1 can substitute variable antibody regions in different formats to function in a new therapeutic approach to treat MCL.
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Simons JF, Lim YW, Carter KP, Wagner EK, Wayham N, Adler AS, Johnson DS. Affinity maturation of antibodies by combinatorial codon mutagenesis versus error-prone PCR. MAbs 2021; 12:1803646. [PMID: 32744131 PMCID: PMC7531523 DOI: 10.1080/19420862.2020.1803646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
IN VITRO affinity maturation of therapeutic monoclonal antibodies is commonly applied to achieve desired properties, such as improved binding kinetics and affinity. Currently there are no universally accepted protocols for generation of variegated antibody libraries or selection thereof. Here, we performed affinity maturation using a yeast-based single-chain variable fragment (scFv) expression system to compare two mutagenesis methods: random mutagenesis across the entire V(D)J region by error-prone PCR, and a novel combinatorial mutagenesis process limited to the complementarity-determining regions (CDRs). We applied both methods of mutagenesis to four human antibodies against well-known immuno-oncology target proteins. Detailed sequence analysis showed an even mutational distribution across the entire length of the scFv for the error-prone PCR method and an almost exclusive targeting of the CDRs for the combinatorial method. Though there were distinct mutagenesis profiles for each target antibody and mutagenesis method, we found that both methods improved scFv affinity with similar efficiency. When a subset of the affinity-matured antibodies was expressed as full-length immunoglobulin, the measured affinity constants were mostly comparable to those of the respective scFv, but the full-length antibodies were inferior to their scFv counterparts for one of the targets. Furthermore, we found that improved affinity for the full-length antibody did not always translate into enhanced binding to cell-surface expressed antigen or improved immune checkpoint blocking ability, suggesting that screening with full-length antibody or antigen-binding fragment formats might be advantageous and the subject of a future study.
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Guliy O, Zaitsev B, Teplykh A, Balashov S, Fomin A, Staroverov S, Borodina I. Acoustical Slot Mode Sensor for the Rapid Coronaviruses Detection. SENSORS 2021; 21:s21051822. [PMID: 33807879 PMCID: PMC7961855 DOI: 10.3390/s21051822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/26/2021] [Accepted: 02/28/2021] [Indexed: 12/02/2022]
Abstract
A method for the rapid detection of coronaviruses is presented on the example of the transmissible gastroenteritis virus (TGEV) directly in aqueous solutions with different conductivity. An acoustic sensor based on a slot wave in an acoustic delay line was used for the research. The addition of anti-TGEV antibodies (Abs) diluted in an aqueous solution led to a change in the depth and frequency of resonant peaks on the frequency dependence of the insertion loss of the sensor. The difference in the output parameters of the sensor before and after the biological interaction of the TGE virus in solutions with the specific antibodies allows drawing a conclusion about the presence/absence of the studied viruses in the analyzed solution. The possibility for virus detection in aqueous solutions with the conductivity of 1.9–900 μs/cm, as well as in the presence of the foreign viral particles, has been demonstrated. The analysis time did not exceed 10 min.
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Affiliation(s)
- Olga Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov 410049, Russia; (O.G.); (A.F.); (S.S.)
| | - Boris Zaitsev
- Kotel’nikov Institute of Radio Engineering and Electronics of RAS, Saratov Branch, Saratov 410019, Russia; (B.Z.); (A.T.)
| | - Andrey Teplykh
- Kotel’nikov Institute of Radio Engineering and Electronics of RAS, Saratov Branch, Saratov 410019, Russia; (B.Z.); (A.T.)
| | - Sergey Balashov
- Information Technology Center Renato Archer, Campinas CEP, SP 13069-901, Brazil;
| | - Alexander Fomin
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov 410049, Russia; (O.G.); (A.F.); (S.S.)
| | - Sergey Staroverov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov 410049, Russia; (O.G.); (A.F.); (S.S.)
| | - Irina Borodina
- Kotel’nikov Institute of Radio Engineering and Electronics of RAS, Saratov Branch, Saratov 410019, Russia; (B.Z.); (A.T.)
- Correspondence: ; Tel.: +7-8452-272401
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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Seidel-Greven M, Addai-Mensah O, Spiegel H, Chiegoua Dipah GN, Schmitz S, Breuer G, Frempong M, Reimann A, Klockenbring T, Fischer R, Barth S, Fendel R. Isolation and light chain shuffling of a Plasmodium falciparum AMA1-specific human monoclonal antibody with growth inhibitory activity. Malar J 2021; 20:37. [PMID: 33430886 PMCID: PMC7798374 DOI: 10.1186/s12936-020-03548-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/12/2020] [Indexed: 11/25/2022] Open
Abstract
Background Plasmodium falciparum, the parasite causing malaria, affects populations in many endemic countries threatening mainly individuals with low malaria immunity, especially children. Despite the approval of the first malaria vaccine Mosquirix™ and very promising data using cryopreserved P. falciparum sporozoites (PfSPZ), further research is needed to elucidate the mechanisms of humoral immunity for the development of next-generation vaccines and alternative malaria therapies including antibody therapy. A high prevalence of antibodies against AMA1 in immune individuals has made this antigen one of the major blood-stage vaccine candidates. Material and methods Using antibody phage display, an AMA1-specific growth inhibitory human monoclonal antibody from a malaria-immune Fab library using a set of three AMA1 diversity covering variants (DiCo 1–3), which represents a wide range of AMA1 antigen sequences, was selected. The functionality of the selected clone was tested in vitro using a growth inhibition assay with P. falciparum strain 3D7. To potentially improve affinity and functional activity of the isolated antibody, a phage display mediated light chain shuffling was employed. The parental light chain was replaced with a light chain repertoire derived from the same population of human V genes, these selected antibodies were tested in binding tests and in functionality assays. Results The selected parental antibody achieved a 50% effective concentration (EC50) of 1.25 mg/mL. The subsequent light chain shuffling led to the generation of four derivatives of the parental clone with higher expression levels, similar or increased affinity and improved EC50 against 3D7 of 0.29 mg/mL. Pairwise epitope mapping gave evidence for binding to AMA1 domain II without competing with RON2. Conclusion We have thus shown that a compact immune human phage display library is sufficient for the isolation of potent inhibitory monoclonal antibodies and that minor sequence mutations dramatically increase expression levels in Nicotiana benthamiana. Interestingly, the antibody blocks parasite inhibition independently of binding to RON2, thus having a yet undescribed mode of action.
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Affiliation(s)
- Melanie Seidel-Greven
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Otchere Addai-Mensah
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany.,Department of Medical Diagnostics, Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Gwladys Nina Chiegoua Dipah
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Stefan Schmitz
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Gudrun Breuer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Margaret Frempong
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Andreas Reimann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Torsten Klockenbring
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany.,Institute of Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.,Purdue University, West Lafayette, IN, 47907, USA
| | - Stefan Barth
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany.,Department of Experimental Medicine and Immunotherapy, Institute of Applied Medical Engineering, RWTH Aachen University Clinic, Pauwelsstraße 20, 52074, Aachen, Germany.,South African Research Chair in Cancer Biotechnology, Department of Integrative Biomedical Sciences, and Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rolf Fendel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr.6, 52074, Aachen, Germany. .,Institute of Tropical Medicine, University of Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.
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27
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Nannini F, Senicar L, Parekh F, Kong KJ, Kinna A, Bughda R, Sillibourne J, Hu X, Ma B, Bai Y, Ferrari M, Pule MA, Onuoha SC. Combining phage display with SMRTbell next-generation sequencing for the rapid discovery of functional scFv fragments. MAbs 2021; 13:1864084. [PMID: 33382949 PMCID: PMC7781620 DOI: 10.1080/19420862.2020.1864084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Phage display technology in combination with next-generation sequencing (NGS) currently is a state-of-the-art method for the enrichment and isolation of monoclonal antibodies from diverse libraries. However, the current NGS methods employed for sequencing phage display libraries are limited by the short contiguous read lengths associated with second-generation sequencing platforms. Consequently, the identification of antibody sequences has conventionally been restricted to individual antibody domains or to the analysis of single domain binding moieties such as camelid VHH or cartilaginous fish IgNAR antibodies. In this study, we report the application of third-generation sequencing to address this limitation. We used single molecule real time (SMRT) sequencing coupled with hairpin adaptor loop ligation to facilitate the accurate interrogation of full-length single-chain Fv (scFv) libraries. Our method facilitated the rapid isolation and testing of scFv antibodies enriched from phage display libraries within days following panning. Two libraries against CD160 and CD123 were panned and monitored by NGS. Analysis of NGS antibody data sets led to the isolation of several functional scFv antibodies that were not identified by conventional panning and screening strategies. Our approach, which combines phage display selection of immune libraries with the full-length interrogation of scFv fragments, is an easy method to discover functional antibodies, with a range of affinities and biophysical characteristics.
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Affiliation(s)
| | | | | | - Khai J. Kong
- Cancer Institute, University College London, London, UK
| | | | | | | | - Xihao Hu
- GV20 Therapeutics LLC, Cambridge, MA, USA
| | - Biao Ma
- Autolus Therapeutics, London, UK
| | | | | | - Martin A. Pule
- Cancer Institute, University College London, London, UK
- Autolus Therapeutics, London, UK
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Kulkarni A, Mochnáčová E, Majerova P, Čurlík J, Bhide K, Mertinková P, Bhide M. Single Domain Antibodies Targeting Receptor Binding Pockets of NadA Restrain Adhesion of Neisseria meningitidis to Human Brain Microvascular Endothelial Cells. Front Mol Biosci 2020; 7:573281. [PMID: 33425985 PMCID: PMC7785856 DOI: 10.3389/fmolb.2020.573281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/03/2020] [Indexed: 01/02/2023] Open
Abstract
Neisseria adhesin A (NadA), one of the surface adhesins of Neisseria meningitides (NM), interacts with several cell types including human brain microvascular endothelial cells (hBMECs) and play important role in the pathogenesis. Receptor binding pockets of NadA are localized on the globular head domain (A33 to K69) and the first coiled-coil domain (L121 to K158). Here, the phage display was used to develop a variable heavy chain domain (VHH) that can block receptor binding sites of recombinant NadA (rec-NadA). A phage library displaying VHH was panned against synthetic peptides (NadA-gdA33−K69 or NadA-ccL121−K158), gene encoding VHH was amplified from bound phages and re-cloned in the expression vector, and the soluble VHHs containing disulfide bonds were overexpressed in the SHuffle E. coli. From the repertoire of 96 clones, two VHHs (VHHF3–binding NadA-gdA33−K69 and VHHG9–binding NadA-ccL121−K158) were finally selected as they abrogated the interaction between rec-NadA and the cell receptor. Preincubation of NM with VHHF3 and VHHG9 significantly reduced the adhesion of NM on hBMECs in situ and hindered the traversal of NM across the in-vitro BBB model. The work presents a phage display pipeline with a single-round of panning to select receptor blocking VHHs. It also demonstrates the production of soluble and functional VHHs, which blocked the interaction between NadA and its receptor, decreased adhesion of NM on hBMECs, and reduced translocation of NM across BBB in-vitro. The selected NadA blocking VHHs could be promising molecules for therapeutic translation.
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Affiliation(s)
- Amod Kulkarni
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.,Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Evelína Mochnáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Ján Čurlík
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Patrícia Mertinková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.,Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
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Bewarder M, Kiefer M, Moelle C, Goerens L, Stilgenbauer S, Christofyllakis K, Kaddu-Mulindwa D, Fadle N, Regitz E, Neumann F, Hoth M, Preuss KD, Pfreundschuh M, Thurner L. Integration of the B-Cell Receptor Antigen Neurabin-I/SAMD14 Into an Antibody Format as New Therapeutic Approach for the Treatment of Primary CNS Lymphoma. Front Oncol 2020; 10:580364. [PMID: 33282736 PMCID: PMC7689012 DOI: 10.3389/fonc.2020.580364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/15/2020] [Indexed: 12/28/2022] Open
Abstract
Recently, neurabin-I and SAMD14 have been described as the autoantigenic target of approximately 66% of B-cell receptors (BCRs) of primary central nervous system lymphomas (PCNSL). Neurabin-I and SAMD14 share a highly homologous SAM domain that becomes immunogenic after atypical hyper-N-glycosylation (SAMD14 at ASN339 and neurabin-I at ASN1277). This post-translational modification of neurabin-I and SAMD14 seems to lead to a chronic immune reaction with B-cell receptor activation contributing to lymphoma genesis of PCNSLs. The selective tropism of PCNSL to the CNS corresponds well to the neurabin-I and SAMD14 protein expression pattern. When conjugated to Pseudomonas Exotoxin A (ETA´), the PCNSL reactive epitope exerts cytotoxic effects on lymphoma cells expressing a SAMD14/neurabin-I reactive BCR. Thus, the reactive epitopes of SAMD14/neurabin-I might be useful to establish additional therapeutic strategies against PCNSL. To test this possibility, we integrated the PCNSL-reactive epitope of SAMD14/neurabin-I into a heavy-chain-only Fab antibody format in substitution of the variable region. Specific binding of the prokaryotically produced SAMD14/neurabin-I Fab-antibody to lymphoma cells and their internalization were determined by flow cytometry. Since no established EBV-negative PCNSL cell line exists, we used the ABC-DLBCL cell lines OCI-Ly3 and U2932, which were transfected to express a SAMD14/neurabin-I reactive BCR. The SAMD14/neurabin-I Fab antibody bound specifically to DLBCL cells expressing a BCR with reactivity to SAMD14/neurabin-I and not to unmanipulated DLBCL cell lines. Eukaryotically produced full-length IgG antibodies are well established as immunotherapy format. Therefore, the PCNSL-reactive epitope of SAMD14/neurabin-I was cloned into a full-length IgG1 format replacing the variable domains of the light and heavy chains. The IgG1-format SAMD14/neurabin-I construct was found to specifically bind to target lymphoma cells expressing a SAMD14/neurabin-I reactive B cell receptor. In addition, it induced dose-dependent relative cytotoxicity against these lymphoma cells when incubated with PBMCs. Control DLBCL cells are not affected at any tested concentration. When integrated into the Fab-format and IgG1-format, the PCNSL-reactive epitope of SAMD14/neurabin-I functions as B-cell receptor Antigen for Reverse targeting (BAR). In particular, the IgG1-format BAR-body approach represents a very attractive therapeutic format for the treatment of PCNSLs, considering its specificity against SAMD14/neurabin-I reactive BCRs and the well-known pharmacodynamic properties of IgG antibodies.
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Affiliation(s)
- Moritz Bewarder
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany.,Internal Medicine I, Saarland University Medical Center, Homburg, Germany
| | - Maximilian Kiefer
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Clara Moelle
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Lisa Goerens
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Stephan Stilgenbauer
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany.,Internal Medicine I, Saarland University Medical Center, Homburg, Germany
| | | | | | - Natalie Fadle
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Evi Regitz
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Frank Neumann
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Markus Hoth
- Biophysics, CIPMM, Saarland University, Homburg, Germany
| | - Klaus-Dieter Preuss
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Michael Pfreundschuh
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany.,Internal Medicine I, Saarland University Medical Center, Homburg, Germany
| | - Lorenz Thurner
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany.,Internal Medicine I, Saarland University Medical Center, Homburg, Germany
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Nannini F, Parekh F, Wawrzyniecka P, Mekkaoui L, Righi M, Dastjerdi FV, Yeung J, Roddie C, Bai Y, Ma B, Ferrari M, Onuoha S, Chester K, Pule M. A primer set for the rapid isolation of scFv fragments against cell surface antigens from immunised rats. Sci Rep 2020; 10:19168. [PMID: 33154441 PMCID: PMC7644676 DOI: 10.1038/s41598-020-76069-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
Antibody phage display is a powerful platform for discovery of clinically applicable high affinity monoclonal antibodies against a broad range of targets. Libraries generated from immunized animals offer the advantage of in vivo affinity-maturation of V regions prior to library generation. Despite advantages, few studies have described isolation of antibodies from rats using immune phage display. In our study, we describe a novel primer set, covering the full rat heavy chain variable and kappa light chain variable regions repertoire for the generation of an unbiased immune libraries. Since the immune repertoire of rats is poorly understood, we first performed a deep sequencing analysis of the V(D)J regions of VH and VLK genes, demonstrating the high abundance of IGVH2 and IGVH5 families for VH and IGVLK12 and IGVLK22 for VLK. The comparison of gene's family usage in naïve rats have been used to validate the frequency's distribution of the primer set, confirming the absence of PCR-based biases. The primers were used to generate and assemble a phage display library from human CD160-vaccinated rats. CD160 represents a valid therapeutic target as it has been shown to be expressed on chronic lymphocytic leukaemia cells and on the surface of newly formed vessels. We utilised a novel phage display panning strategy to isolate a high affinity pool (KD range: 0.399-233 nM) of CD160 targeting monoclonal antibodies. Subsequently, identified binders were tested for function as third generation Chimeric Antigen Receptors (CAR) T cells demonstrating specific cytolytic activity. Our novel primer set coupled with a streamlined strategy for phage display panning enable the rapid isolation and identification of high affinity antibodies from immunised rats. The therapeutic utility of these antibodies was demonstrated in CAR format.
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Affiliation(s)
- Francesco Nannini
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Farhaan Parekh
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Patrycja Wawrzyniecka
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Leila Mekkaoui
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Matteo Righi
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | | | - Jenny Yeung
- Research Department of Oncology, UCL Cancer Institute, London, UK
| | - Claire Roddie
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | | | - Biao Ma
- Autolus Therapeutics, London, UK
| | | | | | - Kerry Chester
- Research Department of Oncology, UCL Cancer Institute, London, UK
| | - Martin Pule
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK.
- Autolus Therapeutics, London, UK.
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Kawecki C, Aymonnier K, Ferrière S, Venisse L, Arocas V, Boulaftali Y, Christophe OD, Lenting PJ, Bouton MC, Denis CV. Development and characterization of single-domain antibodies neutralizing protease nexin-1 as tools to increase thrombin generation. J Thromb Haemost 2020; 18:2155-2168. [PMID: 32495984 DOI: 10.1111/jth.14940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 01/29/2023]
Abstract
BACKGROUND Protease nexin-1 (PN-1) is a member of the serine protease inhibitor (Serpin)-family, with thrombin as its main target. Current polyclonal and monoclonal antibodies against PN-1 frequently cross-react with plasminogen activator inhibitor-1 (PAI-1), a structurally and functionally homologous Serpin. OBJECTIVES Here, we aimed to develop inhibitory single-domain antibodies (VHHs) that show specific binding to both human (hPN-1) and murine (mPN-1) PN-1. METHODS PN-1-binding VHHs were isolated via phage-display using llama-derived or synthetic VHH-libraries. Following bacterial expression, purified VHHs were analyzed in binding and activity assays. RESULTS AND CONCLUSIONS By using a llama-derived library, 2 PN-1 specific VHHs were obtained (KB-PN1-01 and KB-PN1-02). Despite their specificity, none displayed inhibitory activity toward hPN-1 or mPN-1. From the synthetic library, 4 VHHs (H12, B11, F06, A08) could be isolated that combined efficient binding to both hPN-1 and mPN-1 with negligible binding to PAI-1. Of these, B11, F06, and A08 were able to fully restore thrombin activity by blocking PN-1. As monovalent VHH, half-maximal inhibitory concentration values for hPN-1 were 50 ± 10, 290 ± 30, and 960 ± 390 nmol/L, for B11, F06, and A08, respectively, and 1580 ± 240, 560 ± 130, and 2880 ± 770 nmol/L for mPN-1. The inhibitory potential was improved 4- to 7-fold when bivalent VHHs were engineered. Importantly, all VHHs could block PN-1 activity in plasma as well as PN-1 released from activated platelets, one of the main sources of PN-1 during hemostasis. In conclusion, we report the generation of inhibitory anti-PN-1 antibodies using a specific approach to avoid cross-reactivity with the homologous Serpin PAI-1.
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Affiliation(s)
- Charlotte Kawecki
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1176, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1148, Université de Paris, Paris, France
| | - Karen Aymonnier
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1148, Université de Paris, Paris, France
| | - Stephen Ferrière
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1176, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Laurence Venisse
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1148, Université de Paris, Paris, France
| | - Véronique Arocas
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1148, Université de Paris, Paris, France
| | - Yacine Boulaftali
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1148, Université de Paris, Paris, France
| | - Olivier D Christophe
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1176, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Peter J Lenting
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1176, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Marie-Christine Bouton
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1148, Université de Paris, Paris, France
| | - Cécile V Denis
- Institut National de la Santé et de la Recherche Médicale, UMR_S 1176, Université Paris-Saclay, Le Kremlin-Bicêtre, France
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Ishina IA, Filimonova IN, Zakharova MY, Ovchinnikova LA, Mamedov AE, Lomakin YA, Belogurov AA. Exhaustive Search of the Receptor Ligands by the CyCLOPS (Cytometry Cell-Labeling Operable Phage Screening) Technique. Int J Mol Sci 2020; 21:ijms21176258. [PMID: 32872428 PMCID: PMC7504098 DOI: 10.3390/ijms21176258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 01/01/2023] Open
Abstract
Effective and versatile screening of the peptide ligands capable of selectively binding to diverse receptors is in high demand for the state-of-the-art technologies in life sciences, including probing of specificity of the cell surface receptors and drug development. Complex microenvironment and structure of the surface receptors significantly reduce the possibility to determine their specificity, especially when in vitro conditions are utilized. Previously, we designed a publicly available platform for the ultra-high-throughput screening (uHTS) of the specificity of surface-exposed receptors of the living eukaryotic cells, which was done by consolidating the phage display and flow cytometry techniques. Here, we significantly improved this methodology and designed the fADL-1e-based phage vectors that do not require a helper hyperphage for the virion assembly. The enhanced screening procedure was tested on soluble human leukocyte antigen (HLA) class II molecules and transgenic antigen-specific B cells that express recombinant lymphoid B-cell receptor (BCR). Our data suggest that the improved vector system may be successfully used for the comprehensive search of the receptor ligands in either cell-based or surface-immobilized assays.
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Affiliation(s)
- Irina A. Ishina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
| | - Ioanna N. Filimonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
| | - Maria Y. Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Leyla A. Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
| | - Azad E. Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
| | - Yakov A. Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
- Correspondence: (Y.A.L.); (A.A.B.J.)
| | - Alexey A. Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (I.A.I.); (I.N.F.); (M.Y.Z.); (L.A.O.); (A.E.M.)
- Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (Y.A.L.); (A.A.B.J.)
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Muyldermans S. A guide to: generation and design of nanobodies. FEBS J 2020; 288:2084-2102. [PMID: 32780549 PMCID: PMC8048825 DOI: 10.1111/febs.15515] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/03/2020] [Accepted: 08/07/2020] [Indexed: 01/09/2023]
Abstract
A nanobody (Nb) is a registered trademark of Ablynx, referring to the single antigen-binding domain of heavy chain-only antibodies (HCAbs) that are circulating in Camelidae. Nbs are produced recombinantly in micro-organisms and employed as research tools or for diagnostic and therapeutic applications. They were - and still are - also named single-domain antibodies (sdAbs) or variable domain of the heavy chain of HCAbs (VHH). A variety of methods are currently in use for the fast and efficient generation of target-specific Nbs. Such Nbs are produced at low cost and associate with high affinity to their cognate antigen. They are robust, strictly monomeric and easy to tailor into more complex entities to meet the requirements of their application. Here, we review the various sources and different strategies that have been developed to identify rapidly, target-specific Nbs. We further discuss a variety of engineering technologies that have been explored to broaden the application range of Nbs and summarise those applications where designed Nbs might offer a marked advantage over other affinity reagents.
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Affiliation(s)
- Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Belgium.,Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, China
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Bewarder M, Held G, Thurner L, Stilgenbauer S, Smola S, Preuss KD, Carbon G, Bette B, Christofyllakis K, Bittenbring JT, Felbel A, Hasse A, Murawski N, Kaddu-Mulindwa D, Neumann F. Characterization of an HLA-restricted and human cytomegalovirus-specific antibody repertoire with therapeutic potential. Cancer Immunol Immunother 2020; 69:1535-1548. [PMID: 32300857 PMCID: PMC7347513 DOI: 10.1007/s00262-020-02564-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 04/02/2020] [Indexed: 01/04/2023]
Abstract
With an infection rate of 60-90%, the human cytomegalovirus (HCMV) is very common among adults but normally causes no symptoms. When T cell-mediated immunity is compromised, HCMV reactivation can lead to increased morbidity and mortality. HCMV antigens are processed and presented as peptides on the cell surface via HLA I complexes to the T cell receptor (TCR) of T cells. The generation of antibodies against HCMV peptides presented on HLA complexes (TCR-like antibodies) has been described, but is without therapeutic applications to date due to the polygenic and polymorphic nature of HLA genes. We set out to obtain antibodies specific for HLA/HCMV-peptides, covering the majority of HLA alleles present in European populations. Using phage display technology, we selected 10 Fabs, able to bind to HCMV-peptides presented in the 6 different HLA class I alleles A*0101, A*0201, A*2402, B*0702, B*0801 and B*3501. We demonstrate specific binding of all selected Fabs to HLA-typed lymphoblastoid cell lines (EBV-transformed B cells) and lymphocytes loaded with HCMV-peptides. After infection with HCMV, 4/10 tetramerized Fabs restricted to the alleles HLA-A*0101, HLA-A*0201 and HLA-B*0702 showed binding to infected primary fibroblasts. When linked to the pseudomonas exotoxin A, these Fab antibodies induce highly specific cytotoxicity in HLA matched cell lines loaded with HCMV peptides. TCR-like antibody repertoires therefore represent a promising new treatment modality for viral infections and may also have applications in the treatment of cancers.
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Affiliation(s)
- Moritz Bewarder
- Internal Medicine I, Saarland University Medical Center, 66421, Homburg, Germany.
- José Carreras Center, Saarland University Medical Center, Homburg, Germany.
| | - Gerhard Held
- Internal Medicine I, Westpfalz-Klinikum Kaiserslautern, Kaiserslautern, Germany
| | - Lorenz Thurner
- Internal Medicine I, Saarland University Medical Center, 66421, Homburg, Germany
- José Carreras Center, Saarland University Medical Center, Homburg, Germany
| | - Stephan Stilgenbauer
- Internal Medicine I, Saarland University Medical Center, 66421, Homburg, Germany
- José Carreras Center, Saarland University Medical Center, Homburg, Germany
| | - Sigrun Smola
- Institute of Virology, Saarland University Medical Center, Homburg, Germany
| | | | - Gabi Carbon
- José Carreras Center, Saarland University Medical Center, Homburg, Germany
| | - Birgit Bette
- José Carreras Center, Saarland University Medical Center, Homburg, Germany
| | | | | | - Arne Felbel
- Internal Medicine I, Saarland University Medical Center, 66421, Homburg, Germany
| | - Alexander Hasse
- Internal Medicine I, Saarland University Medical Center, 66421, Homburg, Germany
| | - Niels Murawski
- Internal Medicine I, Saarland University Medical Center, 66421, Homburg, Germany
| | | | - Frank Neumann
- José Carreras Center, Saarland University Medical Center, Homburg, Germany
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Xu Y, Kirk NS, Venugopal H, Margetts MB, Croll TI, Sandow JJ, Webb AI, Delaine CA, Forbes BE, Lawrence MC. How IGF-II Binds to the Human Type 1 Insulin-like Growth Factor Receptor. Structure 2020; 28:786-798.e6. [PMID: 32459985 PMCID: PMC7343240 DOI: 10.1016/j.str.2020.05.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/23/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023]
Abstract
Human type 1 insulin-like growth factor receptor (IGF-1R) signals chiefly in response to the binding of insulin-like growth factor I. Relatively little is known about the role of insulin-like growth factor II signaling via IGF-1R, despite the affinity of insulin-like growth factor II for IGF-1R being within an order of magnitude of that of insulin-like growth factor I. Here, we describe the cryoelectron microscopy structure of insulin-like growth factor II bound to a leucine-zipper-stabilized IGF-1R ectodomain, determined in two conformations to a maximum average resolution of 3.2 Å. The two conformations differ in the relative separation of their respective points of membrane entry, and comparison with the structure of insulin-like growth factor I bound to IGF-1R reveals long-suspected differences in the way in which the critical C domain of the respective growth factors interact with IGF-1R.
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Affiliation(s)
- Yibin Xu
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Nicholas S Kirk
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC 3800, Australia
| | - Mai B Margetts
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, UK
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia
| | - Carlie A Delaine
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, SA 5042, Australia
| | - Briony E Forbes
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, SA 5042, Australia
| | - Michael C Lawrence
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3050, Australia.
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36
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Barbon E, Ayme G, Mohamadi A, Ottavi J, Kawecki C, Casari C, Verhenne S, Marmier S, van Wittenberghe L, Charles S, Collaud F, Denis CV, Christophe OD, Mingozzi F, Lenting PJ. Single-domain antibodies targeting antithrombin reduce bleeding in hemophilic mice with or without inhibitors. EMBO Mol Med 2020; 12:e11298. [PMID: 32159286 PMCID: PMC7136963 DOI: 10.15252/emmm.201911298] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 01/08/2023] Open
Abstract
Novel therapies for hemophilia, including non-factor replacement and in vivo gene therapy, are showing promising results in the clinic, including for patients having a history of inhibitor development. Here, we propose a novel therapeutic approach for hemophilia based on llama-derived single-domain antibody fragments (sdAbs) able to restore hemostasis by inhibiting the antithrombin (AT) anticoagulant pathway. We demonstrated that sdAbs engineered in multivalent conformations were able to block efficiently AT activity in vitro, restoring the thrombin generation potential in FVIII-deficient plasma. When delivered as a protein to hemophilia A mice, a selected bi-paratopic sdAb significantly reduced the blood loss in a model of acute bleeding injury. We then packaged this sdAb in a hepatotropic AAV8 vector and tested its safety and efficacy profile in hemophilic mouse models. We show that the long-term expression of the bi-paratopic sdAb in the liver is safe and poorly immunogenic, and results in sustained correction of the bleeding phenotype in hemophilia A and B mice, even in the presence of inhibitory antibodies to the therapeutic clotting factor.
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Affiliation(s)
- Elena Barbon
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Gabriel Ayme
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Amel Mohamadi
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | | | - Charlotte Kawecki
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Caterina Casari
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Sebastien Verhenne
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Solenne Marmier
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Laetitia van Wittenberghe
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Severine Charles
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Fanny Collaud
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Cecile V Denis
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Olivier D Christophe
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
| | - Federico Mingozzi
- Genethon, Institut National de la Santé et de la Recherche Médicale U951 IntegrareUniversité Paris‐SaclayUniversity of EvryEvryFrance
| | - Peter J Lenting
- HITh, UMR_S1176Institut National de la Santé et de la Recherche MédicaleUniversité Paris‐SaclayLe Kremlin‐BicêtreFrance
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Guliy OI, Zaitsev BD, Mehta SK, Borodina IA. Analysis of Microbial Cell Viability in a Liquid Using an Acoustic Sensor. ULTRASOUND IN MEDICINE & BIOLOGY 2020; 46:1026-1039. [PMID: 31932157 DOI: 10.1016/j.ultrasmedbio.2019.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
A method was developed for the rapid analysis and evaluation of the viability of bacteriophage-infected Escherichia coli (E.coli) XL-1 directly in a conducting suspension by using a slot-mode sensor. The method is based on recording the changes in the depth and frequency of resonant absorption peaks in the frequency dependence of the insertion loss of the sensor before and after the biologic interaction of E. coli with specific bacteriophages. The possibility was shown of recording the infection of E. coli with specific bacteriophages and assessing its viability in suspensions with a conductivity of 4.5-30 μS/cm. Сontrol experiments were carried out with non-specific interactions of E. coli cells with bacteriophages, in which no changes in the sensor variables were observed. The optimal informational variable for estimating the number of viable cells was the degree of change in the depth of the resonant peaks in the frequency dependence of the insertion loss of the sensor. The limit of cell detection was ∼102-103 cells mL-1, with an analysis time of about 5 min. An additional advantage of the sensor was the availability of a removable liquid container, which allows one to use it repeatedly and to facilitate the cleaning of the container from spent samples. The results are promising for the detection of bacteria and assessment of their viability in solutions with conductivity in the range 4.5-30 µS/cm.
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Affiliation(s)
- Olga I Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences Saratov, Russia.
| | - Boris D Zaitsev
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Saratov, Russia
| | | | - Irina A Borodina
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Saratov, Russia
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Leyton-Castro NF, Brigido MM, Maranhão AQ. Selection of Antibody Fragments for CAR-T Cell Therapy from Phage Display Libraries. Methods Mol Biol 2020; 2086:13-26. [PMID: 31707665 DOI: 10.1007/978-1-0716-0146-4_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CAR-T cell therapy emerged in the last years as a great promise to cancer treatment. Nowadays, there is a run to improve the breadth of its use, and thus, new chimeric antigen receptors (CAR) are being proposed. The antigen-binding counterpart of CAR is an antibody fragment, scFv (single chain variable fragment), that recognizes a membrane protein associated to a cancer cell. In this chapter, the use of human scFv phage display libraries as a source of new mAbs against surface antigen is discussed. Protocols focusing in the use of extracellular domains of surface protein in biotinylated format are proposed as selection antigen. Elution with unlabeled peptide and selection in solution is described. The analysis of enriched scFvs throughout the selection using NGS is also outlined. Taken together these protocols allow for the isolation of new scFvs able to be useful in the construction of new chimeric antigen receptors for application in cancer therapy.
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Affiliation(s)
- Nestor F Leyton-Castro
- Molecular Pathology Graduation Programme, School of Medicine, University of Brasilia, Brasilia, Brazil
| | - Marcelo M Brigido
- Molecular Pathology Graduation Programme, School of Medicine, University of Brasilia, Brasilia, Brazil
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Andrea Q Maranhão
- Molecular Pathology Graduation Programme, School of Medicine, University of Brasilia, Brasilia, Brazil.
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil.
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Antibody-based therapies for Huntington’s disease: current status and future directions. Neurobiol Dis 2019; 132:104569. [DOI: 10.1016/j.nbd.2019.104569] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 12/12/2022] Open
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Winter G. Harnessing Evolution to Make Medicines (Nobel Lecture). Angew Chem Int Ed Engl 2019; 58:14438-14445. [DOI: 10.1002/anie.201909343] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Gregory Winter
- MRC Laboratory of Molecular Biology Cambridge and Trinity College Cambridge UK
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Affiliation(s)
- Gregory Winter
- MRC Laboratory of Molecular Biology Cambridge and Trinity College Cambridge UK
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Godakova SA, Noskov AN, Vinogradova ID, Ugriumova GA, Solovyev AI, Esmagambetov IB, Tukhvatulin AI, Logunov DY, Naroditsky BS, Shcheblyakov DV, Gintsburg AL. Camelid VHHs Fused to Human Fc Fragments Provide Long Term Protection Against Botulinum Neurotoxin A in Mice. Toxins (Basel) 2019; 11:E464. [PMID: 31394847 PMCID: PMC6723419 DOI: 10.3390/toxins11080464] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/29/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022] Open
Abstract
The bacterium Clostridium botulinum is the causative agent of botulism-a severe intoxication caused by botulinum neurotoxin (BoNT) and characterized by damage to the nervous system. In an effort to develop novel C. botulinum immunotherapeutics, camelid single-domain antibodies (sdAbs, VHHs, or nanobodies) could be used due to their unique structure and characteristics. In this study, VHHs were produced using phage display technology. A total of 15 different monoclonal VHHs were selected based on their comlementarity-determining region 3 (CDR3) sequences. Different toxin lethal dose (LD50) challenges with each selected phage clone were conducted in vivo to check their neutralizing potency. We demonstrated that modification of neutralizing VHHs with a human immunoglobulin G (IgG)1 Fc (fragment crystallizable) fragment (fusionbody, VHH-Fc) significantly increased the circulation time in the blood (up to 14 days). At the same time, VHH-Fc showed the protective activity 1000 times higher than monomeric form when challenged with 5 LD50. Moreover, VHH-Fcs remained protective even 14 days after antibody administration. These results indicate that this VHH-Fc could be used as an effective long term antitoxin protection against botulinum type A.
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Affiliation(s)
- Svetlana A Godakova
- Department of Genetics and Bacteria Molecular Biology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Anatoly N Noskov
- Department of Bacteriology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Irina D Vinogradova
- Department of Bacteriology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Galina A Ugriumova
- Department of Bacteriology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Andrey I Solovyev
- Department of Bacteriology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Ilias B Esmagambetov
- Department of Genetics and Bacteria Molecular Biology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Amir I Tukhvatulin
- Department of Medical Microbiology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Denis Y Logunov
- Department of Medical Microbiology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Boris S Naroditsky
- Department of Genetics and Bacteria Molecular Biology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
| | - Dmitry V Shcheblyakov
- Department of Genetics and Bacteria Molecular Biology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia.
| | - Aleksandr L Gintsburg
- Department of Genetics and Bacteria Molecular Biology, Gamaleya Research Center of Epidemiology and Microbiology, 18 Gamaleya Street, Moscow 123098, Russia
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43
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A Novel DT40 Antibody Library for the Generation of Monoclonal Antibodies. Virol Sin 2019; 34:641-647. [PMID: 31240617 DOI: 10.1007/s12250-019-00142-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022] Open
Abstract
Early etiological diagnosis is very important for the control of sudden viral infections, and requires antibodies with both high sensitivity and high specificity. Traditional antibody preparation methods have limitations, such as a long and arduous cycle, complicated operation, and high expenses. A chicken lymphoma cell line, DT40, is known to produce IgM-type antibodies and undergo gene conversion and somatic mutation in the variable region of the immunoglobulin gene during culture. Here, the DT40 cell line was developed to produce antibody libraries and prepare antibody rapidly in vitro. Since hypermutation in DT40 cells was regulated by the activation-induced cytidine deaminase (AID) gene, AID expression needs to be controlled to either fix the Ig sequence by stopping mutation or improve affinity by resuming mutation after the antibodies have been selected. In this study, we generated a novel AID-inducible DT40 cell line (DT40-H7), in which the endogenous AID gene was knocked out using the CRISPR/Cas9 genome editing system, and an inducible AID gene, based on the Tet-Off expression system, was stably transfected. AID expression was controlled in DT40-H7 cells in a simple and efficient manner; gene conversion and point mutations were observed only when AID was expressed. Using the antibody library generated from this cell line, we successfully obtained monoclonal antibodies against the NS1 protein of Zika virus. The DT40-H7 cell line represents a useful tool for the selection and evolution of antibodies and may also be a powerful tool for the rapid selection and generation of diagnostic antibodies for emerging infectious diseases.
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Kotlan B, Horvath S, Eles K, Plotar VK, Naszados G, Czirbesz K, Blank M, Farkas E, Toth L, Tovari J, Szekacs A, Shoenfeld Y, Godeny M, Kasler M, Liszkay G. Tumor-Associated Disialylated Glycosphingolipid Antigen-Revealing Antibodies Found in Melanoma Patients' Immunoglobulin Repertoire Suggest a Two-Direction Regulation Mechanism Between Immune B Cells and the Tumor. Front Immunol 2019; 10:650. [PMID: 31024530 PMCID: PMC6459966 DOI: 10.3389/fimmu.2019.00650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/11/2019] [Indexed: 12/24/2022] Open
Abstract
There is far less information available about the tumor infiltrating B (TIL-B) cells, than about the tumor infiltrating T cells. We focused on discovering the features and potential role of B lymphocytes in solid tumors. Our project aimed to develop innovative strategies to define cancer membrane structures. We chose two solid tumor types, with variable to considerable B cell infiltration. The strategy we set up with invasive breast carcinoma, showing medullary features, has been introduced and standardized in metastatic melanoma. After detecting B lymphocytes by immunohistochemistry, VH-JH, Vκ-Jκ immunoglobulin rearranged V region genes were amplified by RT-PCR, from TIL-B cDNA. Immunoglobulin variable-region genes of interest were cloned, sequenced, and subjected to a comparative DNA analysis. Single-chain variable (scFv) antibody construction was performed in selected cases to generate a scFv library and to test tumor binding capacity. DNA sequence analysis revealed an overrepresented VH3-1 cluster, represented both in the breast cancer and the melanoma TIL-B immunoglobulin repertoire. We observed that our previously defined anti GD3 ganglioside-binder antibody-variable region genes were present in melanoma as well. Our antibody fragments showed binding potential to disialylated glycosphingolipids (GD3 ganglioside) and their O acetylated forms on melanoma cancer cells. We conclude that our results have a considerable tumor immunological impact, as they reveal the power of TIL-B cells to recognize strong tumor-associated glycosphingolipid structures on melanomas and other solid tumors. As tumor-derived gangliosides affect immune cell functions and reduce the B lymphocytes' antibody production, we suspect an important B lymphocyte and cancer cell crosstalk mechanism. We not only described the isolation and specificity testing of the tumor infiltrating B cells, but also showed the TIL-B cells' highly tumor-associated GD3 ganglioside-revealing potential in melanomas. The present data help to identify new cancer-associated biomarkers that may serve for novel cancer diagnostics. The two-direction regulation mechanism between immune B cells and the tumor could eventually be developed into an innovative cancer treatment strategy.
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Affiliation(s)
- Beatrix Kotlan
- Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary
| | - Szabolcs Horvath
- Center of Surgical and Molecular Pathology, National Institute of Oncology, Budapest, Hungary
| | - Klara Eles
- Center of Surgical and Molecular Pathology, National Institute of Oncology, Budapest, Hungary
| | - Vanda K Plotar
- Center of Surgical and Molecular Pathology, National Institute of Oncology, Budapest, Hungary
| | - Gyorgy Naszados
- Center of Image Analysis and Radiological Diagnostics, National Institute of Oncology, Budapest, Hungary
| | - Katalin Czirbesz
- Department of Oncodermatology, National Institute of Oncology, Budapest, Hungary
| | - Miri Blank
- Zabludowitz Center for Autoimmune Diseases, Sheba Medical Center Affiliated to Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Emil Farkas
- Center of Oncosurgery, National Institute of Oncology, Budapest, Hungary
| | - Laszlo Toth
- Center of Oncosurgery, National Institute of Oncology, Budapest, Hungary
| | - Jozsef Tovari
- Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary
| | - Andras Szekacs
- Agro-Environmental Research Institute, National Agricultural Research and Innovation Centre, Budapest, Hungary
| | - Yehuda Shoenfeld
- Zabludowitz Center for Autoimmune Diseases, Sheba Medical Center Affiliated to Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Maria Godeny
- Center of Image Analysis and Radiological Diagnostics, National Institute of Oncology, Budapest, Hungary
| | - Miklos Kasler
- National Institute of Oncology, Budapest, Hungary.,Ministry of Human Capacities, Budapest, Hungary
| | - Gabriella Liszkay
- Department of Oncodermatology, National Institute of Oncology, Budapest, Hungary
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Kang JC, Sun W, Khare P, Karimi M, Wang X, Shen Y, Ober RJ, Ward ES. Engineering a HER2-specific antibody-drug conjugate to increase lysosomal delivery and therapeutic efficacy. Nat Biotechnol 2019; 37:523-526. [PMID: 30936563 PMCID: PMC6668989 DOI: 10.1038/s41587-019-0073-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/20/2019] [Indexed: 12/11/2022]
Abstract
We improve the potency of antibody-drug conjugates (ADCs) containing the
HER2-specific antibody pertuzumab by reducing their affinity for HER2 by
>250-fold at acidic endosomal pH relative to near neutral pH. These
engineered pertuzumab variants show increased lysosomal delivery and
cytotoxicity towards tumor cells expressing intermediate HER2 levels. In
HER2int xenograft tumor models in mice, the variants show higher
therapeutic efficacy than the parent ADC and a clinically-approved HER2-specific
ADC.
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Affiliation(s)
- Jeffrey C Kang
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - Wei Sun
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - Priyanka Khare
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - Mostafa Karimi
- Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Xiaoli Wang
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - Yang Shen
- Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Raimund J Ober
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA. .,Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA. .,Cancer Sciences Unit, Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK.
| | - E Sally Ward
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA. .,Cancer Sciences Unit, Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK. .,Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA.
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Barderas R, Benito-Peña E. The 2018 Nobel Prize in Chemistry: phage display of peptides and antibodies. Anal Bioanal Chem 2019; 411:2475-2479. [PMID: 30888467 DOI: 10.1007/s00216-019-01714-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/25/2019] [Indexed: 12/29/2022]
Abstract
One-half of the 2018 Nobel Prize in Chemistry was awarded jointly to George P. Smith and Sir Gregory P. Winter "for the phage display of peptides and antibodies". This feature article summarizes significant achievements leading to the development of phage display of peptides and antibodies, where a bacteriophage is genetically modified to display peptides and proteins, with the primary aim of producing new biopharmaceuticals. These significant achievements are proven to be useful for the development of phage-based bioassays and biosensors.
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Affiliation(s)
- Rodrigo Barderas
- Functional Proteomics Unit, UFIEC, Chronic Disease Programme, Instituto de Salud Carlos III, Majadahonda, 28220, Madrid, Spain.
| | - Elena Benito-Peña
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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Phage Display Libraries: From Binders to Targeted Drug Delivery and Human Therapeutics. Mol Biotechnol 2019; 61:286-303. [DOI: 10.1007/s12033-019-00156-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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.
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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
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Hyper- N-glycosylated SAMD14 and neurabin-I as driver autoantigens of primary central nervous system lymphoma. Blood 2018; 132:2744-2753. [PMID: 30249786 DOI: 10.1182/blood-2018-03-836932] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 09/12/2018] [Indexed: 01/01/2023] Open
Abstract
To address the role of chronic antigenic stimulation in primary central nervous system lymphoma (PCNSL), we searched for autoantigens and identified sterile α-motif domain containing protein 14 (SAMD14) and neural tissue-specific F-actin binding protein I (neurabin-I) as autoantigenic targets of the B-cell receptors (BCRs) from 8/12 PCNSLs. In the respective cases, SAMD14 and neurabin-I were atypically hyper-N-glycosylated (SAMD14 at ASN339 and neurabin-I at ASN1277), explaining their autoimmunogenicity. SAMD14 and neurabin-I induced BCR pathway activation and proliferation of aggressive lymphoma cell lines transfected with SAMD14- and neurabin-I-reactive BCRs. Moreover, the BCR binding epitope of neurabin-I conjugated to truncated Pseudomonas exotoxin-killed lymphoma cells expressing the respective BCRs. These results support the role of chronic antigenic stimulation by posttranslationally modified central nervous system (CNS) driver autoantigens in the pathogenesis of PCNSL, serve as an explanation for their CNS tropism, and provide the basis for a novel specific treatment approach.
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50
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Thiesen HJ. From repression domains to designer zinc finger proteins: a novel strategy of intracellular immunization against HIV. Gene Expr 2018; 5:229-43. [PMID: 8723389 PMCID: PMC6138030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Tissue-specific gene regulation of eukaryotic organisms is to a large extent mediated by transcription factors that interact with genomic DNA sequences in a sequence-specific manner. The purpose of this synopsis is to put forward the potential of designer zinc finger proteins in treating infections of human immunodeficiency virus (HIV). Artificial transcription factors containing designer zinc finger structures fused to activator or repressor domains have been designated Transcription Response Modifiers (TRMs). The principle of engineering TRMs has been derived from the analysis of human Krüppel-type zinc finger genes and their products. Our research efforts encompass two fascinating features that are displayed by the human Krüppel-type zinc finger protein KOX1: 1) the Krüppel-type zinc finger domains display rules of sequence-specific DNA recognition, and 2) the evolutionarily conserved Krüppel-associated box (KRAB) presents one of the strongest transcriptional repressors identified so far in mammalian organisms. The KRAB repressor activity is postulated to be mediated through co-repressor molecules, such as Silencing Mediating Protein-1 (SMP-1). Thus, the structural organization and functional analysis of zinc finger proteins revealed principles of zinc finger transcription factors that are applicable for reducing the viral load in individuals infected with HIV. In this article, a novel concept of generating therapeutic proteins is outlined that might be conceptually promising in modulating gene expressions of any kind.
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