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Barrett J, Leysen S, Galmiche C, Al-Mossawi H, Bowness P, Edwards TE, Lawson AD. Chimeric antigens displaying GPR65 extracellular loops on a soluble scaffold enabled the discovery of antibodies, which recognized native receptor. Bioengineered 2024; 15:2299522. [PMID: 38184821 PMCID: PMC10773626 DOI: 10.1080/21655979.2023.2299522] [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: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024] Open
Abstract
GPR65 is a proton-sensing G-protein coupled receptor associated with multiple immune-mediated inflammatory diseases, whose function is relatively poorly understood. With few reagents commercially available to probe the biology of receptor, generation of an anti-GPR65 monoclonal antibody was desired. Using soluble chimeric scaffolds, such as ApoE3, displaying the extracellular loops of GPR65, together with established phage display technology, native GPR65 loop-specific antibodies were identified. Phage-derived loop-binding antibodies recognized the wild-type native receptor to which they had not previously been exposed, generating confidence in the use of chimeric soluble proteins to act as efficient surrogates for membrane protein extracellular loop antigens. This technique provides promise for the rational design of chimeric antigens in facilitating the discovery of specific antibodies to GPCRs.
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Affiliation(s)
- Janine Barrett
- UK Research Department, UCB Pharma, Slough, UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | | | - Hussein Al-Mossawi
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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2
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Jahandar-Lashaki S, Farajnia S, Faraji-Barhagh A, Hosseini Z, Bakhtiyari N, Rahbarnia L. Phage Display as a Medium for Target Therapy Based Drug Discovery, Review and Update. Mol Biotechnol 2024:10.1007/s12033-024-01195-6. [PMID: 38822912 DOI: 10.1007/s12033-024-01195-6] [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: 11/01/2023] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Phage libraries are now amongst the most prominent approaches for the identification of high-affinity antibodies/peptides from billions of displayed phages in a specific library through the biopanning process. Due to its ability to discover potential therapeutic candidates that bind specifically to targets, phage display has gained considerable attention in targeted therapy. Using this approach, peptides with high-affinity and specificity can be identified for potential therapeutic or diagnostic use. Furthermore, phage libraries can be used to rapidly screen and identify novel antibodies to develop immunotherapeutics. The Food and Drug Administration (FDA) has approved several phage display-derived peptides and antibodies for the treatment of different diseases. In the current review, we provided a comprehensive insight into the role of phage display-derived peptides and antibodies in the treatment of different diseases including cancers, infectious diseases and neurological disorders. We also explored the applications of phage display in targeted drug delivery, gene therapy, and CAR T-cell.
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Affiliation(s)
- Samaneh Jahandar-Lashaki
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Aref Faraji-Barhagh
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Hosseini
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Nasim Bakhtiyari
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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3
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Chomicz D, Kończak J, Wróbel S, Satława T, Dudzic P, Janusz B, Tarkowski M, Deszyński P, Gawłowski T, Kostyn A, Orłowski M, Klaus T, Schulte L, Martin K, Comeau SR, Krawczyk K. Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications. Front Mol Biosci 2024; 11:1352508. [PMID: 38606289 PMCID: PMC11008471 DOI: 10.3389/fmolb.2024.1352508] [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: 12/08/2023] [Accepted: 02/09/2024] [Indexed: 04/13/2024] Open
Abstract
Antibodies are proteins produced by our immune system that have been harnessed as biotherapeutics. The discovery of antibody-based therapeutics relies on analyzing large volumes of diverse sequences coming from phage display or animal immunizations. Identification of suitable therapeutic candidates is achieved by grouping the sequences by their similarity and subsequent selection of a diverse set of antibodies for further tests. Such groupings are typically created using sequence-similarity measures alone. Maximizing diversity in selected candidates is crucial to reducing the number of tests of molecules with near-identical properties. With the advances in structural modeling and machine learning, antibodies can now be grouped across other diversity dimensions, such as predicted paratopes or three-dimensional structures. Here we benchmarked antibody grouping methods using clonotype, sequence, paratope prediction, structure prediction, and embedding information. The results were benchmarked on two tasks: binder detection and epitope mapping. We demonstrate that on binder detection no method appears to outperform the others, while on epitope mapping, clonotype, paratope, and embedding clusterings are top performers. Most importantly, all the methods propose orthogonal groupings, offering more diverse pools of candidates when using multiple methods than any single method alone. To facilitate exploring the diversity of antibodies using different methods, we have created an online tool-CLAP-available at (clap.naturalantibody.com) that allows users to group, contrast, and visualize antibodies using the different grouping methods.
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Affiliation(s)
| | | | - Sonia Wróbel
- NaturalAntibody, Szczecin, West Pomeranian, Poland
| | | | - Paweł Dudzic
- NaturalAntibody, Szczecin, West Pomeranian, Poland
| | | | | | | | | | | | - Marek Orłowski
- Pure Biologics, Wrocław, Poland
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | | | - Lukas Schulte
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Kyle Martin
- Biotherapeutics Discovery, Boehringer Ingelheim, Biberach, Germany
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4
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Lima MIS, Corrêa MBC, Moraes ECDS, Oliveira JDDD, de Souza Santos P, de Souza AG, Goulart IMB, Goulart LR. HSP60 mimetic peptides from Mycobacterium leprae as new antigens for immunodiagnosis of Leprosy. AMB Express 2023; 13:120. [PMID: 37891336 PMCID: PMC10611693 DOI: 10.1186/s13568-023-01625-9] [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: 03/15/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The early diagnosis of leprosy serves as an important tool to reduce the incidence of this disease in the world. Phage display (PD) technology can be used for mapping new antigens to the development of immunodiagnostic platforms. Our objective was to identify peptides that mimic Mycobacterium leprae proteins as serological markers using phage display technology. The phages were obtained in the biopanning using negative and positive serum from household contacts and leprosy patients, respectively. Then, the peptides were synthesized and validated in silico and in vitro for detection of IgG from patients and contacts. To characterize the native protein of M. leprae, scFv antibodies were selected against the synthetic peptides by PD. The scFv binding protein was obtained by immunocapture and confirmed using mass spectrometry. We selected two phase-fused peptides, MPML12 and MPML14, which mimic the HSP60 protein from M. leprae. The peptides MPML12 and MPML14 obtained 100% and 92.85% positivity in lepromatous patients. MPML12 and MPM14 detect IgG, especially in the multibacillary forms. The MPML12 and MPML14 peptides had positivity of 11.1% and 16.6% in household contacts, respectively. There was no cross-reaction in patient's samples with visceral leishmaniasis, tuberculosis and other mycobacteriosis for both peptides. Given these results and the easy obtainment of mimetic antigens, our peptides are promising markers for application in the diagnosis of leprosy, especially in endemic and hyperendemic regions.
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Affiliation(s)
- Mayara Ingrid Sousa Lima
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, MA, Brazil.
- Postgraduate Program on Health and Environment and Postgraduate Program on Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil.
| | | | | | | | - Paula de Souza Santos
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Aline Gomes de Souza
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Isabela Maria Bernardes Goulart
- National Reference Center in Sanitary Dermatology and Leprosy, School of Medicine, Clinics' Hospital, Federal University of Uberlandia, Uberlandia, MG, Brazil.
| | - Luiz Ricardo Goulart
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, MG, Brazil
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
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5
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Liu C, Song G, Yan S, He Y, Hu C, Hou Y, Wen X, Li L, Zhang F, Zhu H, Li Y. Identification of Anti-SNRPA as a Novel Serological Biomarker for Systemic Sclerosis Diagnosis. J Proteome Res 2023; 22:3254-3263. [PMID: 37639699 PMCID: PMC10563158 DOI: 10.1021/acs.jproteome.3c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Indexed: 08/31/2023]
Abstract
Systemic sclerosis (SSc) is a systemic autoimmune disorder that leads to vasculopathy and tissue fibrosis. A lack of reliable biomarkers has been a challenge for clinical diagnosis of the disease. We employed a protein array-based approach to identify and validate SSc-specific autoantibodies. Phase I involved profiled autoimmunity using human proteome microarray (HuProt arrays) with 90 serum samples: 40 patients with SSc, 30 patients diagnosed with autoimmune diseases, and 20 healthy subjects. In Phase II, we constructed a focused array with candidates identified antigens and used this to profile a much larger cohort comprised of serum samples. Finally, we used a western blot analysis to validate the serum of validated proteins with high signal values. Bioinformatics analysis allowed us to identify 113 candidate autoantigens that were significantly associated with SSc. This two-phase strategy allowed us to identify and validate anti-small nuclear ribonucleoprotein polypeptide A (SNRPA) as a novel SSc-specific serological biomarker. The observed positive rate of anti-SNRPA antibody in patients with SSc was 11.25%, which was significantly higher than that of any disease control group (3.33%) or healthy controls (1%). In conclusion, anti-SNRPA autoantibody serves as a novel biomarker for SSc diagnosis and may be promising for clinical applications.
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Affiliation(s)
- Chenxi Liu
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical
Sciences, Beijing 100730, P. R. China
- Department
of Clinical Laboratory, West China Second
University Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Guang Song
- School
of Life Sciences, Central China Normal University, Wuhan 430079, P. R. China
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Songxin Yan
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical
Sciences, Beijing 100730, P. R. China
| | - Yangzhige He
- Central
Research Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical
Sciences, Beijing 100730, P. R. China
| | - Chaojun Hu
- Department
of Rheumatology and Clinical Immunology, Key Laboratory of Rheumatology
and Clinical Immunology, Ministry of Education, Peking Union Medical
College Hospital, Peking Union Medical College,
Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Yong Hou
- Department
of Rheumatology and Clinical Immunology, Key Laboratory of Rheumatology
and Clinical Immunology, Ministry of Education, Peking Union Medical
College Hospital, Peking Union Medical College,
Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Xiaoting Wen
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical
Sciences, Beijing 100730, P. R. China
| | - Liubing Li
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical
Sciences, Beijing 100730, P. R. China
| | - Fengchun Zhang
- Department
of Rheumatology and Clinical Immunology, Key Laboratory of Rheumatology
and Clinical Immunology, Ministry of Education, Peking Union Medical
College Hospital, Peking Union Medical College,
Chinese Academy of Medical Sciences, Beijing 100730, P. R. China
| | - Heng Zhu
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Yongzhe Li
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical
Sciences, Beijing 100730, P. R. China
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6
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Kumari S, Singh K, Singh N, Khan S, Kumar A. Phage display and human disease detection. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:151-172. [PMID: 37770169 DOI: 10.1016/bs.pmbts.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Phage display is a significant and active molecular method and has continued crucial for investigative sector meanwhile its unearthing in 1985. This practice has numerous benefits: the association among physiology and genome, the massive variety of variant proteins showed in sole collection and the elasticity of collection that can be achieved. It suggests a diversity of stages for manipulating antigen attachment; yet, variety and steadiness of exhibited library are an alarm. Additional improvements, like accumulation of non-canonical amino acids, resulting in extension of ligands that can be recognized through collection, will support in expansion of the probable uses and possibilities of technology. Epidemic of COVID-19 had taken countless lives, and while indicative prescriptions were provided to diseased individuals, still no prevention was observed for the contamination. Phage demonstration has presented an in-depth understanding into protein connections included in pathogenesis. Phage display knowledge is developing as an influential, inexpensive, quick, and effectual method to grow novel mediators for the molecular imaging and analysis of cancer.
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Affiliation(s)
- Sonu Kumari
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
| | - Krati Singh
- Department of Biotechnology, Banasthali University, Newai, Rajasthan, India
| | - Neha Singh
- Department of Biotechnology, Banasthali University, Newai, Rajasthan, India
| | - Suphiya Khan
- Department of Biotechnology, Banasthali University, Newai, Rajasthan, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
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7
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Choi HL, Yang HR, Shin HG, Hwang K, Kim JW, Lee JH, Ryu T, Jung Y, Lee S. Generation and Next-Generation Sequencing-Based Characterization of a Large Human Combinatorial Antibody Library. Int J Mol Sci 2023; 24:ijms24066011. [PMID: 36983085 PMCID: PMC10057307 DOI: 10.3390/ijms24066011] [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: 01/30/2023] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Antibody phage display is a key technology for the discovery and development of target-specific monoclonal antibodies (mAbs) for use in research, diagnostics, and therapy. The construction of a high-quality antibody library, with larger and more diverse antibody repertoires, is essential for the successful development of phage display-derived mAbs. In this study, a large human combinatorial single-chain variable fragment library (1.5 × 1011 colonies) was constructed from Epstein-Barr virus-infected human peripheral blood mononuclear cells stimulated with a combination of two of the activators of human B cells, the Toll-like receptor 7/8 agonist R848 and interleukin-2. Next-generation sequencing analysis with approximately 1.9 × 106 and 2.7 × 106 full-length sequences of heavy chain variable (VH) and κ light chain variable (Vκ) domains, respectively, revealed that the library consists of unique VH (approximately 94%) and Vκ (approximately 91%) sequences with greater diversity than germline sequences. Lastly, multiple unique mAbs with high affinity and broad cross-species reactivity could be isolated from the library against two therapeutically relevant target antigens, validating the library quality. These findings suggest that the novel antibody library we have developed may be useful for the rapid development of target-specific phage display-derived recombinant human mAbs for use in therapeutic and diagnostic applications.
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Affiliation(s)
- Hye Lim Choi
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ha Gyeong Shin
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Kyusang Hwang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ji Woong Kim
- Department of Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ji Hyun Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul 08507, Republic of Korea
| | - Yushin Jung
- ATG Lifetech Inc., Seoul 08507, Republic of Korea
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul 02707, Republic of Korea
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8
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Jaiswal D, Kumar U, Gaur V, Salunke DM. Epitope-directed anti-SARS-CoV-2 scFv engineered against the key spike protein region could block membrane fusion. Protein Sci 2023; 32:e4575. [PMID: 36691733 PMCID: PMC9926471 DOI: 10.1002/pro.4575] [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] [Received: 10/29/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023]
Abstract
The newly emerged SARS-CoV-2 causing coronavirus disease (COVID-19) resulted in >500 million infections. A great deal about the molecular processes of virus infection in the host is getting uncovered. Two sequential proteolytic cleavages of viral spike protein by host proteases are prerequisites for the entry of the virus into the host cell. The first cleavage occurs at S1/S2 site by the furin protease, and the second cleavage at a fusion activation site, the S2' site, by the TMPRSS2 protease. S2' cleavage site is present in the S2 domain of spike protein followed by a fusion peptide. Given the S2' site to be conserved among all the SARS-CoV-2 variants, we chose an S2' epitope encompassing the S2' cleavage site and generated single-chain antibodies (scFvs) through an exhaustive phage display library screening. Crystal structure of a scFv in complex with S2' epitope was determined. Incidentally, S2' epitope in the scFv bound structure adopts an alpha-helical conformation equivalent to the conformation of the epitope in the spike protein. Furthermore, these scFvs can bind to the spike protein expressed either in vitro or on the mammalian cell surface. We illustrate a molecular model based on structural and biochemical insights into the antibody-S2' epitope interaction emphasizing scFvs mediated blocking of virus entry into the host cell by restricting the access of TMPRSS2 protease and consequently inhibiting the S2' cleavage competitively.
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Affiliation(s)
- Deepika Jaiswal
- International Centre for Genetic Engineering and BiotechnologyNew DelhiDelhiIndia
| | - Ujjwal Kumar
- International Centre for Genetic Engineering and BiotechnologyNew DelhiDelhiIndia
| | - Vineet Gaur
- National Institute of Plant Genome ResearchNew DelhiDelhiIndia
| | - Dinakar M. Salunke
- International Centre for Genetic Engineering and BiotechnologyNew DelhiDelhiIndia
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9
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Hu X, Li M, Zhang Y, Sang K, Zhang Y, Li W, Liu B, Wan L, Du B, Qian J, Meng F, Fu Y, Dai M, Gao G, Ye H. An innovative immunotherapeutic strategy for rheumatoid arthritis: Selectively suppressing angiogenesis and osteoclast differentiation by fully human antibody targeting thymocyte antigen-1. Exp Cell Res 2023; 424:113490. [PMID: 36706943 DOI: 10.1016/j.yexcr.2023.113490] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/14/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023]
Abstract
Thymocyte antigen-1 (THY-1)is a potential target for rheumatoid arthritis (RA) treatment, and THY-1 positive fibroblast-like synoviocytes (FLS) are enriched in the synovium of RA patients and participate in angiogenesis to accelerate RA progression. In this study, we screened an antibody targeting THY-1 (THY-1 Ab) and explored its mechanism in alleviating RA progression. THY-1 Ab was screened from ScFv phage antibody library by phage display technology (PDT). THY-1 Ab-treated collagen induced arthritis (CIA) mice had lower degree of arthritis scores. We explore the mechanism of THY-1 Ab in alleviating RA progression. THY-1 Ab can remarkably inhibit the secretion of pro-inflammatory factors and promote the secretion of anti-inflammatory factors. Further experiments showed that THY1 Ab downregulated the expression of JUNB by the hsa_circ_0094342/miRNA-155-5P/SPI1 axis, inhibited RA angiogenesis and osteoclast differentiation, and relieved RA progression. These findings support that THY-1 Ab is a promising therapeutic antibody for RA treatment.
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Affiliation(s)
- Xuanxuan Hu
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Meiqi Li
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yu Zhang
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Kanru Sang
- The First School of Clinical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yejun Zhang
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Wulan Li
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Bo Liu
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Leyu Wan
- School of Stomatology, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Bang Du
- The First School of Clinical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jinheng Qian
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Fanxi Meng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yanneng Fu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Meijuan Dai
- The Second School of Clinical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Guohui Gao
- School of Laboratory Medicine and Life Sciences, WenZhou Medical University, Wenzhou, Zhejiang, 325035, China; Key Laboratory of Laboratory Medicine, Ministry Education, Wenzhou, Zhejiang, 325035, China.
| | - Hui Ye
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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10
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Development of a human phage display-derived anti-PD-1 scFv antibody: an attractive tool for immune checkpoint therapy. BMC Biotechnol 2022; 22:22. [PMID: 35996120 PMCID: PMC9396865 DOI: 10.1186/s12896-022-00752-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/18/2022] [Indexed: 12/13/2022] Open
Abstract
Background The PD-1 checkpoint pathway plays a major role in tumor immune evasion and the development of the tumor microenvironment. Clinical studies show that therapeutic antibodies blocking the PD-1 pathway can restore anti-tumor or anti-virus immune responses by the reinvigoration of exhausted T cells. Because of the promising results of anti-PD-1 monoclonal antibodies in cancer treatment, autoimmune disorders, and infectious diseases, the PD-1 has emerged as an encouraging target for different diseases. Results In the present study, we employed a human semi-synthetic phage library for isolation of some scFvs against the extracellular domain of PD-1 protein by panning process. After the panning, a novel anti-PD-1 scFv (SS107) was found that exhibited specific binding to PD-1 antigen and stimulated Jurkat T cells. The selected anti-PD-1 scFv could restore the production of IL-2 and IFN-γ by Jurkat T cells that were co-cultured with PD-L1 positive tumor cells. Conclusion This anti-PD-1 scFv with high specificity and the ability to reactivate exhausted T cells has the potential to be developed as an anti-cancer agent or to be used in combination with other therapeutic approaches.
Supplementary Information The online version contains supplementary material available at 10.1186/s12896-022-00752-8.
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11
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Rutkauskaite J, Berger S, Stavrakis S, Dressler O, Heyman J, Casadevall I Solvas X, deMello A, Mazutis L. High-throughput single-cell antibody secretion quantification and enrichment using droplet microfluidics-based FRET assay. iScience 2022; 25:104515. [PMID: 35733793 PMCID: PMC9207670 DOI: 10.1016/j.isci.2022.104515] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/05/2021] [Accepted: 05/29/2022] [Indexed: 01/30/2023] Open
Abstract
High-throughput screening and enrichment of antibody-producing cells have many important applications. Herein, we present a droplet microfluidic approach for high-throughput screening and sorting of antibody-secreting cells using a Förster resonance electron transfer (FRET)-based assay. The FRET signal is mediated by the specific binding of the secreted antibody to two fluorescently labeled probes supplied within a droplet. Functional hybridoma cells expressing either membrane-bound or secreted monoclonal antibodies (mAbs), or both, were efficiently differentiated in less than 30 min. The antibody secretion rate by individual hybridoma cells was recorded in the range of 14,000 Abs/min, while the density of membrane-bound fraction was approximately 100 Abs/μm2. Combining the FRET assay with droplet-based single-cell sorting, an 800-fold enrichment of antigen-specific cells was achieved after one round of sorting. The presented system overcomes several key limitations observed in conventional FACS-based screening methods and should be applicable to assaying various other secreted proteins. FRET-based screening assay of antibody-secreting cells in microfluidic droplets Membrane-bound and secreted antibodies of the same cell are efficiently differentiated Using mouse hybridoma cells antibody secretion assay is completed in 30 min FRET-based droplet sorting enables over 800-fold enrichment in one round of sorting
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Affiliation(s)
- Justina Rutkauskaite
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, 7 Sauletekio ave., 10257 Vilnius, Lithuania.,Institute for Chemical and Bioengineering, ETH Zurich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Simon Berger
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Oliver Dressler
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - John Heyman
- Harvard University, SEAS, 9 Oxford St., Cambridge, MA 02139, USA
| | | | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Linas Mazutis
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, 7 Sauletekio ave., 10257 Vilnius, Lithuania
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12
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Morris NM, Blee JA, Hauert S. Developing a computational pharmacokinetic model of systemic snakebite envenomation and antivenom treatment. Toxicon 2022; 215:77-90. [PMID: 35716719 DOI: 10.1016/j.toxicon.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 11/19/2022]
Abstract
Snakebite envenomation is responsible for over 100,000 deaths and 400,000 cases of disability annually, most of which are preventable through access to safe and effective antivenoms. Snake venom toxins span a wide molecular weight range, influencing their absorption, distribution, and elimination within the body. In recent years, a range of scaffolds have been applied to antivenom development. These scaffolds similarly span a wide molecular weight range and subsequently display diverse pharmacokinetic behaviours. Computational simulations represent a powerful tool to explore the interplay between these varied antivenom scaffolds and venoms, to assess whether a pharmacokinetically optimal antivenom exists. The purpose of this study was to establish a computational model of systemic snakebite envenomation and treatment, for the quantitative assessment and comparison of conventional and next-generation antivenoms. A two-compartment mathematical model of envenomation and treatment was defined and the system was parameterised using existing data from rabbits. Elimination and biodistribution parameters were regressed against molecular weight to predict the dynamics of IgG, F(ab')2, Fab, scFv, and nanobody antivenoms, spanning a size range of 15-150 kDa. As a case study, intramuscular envenomation by Naja sumatrana (equatorial spitting cobra) and its treatment using Fab, F(ab')2, and IgG antivenoms was simulated. Variable venom dose tests were applied to visualise effective antivenom dose levels. Comparisons to existing antivenoms and experimental rescue studies highlight the large dose reductions that could result from recombinant antivenom use. This study represents the first comparative in silico model of snakebite envenomation and treatment.
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Affiliation(s)
- Natalie M Morris
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
| | - Johanna A Blee
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
| | - Sabine Hauert
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
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13
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Mahdavi SZB, Oroojalian F, Eyvazi S, Hejazi M, Baradaran B, Pouladi N, Tohidkia MR, Mokhtarzadeh A, Muyldermans S. An overview on display systems (phage, bacterial, and yeast display) for production of anticancer antibodies; advantages and disadvantages. Int J Biol Macromol 2022; 208:421-442. [PMID: 35339499 DOI: 10.1016/j.ijbiomac.2022.03.113] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 03/17/2022] [Indexed: 11/05/2022]
Abstract
Antibodies as ideal therapeutic and diagnostic molecules are among the top-selling drugs providing considerable efficacy in disease treatment, especially in cancer therapy. Limitations of the hybridoma technology as routine antibody generation method in conjunction with numerous developments in molecular biology led to the development of alternative approaches for the streamlined identification of most effective antibodies. In this regard, display selection technologies such as phage display, bacterial display, and yeast display have been widely promoted over the past three decades as ideal alternatives to traditional methods. The display of antibodies on phages is probably the most widespread of these methods, although surface display on bacteria or yeast have been employed successfully, as well. These methods using various sizes of combinatorial antibody libraries and different selection strategies possessing benefits in screening potency, generating, and isolation of high affinity antibodies with low risk of immunogenicity. Knowing the basics of each method assists in the design and retrieval process of antibodies suitable for different diseases, including cancer. In this review, we aim to outline the basics of each library construction and its display method, screening and selection steps. The advantages and disadvantages in comparison to alternative methods, and their applications in antibody engineering will be explained. Finally, we will review approved or non-approved therapeutic antibodies developed by employing these methods, which may serve as therapeutic antibodies in cancer therapy.
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Affiliation(s)
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran; Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Shirin Eyvazi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran; Biotechnology Research Center, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Maryam Hejazi
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Pouladi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mohammad Reza Tohidkia
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, China..
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14
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Cho JH, Ju WS, Seo SY, Kim BH, Kim JS, Kim JG, Park SJ, Choo YK. The Potential Role of Human NME1 in Neuronal Differentiation of Porcine Mesenchymal Stem Cells: Application of NB-hNME1 as a Human NME1 Suppressor. Int J Mol Sci 2021; 22:ijms222212194. [PMID: 34830075 PMCID: PMC8619003 DOI: 10.3390/ijms222212194] [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: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022] Open
Abstract
This study aimed to investigate the effects of the human macrophage (MP) secretome in cellular xenograft rejection. The role of human nucleoside diphosphate kinase A (hNME1), from the secretome of MPs involved in the neuronal differentiation of miniature pig adipose tissue-derived mesenchymal stem cells (mp AD-MSCs), was evaluated by proteomic analysis. Herein, we first demonstrate that hNME1 strongly binds to porcine ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1 (pST8SIA1), which is a ganglioside GD3 synthase. When hNME1 binds with pST8SIA1, it induces degradation of pST8SIA1 in mp AD-MSCs, thereby inhibiting the expression of ganglioside GD3 followed by decreased neuronal differentiation of mp AD-MSCs. Therefore, we produced nanobodies (NBs) named NB-hNME1 that bind to hNME1 specifically, and the inhibitory effect of NB-hNME1 was evaluated for blocking the binding between hNME1 and pST8SIA1. Consequently, NB-hNME1 effectively blocked the binding of hNME1 to pST8SIA1, thereby recovering the expression of ganglioside GD3 and neuronal differentiation of mp AD-MSCs. Our findings suggest that mp AD-MSCs could be a potential candidate for use as an additive, such as an immunosuppressant, in stem cell transplantation.
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Affiliation(s)
- Jin Hyoung Cho
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
- GreenBio Corp. Central Research, 201-19, Bubaljungand-ro, Bubal-eup, Icheon-si 17321, Korea
| | - Won Seok Ju
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
- Institute for Glycoscience, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea
| | - Sang Young Seo
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
| | - Bo Hyun Kim
- CHA Fertility Center Bundang, 59, Yatap-ro, Bundang-gu, Seongnam-si 13496, Korea;
| | - Ji-Su Kim
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology, 181, Ipsin-gil, Jeongeup-si 56216, Korea;
| | - Jong-Geol Kim
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
| | - Soon Ju Park
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
| | - Young-Kug Choo
- Department of Biological Science, College of Natural Sciences, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea; (J.H.C.); (W.S.J.); (S.Y.S.); (J.-G.K.); (S.J.P.)
- Institute for Glycoscience, Wonkwang University, 460, Iksan-daero, Iksan-si 54538, Korea
- Correspondence: ; Tel.: +82-63-850-6087; Fax: +82-63-857-8837
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15
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Jaroszewicz W, Morcinek-Orłowska J, Pierzynowska K, Gaffke L, Węgrzyn G. Phage display and other peptide display technologies. FEMS Microbiol Rev 2021; 46:6407522. [PMID: 34673942 DOI: 10.1093/femsre/fuab052] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 "for the phage display of peptides and antibodies". In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine, and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.
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Affiliation(s)
- Weronika Jaroszewicz
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | | | - Karolina Pierzynowska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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16
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Chikaev AN, Chikaev AN, Rudometov AP, Merkulyeva YA, Karpenko LI. Phage display as a tool for identifying HIV-1 broadly neutralizing antibodies. Vavilovskii Zhurnal Genet Selektsii 2021; 25:562-572. [PMID: 34595378 PMCID: PMC8453360 DOI: 10.18699/vj21.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/14/2021] [Accepted: 03/22/2021] [Indexed: 11/19/2022] Open
Abstract
Combinatorial biology methods offer a good solution for targeting interactions of specif ic molecules
by a high-throughput screening and are widely used for drug development, diagnostics, identif ication of novel
monoclonal antibodies, search for linear peptide mimetics of discontinuous epitopes for the development of
immunogens or vaccine components. Among all currently available techniques, phage display remains one of
the most popular approaches. Despite being a fairly old method, phage display is still widely used for studying
protein-protein, peptide-protein and DNA-protein interactions due to its relative simplicity and versatility. Phage
display allows highly representative libraries of peptides, proteins or their fragments to be created. Each phage
particle in a library displays peptides or proteins fused to its coat protein and simultaneously carries the DNA
sequence encoding the displayed peptide/protein in its genome. The biopanning procedure allows isolation of
specif ic clones for almost any target, and due to the physical link between the genotype and the phenotype of
recombinant phage particles it is possible to determine the structure of selected molecules. Phage display technology
continues to play an important role in HIV research. A major obstacle to the development of an effective
HIV vaccine is an extensive genetic and antigenic variability of the virus. According to recent data, in order to provide
protection against HIV infection, the so-called broadly neutralizing antibodies that are cross-reactive against
multiple viral strains of HIV must be induced, which makes the identif ication of such antibodies a key area of HIV
vaccinology. In this review, we discuss the use of phage display as a tool for identif ication of HIV-specif ic antibodies
with broad neutralizing activity. We provide an outline of phage display technology, brief ly describe the
design of antibody phage libraries and the affinity selection procedure, and discuss the biology of HIV-1-specif ic
broadly neutralizing antibodies. Finally, we summarize the studies aimed at identif ication of broadly neutralizing
antibodies using various types of phage libraries.
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Affiliation(s)
| | - A N Chikaev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A P Rudometov
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
| | - Yu A Merkulyeva
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
| | - L I Karpenko
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
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17
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Van Lent J, Breukers J, Ven K, Ampofo L, Horta S, Pollet F, Imbrechts M, Geukens N, Vanhoorelbeke K, Declerck P, Lammertyn J. Miniaturized single-cell technologies for monoclonal antibody discovery. LAB ON A CHIP 2021; 21:3627-3654. [PMID: 34505611 DOI: 10.1039/d1lc00243k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.
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Affiliation(s)
- Julie Van Lent
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Louanne Ampofo
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
| | - Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
| | - Francesca Pollet
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Maya Imbrechts
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Paul Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
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18
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Rossotti MA, Bélanger K, Henry KA, Tanha J. Immunogenicity and humanization of single‐domain antibodies. FEBS J 2021; 289:4304-4327. [DOI: 10.1111/febs.15809] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Martin A. Rossotti
- Life Sciences Division Human Health Therapeutics Research Centre National Research Council Canada Ottawa Canada
| | - Kasandra Bélanger
- Life Sciences Division Human Health Therapeutics Research Centre National Research Council Canada Ottawa Canada
| | - Kevin A. Henry
- Life Sciences Division Human Health Therapeutics Research Centre National Research Council Canada Ottawa Canada
- Department of Biochemistry, Microbiology and Immunology Faculty of Medicine University of Ottawa Canada
| | - Jamshid Tanha
- Life Sciences Division Human Health Therapeutics Research Centre National Research Council Canada Ottawa Canada
- Department of Biochemistry, Microbiology and Immunology Faculty of Medicine University of Ottawa Canada
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19
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Torikai M, Higuchi H, Yamamoto N, Ishikawa D, Fujita H, Taguchi K, Sakai F, Soejima K, Nakashima T. A novel monoclonal antibody cross-reactive with both human and mouse α9 integrin useful for therapy against rheumatoid arthritis. J Biochem 2021; 168:231-241. [PMID: 32271918 DOI: 10.1093/jb/mvaa040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/28/2020] [Indexed: 11/14/2022] Open
Abstract
This study introduces a novel monoclonal anti-α9 integrin antibody (MA9-413) with human variable regions, isolated by phage display technology. MA9-413 specifically binds to both human and mouse α9 integrin by recognizing a conserved loop region designated as L1 (amino acids 104-122 of human α9 integrin). MA9-413 inhibits human and mouse α9 integrin-dependent cell adhesion to ligands and suppresses synovial inflammation and osteoclast activation in a mouse model of arthritis. This is the first monoclonal anti-α9 integrin antibody that can react with and functionally inhibit both human and mouse α9 integrin. MA9-413 allows data acquisition both in animal and human pharmacological studies without resorting to surrogate antibodies. Since MA9-413 showed certain therapeutic effects in the mouse arthritis model, it can be considered as a useful therapy against rheumatoid arthritis and other α9 integrin-associated diseases.
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Affiliation(s)
- Masaharu Torikai
- Research & Development Division, KM Biologics Co., Ltd, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Hirofumi Higuchi
- Research & Development Division, KM Biologics Co., Ltd, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | | | - Daisuke Ishikawa
- Research & Development Division, KM Biologics Co., Ltd, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Hirotada Fujita
- Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
| | - Katsunari Taguchi
- Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
| | - Fumihiko Sakai
- EVEC Inc., 6 Odori Nishi, Chuo-ku, Sapporo 060-0042, Japan
| | - Kenji Soejima
- Research & Development Division, KM Biologics Co., Ltd, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Toshihiro Nakashima
- The Chemo-Sero-Therapeutic Research Institute (Kaketsuken), 4-7 Hanabatacho, Chuo-ku, Kumamoto 860-0806, Japan
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20
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Ferrara F, Teixeira AA, Naranjo L, Erasmus MF, D'Angelo S, Bradbury ARM. Exploiting next-generation sequencing in antibody selections - a simple PCR method to recover binders. MAbs 2021; 12:1701792. [PMID: 31829073 PMCID: PMC7009332 DOI: 10.1080/19420862.2019.1701792] [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] [Indexed: 11/09/2022] Open
Abstract
Antibody discovery using invitro display technologies such as phage and/or yeast display has become acornerstone in many research and development projects, including the creation of new drugs for clinical use. Traditionally, after the selection phase, random clones are isolated for binding validation and Sanger sequencing. More recently, next-generation sequencing (NGS) technology has allowed deeper insight into the antibody population after aselection campaign, enabling the identification of many more specific binders. However, this approach only provides the DNA sequences of potential binders, the properties of which need to be fully elucidated by obtaining corresponding clones and expressing them for further validation. Here we present arapid novel method to harvest potential clones identified by NGS that uses asimple PCR and yeast recombination approach. The protocol was tested in selections against three different targets and was able to recover clones at an abundance level that would be impractical to identify using traditional methods.
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Affiliation(s)
| | - Andre A Teixeira
- Specifica Inc., Santa Fe, NM, USA.,Bioscience Division, New Mexico Consortium, Los Alamos, NM, USA
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21
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Abstract
Ever since the discovery of antibodies, they have been generated by complicated multi-step procedures. Typically, these involve sequencing, cloning, and screening after expression of the antibodies in a suitable organism and format. Here, a staphylococcal nanobody display is described that omits many the abovementioned intermediate steps and allows for simultaneous screening of multiple targets without prior knowledge nor expression of the binders. This paper reports a detailed, general step-by-step protocol to achieve nanobodies of high affinity. Apart from its focus on radioactive and fluorescent targets, it gives options for various other target formats and additional applications for the staphylococcal library; including flow cytometry and immunoprecipitation. This provides a system for antibody engineers that can be easily adopted to their specific needs.
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Affiliation(s)
- Marco Cavallari
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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22
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Andrian T, Bakkum T, van Elsland DM, Bos E, Koster AJ, Albertazzi L, van Kasteren SI, Pujals S. Super-resolution correlative light-electron microscopy using a click-chemistry approach for studying intracellular trafficking. Methods Cell Biol 2020; 162:303-331. [PMID: 33707017 DOI: 10.1016/bs.mcb.2020.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Correlative light and electron microscopy (CLEM) entails a group of multimodal imaging techniques that are combined to pinpoint to the location of fluorescently labeled molecules in the context of their ultrastructural cellular environment. Here we describe a detailed workflow for STORM-CLEM, in which STochastic Optical Reconstruction Microscopy (STORM), an optical super-resolution technique, is correlated with transmission electron microscopy (TEM). This protocol has the advantage that both imaging modalities have resolution at the nanoscale, bringing higher synergies on the information obtained. The sample is prepared according to the Tokuyasu method followed by click-chemistry labeling and STORM imaging. Then, after heavy metal staining, electron microscopy imaging is performed followed by correlation of the two images. The case study presented here is on intracellular pathogens, but the protocol is versatile and could potentially be applied to many types of samples.
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Affiliation(s)
- Teodora Andrian
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Thomas Bakkum
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Leiden, The Netherlands
| | - Daphne M van Elsland
- Department of Cell and Chemical Biology, The Institute for Chemical Immunology, Leiden University Medical Center LUMC, Leiden, The Netherlands
| | - Erik Bos
- Department of Cell and Chemical Biology, Section Electron Microscopy, Leiden University Medical Center LUMC, Leiden, The Netherlands
| | - Abraham J Koster
- Department of Cell and Chemical Biology, Section Electron Microscopy, Leiden University Medical Center LUMC, Leiden, The Netherlands
| | - Lorenzo Albertazzi
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain; Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Sander I van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Leiden, The Netherlands.
| | - Sílvia Pujals
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain; Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain.
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23
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Abbaszadeh F, Leylabadlo HE, Alinezhad F, Feizi H, Mobed A, Baghbanijavid S, Baghi HB. Bacteriophages: cancer diagnosis, treatment, and future prospects. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2020. [DOI: 10.1007/s40005-020-00503-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Lee GY, Bong JH, Jung J, Kang MJ, Jose J, Pyun JC. Application of a thermophoretic immunoassay in the diagnosis of lupus using outer membrane particles from E. coli. Biosens Bioelectron 2020; 156:112110. [PMID: 32174550 DOI: 10.1016/j.bios.2020.112110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/02/2020] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
Abstract
Thermophoresis is the physical diffusion of molecules from hot to cold induced by a thermal gradient. Thermophoresis has been used to evaluate the interaction of biomolecules in solution. In this study, the outer membrane from E. coli was isolated and used to produce OM particles with a diameter of approximately 100 nm. These prepared OM particles were applied in a thermophoretic immunoassay. First, outer membrane (OM) particles with lipopolysaccharides (LPS) and anti-LPS antibodies were used as a model to demonstrate proof of concept and the difference in E. coli thermophoresis was explained by the changes in the molecular surface area (A) and effective charge (σeff). The hydrodynamic size of the molecules was measured as a changing parameter, molecular surface area (A), by dynamic laser scattering (DLS), and the zeta potential was measured as a changing parameter of effective charge (σeff) and then evaluated by the Soret equation. Using the hydrodynamic size and zeta potential values, the interaction between the antigen (OM particle with LPS) and antibody (anti-LPS antibodies) could be monitored and the results were fitted to the thermophoretic immunoassay using the Soret coefficient and equation. Finally, this OM-based immunoassay was applied to the medical diagnosis of systemic lupus erythematosus. Here, OM particles with Ro and La proteins were used to analyze the autoantibodies in patient and control sera. Thermophoretic immunoassay results were also compared to the fitted analysis using hydrodynamic size and zeta potential values and the Soret coefficient and equation.
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Affiliation(s)
- Ga-Yeon Lee
- Department of Materials Science and Engineering, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749, South Korea
| | - Ji-Hong Bong
- Department of Materials Science and Engineering, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749, South Korea
| | - Jaeyong Jung
- Department of Materials Science and Engineering, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749, South Korea
| | - Min-Jung Kang
- Korea Institute of Science and Technology, Seoul, South Korea
| | - Joachim Jose
- Institute of Pharmaceutical and Medical Chemistry, University of Münster, Münster, Germany
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749, South Korea.
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25
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Wippold JA, Wang H, Tingling J, Leibowitz J, de Figueiredo P, Han A. PRESCIENT: platform for the rapid evaluation of antibody success using integrated microfluidics enabled technology. LAB ON A CHIP 2020; 20:1628-1638. [PMID: 32196032 PMCID: PMC7269184 DOI: 10.1039/c9lc01165j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Identifying antibodies (Abs) that neutralize infectious agents is the first step for developing therapeutics, vaccines, and diagnostic tools for these infectious agents. However, current approaches for identifying neutralizing Abs (nAbs) typically rely on dilution-based assays that are costly, inefficient, and only survey a small subset of the entire repertoire. There are also intrinsic biases in many steps of conventional nAb identification processes. More importantly, conventional assays rely on simple Ab-antigen binding assays, which may not result in identifying the most potent nAbs, as the strongest binder may not be the most potent nAb. Droplet microfluidic systems have the capability to overcome such limitations by conducting complex multi-step assays with high reliability, resolution, and throughput in a pico-liter volume water-in-oil emulsion droplet format. Here, we describe the development of PRESCIENT (Platform for the Rapid Evaluation of antibody SucCess using Integrated microfluidics ENabled Technology), a droplet microfluidic system that can enable high-throughput single-cell resolution identification of nAb repertoires elicited in response to viral infection. We demonstrate PRESCIENT's ability to identify Abs that neutralize a model viral agent, Murine coronavirus (murine hepatitis virus), which causes high mortality rates in experimentally infected mice. In-droplet infection of host cells by the virus was first demonstrated, followed by demonstration of in-droplet neutralization by nAbs produced from a single Ab-producing hybridoma cell. Finally, fluorescence intensity analyses of two populations of hybridoma cell lines (nAb-producing and non-nAb-producing hybridoma cell lines) successfully discriminated between the two populations. The presented strategy and platform have the potential to identify and investigate neutralizing activities against a broad range of potential infectious agents for which nAbs have yet to be discovered, significantly advancing the nAb identification process as well as reinvigorating the field of Ab discovery, characterization, and development.
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Affiliation(s)
- Jose A. Wippold
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Han Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, CHINA
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Joseph Tingling
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Julian Leibowitz
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA
- Norman Borlaug Center, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Medicine, Texas A&M University, College Station, TX 77843
| | - Arum Han
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, CHINA
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26
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Chen J, Zhao Y, Feng W. Selection, preparation and characterization of scFv against human lipocalin 6 by phage display technology. Protein Expr Purif 2020; 171:105627. [PMID: 32205279 DOI: 10.1016/j.pep.2020.105627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 11/15/2022]
Abstract
Human lipocalin 6 (hLCN6) is a newly discovered epididymal-specific secreted protein, capable of binding to the head and tail of spermatozoa and involved in sperm maturation. Anti-hLCN6 monoclonal antibody coupled immunomagnetic beads (IMBs) can be effectively used for the separation and forensic identification of sperm cells from mixed stains. But the source of monoclonal antibody is limited. In this study, an immunized mouse phage display antibody library was constructed and the single-chain variable fragments (scFvs) against hLCN6 were screened. The selection was performed using four rounds of biopanning and positive clones were validated by phage ELISA. Two anti-hLCN6 scFv clones with highest affinity were selected and sequencing result showed that the two sequences were identical. After prokaryotic expression and purification, the purified scFv could specifically recognize the hLCN6 in the lysate of human sperm cells and epididymis by western blot analysis, without any cross-reactivity with cellular antigens in female epithelial cells. The dissociation constant (Kd) of anti-hLCN6 scFv was 6.69 × 10-7 mol/L measured by indirect ELISA. Therefore, our work not only provides a useful tool for further exploration of the biological functions of hLCN6, but also opens up new research avenues for the separation of sperm cells from mixed stains based on immuno-binding reaction.
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Affiliation(s)
- Jiong Chen
- Department of Forensic Biology, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Yue Zhao
- CITIC Heavy Industries Co., Ltd, Luoyang, 471003, China
| | - Wei Feng
- Department of Forensic Biology, Henan University of Science and Technology, Luoyang, 471023, China
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27
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Ministro JH, Oliveira SS, Oliveira JG, Cardoso M, Aires-da-Silva F, Corte-Real S, Goncalves J. Synthetic antibody discovery against native antigens by CRISPR/Cas9-library generation and endoplasmic reticulum screening. Appl Microbiol Biotechnol 2020; 104:2501-2512. [PMID: 32020276 DOI: 10.1007/s00253-020-10423-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/18/2020] [Accepted: 01/26/2020] [Indexed: 01/03/2023]
Abstract
Despite the significant advances of antibodies as therapeutic agents, there is still much room for improvement concerning the discovery of these macromolecules. Here, we present a new synthetic cell-based strategy that takes advantage of eukaryotic cell biology to produce highly diverse antibody libraries and, simultaneously, link them to a high-throughput selection mechanism, replicating B cell diversification mechanisms. The interference of site-specific recognition by CRISPR/Cas9 with error-prone DNA repair mechanisms was explored for the generation of diversity, in a cell population containing a gene for a light chain antibody fragment. We achieved up to 93% of cells containing a mutated antibody gene after diversification mechanisms, specifically inside one of the antigen-binding sites. This targeted variability strategy was then integrated into an intracellular selection mechanism. By fusing the antibody with a KDEL retention signal, the interaction of antibodies and native membrane antigens occurs inside the endoplasmic reticulum during the process of protein secretion, enabling the detection of high-quality leads for expression and affinity by flow cytometry. We successfully obtained antibody lead candidates against CD3 as proof of concept. In summary, we developed a novel antibody discovery platform against native antigens by endoplasmic synthetic library generation using CRISPR/Cas9, which will contribute to a faster discovery of new biotherapeutic molecules, reducing the time-to-market.
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Affiliation(s)
- Joana H Ministro
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Soraia S Oliveira
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Joana G Oliveira
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Miguel Cardoso
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Frederico Aires-da-Silva
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Sofia Corte-Real
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,Technophage SA, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisbon, Portugal
| | - Joao Goncalves
- iMed.ULisboa - Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.
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28
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Lu RM, Hwang YC, Liu IJ, Lee CC, Tsai HZ, Li HJ, Wu HC. Development of therapeutic antibodies for the treatment of diseases. J Biomed Sci 2020; 27:1. [PMID: 31894001 PMCID: PMC6939334 DOI: 10.1186/s12929-019-0592-z] [Citation(s) in RCA: 1046] [Impact Index Per Article: 261.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
It has been more than three decades since the first monoclonal antibody was approved by the United States Food and Drug Administration (US FDA) in 1986, and during this time, antibody engineering has dramatically evolved. Current antibody drugs have increasingly fewer adverse effects due to their high specificity. As a result, therapeutic antibodies have become the predominant class of new drugs developed in recent years. Over the past five years, antibodies have become the best-selling drugs in the pharmaceutical market, and in 2018, eight of the top ten bestselling drugs worldwide were biologics. The global therapeutic monoclonal antibody market was valued at approximately US$115.2 billion in 2018 and is expected to generate revenue of $150 billion by the end of 2019 and $300 billion by 2025. Thus, the market for therapeutic antibody drugs has experienced explosive growth as new drugs have been approved for treating various human diseases, including many cancers, autoimmune, metabolic and infectious diseases. As of December 2019, 79 therapeutic mAbs have been approved by the US FDA, but there is still significant growth potential. This review summarizes the latest market trends and outlines the preeminent antibody engineering technologies used in the development of therapeutic antibody drugs, such as humanization of monoclonal antibodies, phage display, the human antibody mouse, single B cell antibody technology, and affinity maturation. Finally, future applications and perspectives are also discussed.
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Affiliation(s)
- Ruei-Min Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Yu-Chyi Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - I-Ju Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Chi-Chiu Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Han-Zen Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Hsin-Jung Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan. .,, 128 Academia Rd., Section 2, Nankang, Taipei, 11529, Taiwan.
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29
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Yang X, Xie S, Yang X, Cueva JC, Hou X, Tang Z, Yao H, Mo F, Yin S, Liu A, Lu X. Opportunities and Challenges for Antibodies against Intracellular Antigens. Am J Cancer Res 2019; 9:7792-7806. [PMID: 31695801 PMCID: PMC6831482 DOI: 10.7150/thno.35486] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Therapeutic antibodies are one most significant advances in immunotherapy, the development of antibodies against disease-associated MHC-peptide complexes led to the introduction of TCR-like antibodies. TCR-like antibodies combine the recognition of intracellular proteins with the therapeutic potency and versatility of monoclonal antibodies (mAb), offering an unparalleled opportunity to expand the repertoire of therapeutic antibodies available to treat diseases like cancer. This review details the current state of TCR-like antibodies and describes their production, mechanisms as well as their applications. In addition, it presents an insight on the challenges that they must overcome in order to become commercially and clinically validated.
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30
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Jorgolli M, Nevill T, Winters A, Chen I, Chong S, Lin F, Mock M, Chen C, Le K, Tan C, Jess P, Xu H, Hamburger A, Stevens J, Munro T, Wu M, Tagari P, Miranda LP. Nanoscale integration of single cell biologics discovery processes using optofluidic manipulation and monitoring. Biotechnol Bioeng 2019; 116:2393-2411. [PMID: 31112285 PMCID: PMC6771990 DOI: 10.1002/bit.27024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022]
Abstract
The new and rapid advancement in the complexity of biologics drug discovery has been driven by a deeper understanding of biological systems combined with innovative new therapeutic modalities, paving the way to breakthrough therapies for previously intractable diseases. These exciting times in biomedical innovation require the development of novel technologies to facilitate the sophisticated, multifaceted, high-paced workflows necessary to support modern large molecule drug discovery. A high-level aspiration is a true integration of "lab-on-a-chip" methods that vastly miniaturize cellulmical experiments could transform the speed, cost, and success of multiple workstreams in biologics development. Several microscale bioprocess technologies have been established that incrementally address these needs, yet each is inflexibly designed for a very specific process thus limiting an integrated holistic application. A more fully integrated nanoscale approach that incorporates manipulation, culture, analytics, and traceable digital record keeping of thousands of single cells in a relevant nanoenvironment would be a transformative technology capable of keeping pace with today's rapid and complex drug discovery demands. The recent advent of optical manipulation of cells using light-induced electrokinetics with micro- and nanoscale cell culture is poised to revolutionize both fundamental and applied biological research. In this review, we summarize the current state of the art for optical manipulation techniques and discuss emerging biological applications of this technology. In particular, we focus on promising prospects for drug discovery workflows, including antibody discovery, bioassay development, antibody engineering, and cell line development, which are enabled by the automation and industrialization of an integrated optoelectronic single-cell manipulation and culture platform. Continued development of such platforms will be well positioned to overcome many of the challenges currently associated with fragmented, low-throughput bioprocess workflows in biopharma and life science research.
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Affiliation(s)
| | - Tanner Nevill
- Product ApplicationsBerkeley Lights, IncEmeryvilleCalifornia
| | - Aaron Winters
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Irwin Chen
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Su Chong
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Fen‐Fen Lin
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Marissa Mock
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Ching Chen
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Kim Le
- Drug Substance Technologies, One Amgen Center DriveThousand OaksCalifornia
| | - Christopher Tan
- Drug Substance Technologies, One Amgen Center DriveThousand OaksCalifornia
| | - Philip Jess
- Product ApplicationsBerkeley Lights, IncEmeryvilleCalifornia
| | - Han Xu
- Drug DiscoveryA2 BiotherapeuticsWestlake VillageCalifornia
| | - Agi Hamburger
- Drug DiscoveryA2 BiotherapeuticsWestlake VillageCalifornia
| | - Jennitte Stevens
- Drug Substance Technologies, One Amgen Center DriveThousand OaksCalifornia
| | - Trent Munro
- Drug Substance Technologies, One Amgen Center DriveThousand OaksCalifornia
| | - Ming Wu
- Department of Electrical Engineering and Computer SciencesUniversity of California at BerkeleyBerkeleyCalifornia
| | - Philip Tagari
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Les P. Miranda
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
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31
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Ljungars A, Svensson C, Carlsson A, Birgersson E, Tornberg UC, Frendéus B, Ohlin M, Mattsson M. Deep Mining of Complex Antibody Phage Pools Generated by Cell Panning Enables Discovery of Rare Antibodies Binding New Targets and Epitopes. Front Pharmacol 2019; 10:847. [PMID: 31417405 PMCID: PMC6683657 DOI: 10.3389/fphar.2019.00847] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/02/2019] [Indexed: 01/11/2023] Open
Abstract
Phage display technology is a common approach for discovery of therapeutic antibodies. Drug candidates are typically isolated in two steps: First, a pool of antibodies is enriched through consecutive rounds of selection on a target antigen, and then individual clones are characterized in a screening procedure. When whole cells are used as targets, as in phenotypic discovery, the output phage pool typically contains thousands of antibodies, binding, in theory, hundreds of different cell surface receptors. Clonal expansion throughout the phage display enrichment process is affected by multiple factors resulting in extremely complex output phage pools where a few antibodies are highly abundant and the majority is very rare. This is a huge challenge in the screening where only a fraction of the antibodies can be tested using a conventional binding analysis, identifying mainly the most abundant clones typically binding only one or a few targets. As the expected number of antibodies and specificities in the pool is much higher, complementing methods, to reach deeper into the pool, are required, called deep mining methods. In this study, four deep mining methods were evaluated: 1) isolation of rare sub-pools of specific antibodies through selection on recombinant proteins predicted to be expressed on the target cells, 2) isolation of a sub-pool enriched for antibodies of unknown specificities through depletion of the primary phage pool on recombinant proteins corresponding to receptors known to generate many binders, 3) isolation of a sub-pool enriched for antibodies through selection on cells blocked with antibodies dominating the primary phage pool, and 4) next-generation sequencing-based analysis of isolated antibody pools followed by antibody gene synthesis and production of rare but enriched clones. We demonstrate that antibodies binding new targets and epitopes, not discovered through screening alone, can be discovered using described deep mining methods. Overall, we demonstrate the complexity of phage pools generated through selection on cells and show that a combination of conventional screening and deep mining methods are needed to fully utilize such pools. Deep mining will be important in future phenotypic antibody drug discovery efforts to increase the diversity of identified antibodies and targets.
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Affiliation(s)
- Anne Ljungars
- BioInvent International AB, Lund, Sweden
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | | | | | | | | | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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32
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Kumar R, Parray HA, Shrivastava T, Sinha S, Luthra K. Phage display antibody libraries: A robust approach for generation of recombinant human monoclonal antibodies. Int J Biol Macromol 2019; 135:907-918. [PMID: 31170490 DOI: 10.1016/j.ijbiomac.2019.06.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/02/2019] [Accepted: 06/02/2019] [Indexed: 12/29/2022]
Abstract
Monoclonal antibodies (mAbs) and their derivatives have achieved remarkable success as medicine, targeting both diagnostic and therapeutic applications associated with communicable and non-communicable diseases. In the last 3 to 4 decades, tremendous success has been manifested in the field of cancer therapy, autoimmune diseases, cardiovascular and infectious diseases. MAbs are the fastest growing class of biopharmaceuticals, with more than 25 derivatives are in clinical use and 7 of these have been isolated through phage display technology. Phage display technology has gained impetus in the field of medical and health sciences, as a large repertoire of diverse recombinant antibodies, targeting various antigens have been generated in a short span of time. A prominent number of phage display derived antibodies are already approved for therapy and significant numbers are currently in clinical trials. In this review we have discussed the various strategies employed for generation of monoclonal antibodies; their advantages, limitations and potential therapeutic applications. We also discuss the potential of phage display antibody libraries in isolation of monoclonal antibodies.
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Affiliation(s)
- Rajesh Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India; Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India.
| | - Hilal Ahmed Parray
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Tripti Shrivastava
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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33
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Vostakolaei MA, Molavi O, Hejazi MS, Kordi S, Rahmati S, Barzegari A, Abdolalizadeh J. Isolation and characterization of a novel scFv antibody fragments specific for Hsp70 as a tumor biomarker. J Cell Biochem 2019; 120:14711-14724. [DOI: 10.1002/jcb.28732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/12/2019] [Accepted: 03/22/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Mehdi Asghari Vostakolaei
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy Tabriz University of Medical Sciences Tabriz Iran
| | - Ommoleila Molavi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy Tabriz University of Medical Sciences Tabriz Iran
- Biotechnology Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy Tabriz University of Medical Sciences Tabriz Iran
| | - Shirafkan Kordi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences Tabriz University of Medical Sciences Tabriz Iran
| | - Saman Rahmati
- Medical Biotechnology Department Biotechnology Research Center, Pasteur Institute of Iran Tehran Iran
| | - Abolfazl Barzegari
- Research Centre for Pharmaceutical Nanotechnology Tabriz University of Medical Sciences Tabriz Iran
| | - Jalal Abdolalizadeh
- Drug Applied Research Center Tabriz University of Medical Sciences Tabriz Iran
- Paramedical Faculty Tabriz University of Medical Sciences Tabriz Iran
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34
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Timoshicheva TA, Zabrodskaya YA, Ramsay E, Amosova IV. Use of hexon as an antigen for the production of monoclonal antibodies capable of detecting multiple adenovirus types. Biologicals 2019; 58:44-49. [DOI: 10.1016/j.biologicals.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/10/2018] [Accepted: 01/13/2019] [Indexed: 10/27/2022] Open
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35
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Arslan M, Karadağ D, Kalyoncu S. Protein engineering approaches for antibody fragments: directed evolution and rational design approaches. ACTA ACUST UNITED AC 2019; 43:1-12. [PMID: 30930630 PMCID: PMC6426644 DOI: 10.3906/biy-1809-28] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The number of therapeutic antibodies in preclinical, clinical, or approved phases has been increasing exponentially, mostly due to their known successes. Development of antibody engineering methods has substantially hastened the development of therapeutic antibodies. A variety of protein engineering techniques can be applied to antibodies to improve their afinity and/or biophysical properties such as solubility and stability. Antibody fragments (where all or some parts of constant regions are eliminated while the essential antigen binding region is preserved) are more suitable for protein engineering techniques because there are many in vitro screening technologies available for antibody fragments but not full-length antibodies. Improvement of biophysical characteristics is important in the early development phase because most antibodies fail at the later stage of development and this leads to loss of resources and time. Here, we review directed evolution and rational design methods to improve antibody properties. Recent developments in rational design approaches and antibody display technologies, and especially phage display, which was recently awarded the 2018 Nobel Prize, are discussed to be used in antibody research and development.
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Affiliation(s)
- Merve Arslan
- İzmir Biomedicine and Genome Center , İzmir , Turkey.,İzmir Biomedicine and Genome Institute, Dokuz Eylül University , İzmir , Turkey
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36
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Fluorescence immunoassay of E. coli using anti-lipopolysaccharide antibodies isolated from human serum. Biosens Bioelectron 2019; 126:518-528. [DOI: 10.1016/j.bios.2018.10.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 10/07/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022]
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37
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Busse PJ, Farkas H, Banerji A, Lumry WR, Longhurst HJ, Sexton DJ, Riedl MA. Lanadelumab for the Prophylactic Treatment of Hereditary Angioedema with C1 Inhibitor Deficiency: A Review of Preclinical and Phase I Studies. BioDrugs 2019; 33:33-43. [PMID: 30539362 PMCID: PMC6373397 DOI: 10.1007/s40259-018-0325-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Hereditary angioedema (HAE) with C1 esterase inhibitor (C1-INH) deficiency (C1-INH-HAE) is a rare disease characterized by diminished levels or dysfunctional activity of C1-INH, leading to dysregulated plasma kallikrein activity within the kallikrein-kinin pathway. Symptoms manifest as painful, potentially life-threatening swelling of subcutaneous tissues throughout the body and/or submucosal edema in the upper airway or gastrointestinal tract. Attacks recur with unpredictable frequency, intensity, and duration, placing a heavy burden on patients' daily lives. Despite improved availability of medications for on-demand treatment during attacks and prophylaxis of future attacks, unmet needs remain. Lanadelumab, a fully human monoclonal antibody, may help address some of the limitations of existing prophylactic options (e.g., the need for intravenous administration or frequent dosing). Preclinical studies demonstrate that it is highly potent and specifically inhibits plasma kallikrein, and findings from phase Ia and Ib studies suggest this agent is well tolerated and provides sustained inhibition of plasma kallikrein, allowing for less frequent dosing. The phase III HELP Study (NCT02586805) evaluating the efficacy and safety of lanadelumab in preventing HAE attacks has been completed, and its open-label extension (NCT02741596) is ongoing. Lanadelumab is now approved in the USA and Canada for prophylaxis to prevent attacks of HAE in patients aged ≥ 12 years. This review provides an overview of the discovery and clinical development of lanadelumab, from preclinical through phase Ib studies, characterizing its safety/tolerability, efficacy, and pharmacokinetic and pharmacodynamic profiles. It also highlights how this agent may positively impact clinical care of patients with C1-INH-HAE.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Angioedemas, Hereditary/drug therapy
- Angioedemas, Hereditary/pathology
- Angioedemas, Hereditary/physiopathology
- Angioedemas, Hereditary/prevention & control
- Antibodies, Monoclonal, Humanized/pharmacokinetics
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Clinical Trials, Phase I as Topic
- Drug Evaluation, Preclinical
- Humans
- Middle Aged
- Plasma Kallikrein/antagonists & inhibitors
- Plasma Kallikrein/drug effects
- Young Adult
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Affiliation(s)
- Paula J Busse
- Division of Clinical Immunology and Allergy, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 11-20, New York, NY, 10029, USA.
| | - Henriette Farkas
- Hungarian Angioedema Reference Center, 3rd Department of Internal Medicine, Semmelweis University, Kutvolgyi ut 4, Budapest, 1125, Hungary
| | - Aleena Banerji
- Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Cox 201, Boston, MA, 02114, USA
| | - William R Lumry
- Allergy and Asthma Research Associates, 10100 N. Central Expressway, Suite 100, Dallas, TX, 75231, USA
| | - Hilary J Longhurst
- Department of Immunology, Addenbrookes Hospital Cambridge University NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | | | - Marc A Riedl
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego, 8899 University Center Lane, Suite 230, San Diego, CA, 92122, USA
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Xu C, Liu X, Liu Y, Zhang X, Zhang C, Li J, Liu X. High sensitive single chain variable fragment screening from a microcystin-LR immunized mouse phage antibody library and its application in immunoassay. Talanta 2019; 197:397-405. [PMID: 30771953 DOI: 10.1016/j.talanta.2019.01.064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/03/2019] [Accepted: 01/16/2019] [Indexed: 12/23/2022]
Abstract
Microcystin-LR (MC-LR) is one of common high-toxic biotoxins produced by cyanobacteria in waterbody. A high sensitive and convenient detection method is necessary for monitoring for MC-LR. To establish a high sensitive indirect competitive enzyme-linked immunosorbent assay (IC-ELISA) based on single chain variable fragment (scFv) for detecting MC-LR, 16 positive anti-MC-LR phage scFv particles were screened out from a MC-LR-immunized mouse phage scFv library, which was successfully constructed with the capacity of 8.67 × 107 CFU/mL. The most positive anti-MC-LR phage scFv (MscFv7) was successfully expressed in Escherichia coli (E.coli) HB2151. The molecular weight (M.W.) of expressed protein was about 30 kDa, and the concentration of purified protein was 512.6 μg/mL analyzed by SDS-PAGE and protein quantitative respectively. The IC-ELISA based on MscFv7-scFv for MC-LR shows a half-maximum inhibition (IC50) of 0.471 μg/L and a limit of detection (LOD) of 0.044 μg/L, which is below the maximum residue limit standard (MRLs) of 1.0 μg/L in drinking water. The MscFv7-scFv has a strong cross-recognition for MC-RR and MC-YR with cross-reactivity (CRs) of 93.1% and 85.9%, respectively, but weak for MC-LW with that of 9.7%, even non-recognition for MC-WR, MC-LF and MC-LY. The recovery rates of IC-ELISA to detect MC-LR spiked in different cleanliness of water samples were 81.2-106.3% with CVs of 2.62-10.22% at intra-assay and inter-assay. The results showed that we obtained a high sensitive anti-MC-LR scFv, and the established IC-ELISA based on MscFv7-scFv should be promising for ultrasensitive monitoring MC-LR, MC-RR and MC-YR in water samples.
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Affiliation(s)
- Chongxin Xu
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaoqin Liu
- Huaihua Vocational and Technical College, Huaihua 418007, China
| | - Yuan Liu
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiao Zhang
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Cunzheng Zhang
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jianhong Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Xianjin Liu
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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Ministro J, Manuel AM, Goncalves J. Therapeutic Antibody Engineering and Selection Strategies. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 171:55-86. [PMID: 31776591 DOI: 10.1007/10_2019_116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibody drugs became an increasingly important element of the therapeutic landscape. Their accomplishment has been driven by many unique properties, in particular by their very high specificity and selectivity, in contrast to the off-target liabilities of small molecules (SMs). Antibodies can bring additional functionality to the table with their ability to interact with the immune system, and this can be further manipulated with advances in antibody engineering.The expansion of strategies related to discovery technologies of monoclonal antibodies (mAbs) (phage display, yeast display, ribosome display, bacterial display, mammalian cell surface display, mRNA display, DNA display, transgenic animal, and human B cell derived) opened perspectives for the screening and the selection of therapeutic antibodies for, theoretically, any target from any kind of organism. Moreover, antibody engineering technologies were developed and explored to obtain chosen characteristics of selected leading candidates such as high affinity, low immunogenicity, improved functionality, improved protein production, improved stability, and others. This chapter contains an overview of discovery technologies, mainly display methods and antibody humanization methods for the selection of therapeutic humanized and human mAbs that appeared along the development of these technologies and thereafter. The increasing applications of these technologies will be highlighted in the antibody engineering area (affinity maturation, guided selection to obtain human antibodies) giving promising perspectives for the development of future therapeutics.
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Affiliation(s)
| | - Ana Margarida Manuel
- iMed - Research Institute for Medicines, Faculty of Pharmacy at University of Lisbon, Lisbon, Portugal
| | - Joao Goncalves
- iMed - Research Institute for Medicines, Faculty of Pharmacy at University of Lisbon, Lisbon, Portugal.
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Site-Specific Photocrosslinking to Immunoglobulin G Using Photoreactive Antibody-Binding Domains. Methods Mol Biol 2019; 2033:275-286. [PMID: 31332760 DOI: 10.1007/978-1-4939-9654-4_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The high specificity and strong binding affinity of antibodies, most commonly immunoglobulin G (IgG), have led to their use in a wide range of research, diagnostic and therapeutic applications. Many of these applications require the antibody to be labeled with additional chemical or biological moieties. Here, we describe a method for the rapid and site-specific labeling of nearly any "off-the-shelf" IgG. Our method utilizes small photoreactive antibody-binding domains (pAbBDs) that are produced by modifying the IgG-binding domains of Protein A and Protein G with the unnatural amino acid benzoylphenylalanine (BPA). The pAbBDs are covalently linked to IgG heavy chains upon exposure to ultraviolet light. Fusion of pAbBDs to a given protein of interest or conjugation of pAbBDs with drugs, fluorophores, and/or other chemical moieties, enables the facile production of a diverse range of antibody conjugates.
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Lee NK, Bidlingmaier S, Su Y, Liu B. Modular Construction of Large Non-Immune Human Antibody Phage-Display Libraries from Variable Heavy and Light Chain Gene Cassettes. Methods Mol Biol 2018; 1701:61-82. [PMID: 29116500 DOI: 10.1007/978-1-4939-7447-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Monoclonal antibodies and antibody-derived therapeutics have emerged as a rapidly growing class of biological drugs for the treatment of cancer, autoimmunity, infection, and neurological diseases. To support the development of human antibodies, various display techniques based on antibody gene repertoires have been constructed over the last two decades. In particular, scFv-antibody phage display has been extensively utilized to select lead antibodies against a variety of target antigens. To construct a scFv phage display that enables efficient antibody discovery, and optimization, it is desirable to develop a system that allows modular assembly of highly diverse variable heavy chain and light chain (Vκ and Vλ) repertoires. Here, we describe modular construction of large non-immune human antibody phage-display libraries built on variable gene cassettes from heavy chain and light chain repertoires (Vκ- and Vλ-light can be made into independent cassettes). We describe utility of such libraries in antibody discovery and optimization through chain shuffling.
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Affiliation(s)
- Nam-Kyung Lee
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA
| | - Scott Bidlingmaier
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA
| | - Yang Su
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA
| | - Bin Liu
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA.
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Ryvkin A, Ashkenazy H, Weiss-Ottolenghi Y, Piller C, Pupko T, Gershoni JM. Phage display peptide libraries: deviations from randomness and correctives. Nucleic Acids Res 2018; 46:e52. [PMID: 29420788 PMCID: PMC5961013 DOI: 10.1093/nar/gky077] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/25/2017] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study, we demonstrate that the UAG over-representation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by mass spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications.
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Affiliation(s)
- Arie Ryvkin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yael Weiss-Ottolenghi
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Piller
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan M Gershoni
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Abstract
Rapidly after the clinical success of the first murine therapeutic antibody licensed in 1985 (muromomab-CD3), the first limits of the therapeutic use of antibodies deriving from hybridoma technology appeared. Indeed, the nonhuman nature of these therapeutic antibodies makes them immunogenic when administrated to patients, which develop anti-drug antibodies (ADA). If repeated drug-administrations are needed, the immune response will accelerate the elimination of the drug, leading to a therapeutic failure, or in the worst case to an anaphylactic reaction against the murine protein. Several antibody generations were then developed to obtain better-tolerated molecules: chimeric, humanized, and fully human antibodies. The first antibody generation is fully based on cellular technology (mice hybridoma technology), but the next generations are improved by molecular engineering. Immune antibody phage-display libraries are one successful approach to isolating such engineered antibodies. One strategy to isolate high-affinity and well-tolerated antibodies when no immunized patients are available is based on the phage-display-screening of immune libraries deriving from immunized nonhuman primates, which are phylogenetically close to humans. This chapter presents the strategy for the construction of macaque antibody immune-libraries.
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Affiliation(s)
- Arnaud Avril
- Département des Maladies Infectieuses, unité biothérapies anti-infectieuses et immunité, Institut de Recherche Biomédicale des Armées, 1 place du Général Valérie André, 91220, Brétigny-sur-Orge, France.
| | | | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thibaut Pelat
- BIOTEM, Parc d'activité Bièvre Dauphine 885, rue Alphonse Gourju, 38140, Apprieu, France
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45
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Enhancing vaccine antibody responses by targeting Clec9A on dendritic cells. NPJ Vaccines 2017; 2:31. [PMID: 29263886 PMCID: PMC5674066 DOI: 10.1038/s41541-017-0033-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 09/18/2017] [Accepted: 09/26/2017] [Indexed: 12/23/2022] Open
Abstract
Targeting model antigens (Ags) to Clec9A on DC has been shown to induce, not only cytotoxic T cells, but also high levels of Ab. In fact, Ab responses against immunogenic Ag were effectively generated even in the absence of DC-activating adjuvants. Here we tested if targeting weakly immunogenic putative subunit vaccine Ags to Clec9A could enhance Ab responses to a level likely to be protective. The proposed “universal” influenza Ag, M2e and the enterovirus 71 Ag, SP70 were linked to anti-Clec9A Abs and injected into mice. Targeting these Ags to Clec9A greatly increased Ab titres. For optimal responses, a DC-activating adjuvant was required. For optimal responses, a boost injection was also needed, but the high Ab titres against the targeting construct blocked Clec9A-targeted boosting. Heterologous prime-boost strategies avoiding cross-reactivity between the priming and boosting targeting constructs overcame this limitation. In addition, targeting small amounts of Ag to Clec9A served as an efficient priming for a conventional boost with higher levels of untargeted Ag. Using this Clec9A-targeted priming, conventional boosting strategy, M2e immunisation protected mice from infection with lethal doses of influenza H1N1 virus. Duration and intensity of vaccine response can be boosted using antibodies to target pathogen fragments to specific immune system cells. Dendritic cells exist to take fragments of infectious diseases and present them to the immune system, sparking host defenses. Now, researchers led by Monash University’s Mireille Lahoud, and Ken Shortman of the Walter and Eliza Hall Institute, have successfully used antibodies to target fragments of influenza and hand, foot and mouth disease directly to dendritic cell molecules, specifically chosen to elicit a prolonged immune response. Mice inoculated with the targeted vaccine were protected from lethal influenza exposure, whereas the hand, foot and mouth disease vaccine elicited promising, but less marked results. With further development, this technology could provide a vital boost to vaccines that offer poor immunity on their own.
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46
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Davis AM, Plowright AT, Valeur E. Directing evolution: the next revolution in drug discovery? Nat Rev Drug Discov 2017; 16:681-698. [PMID: 28935911 DOI: 10.1038/nrd.2017.146] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The strong biological rationale to pursue challenging drug targets such as protein-protein interactions has stimulated the development of novel screening strategies, such as DNA-encoded libraries, to allow broader areas of chemical space to be searched. There has also been renewed interest in screening natural products, which are the result of evolutionary selection for a function, such as interference with a key signalling pathway of a competing organism. However, recent advances in several areas, such as understanding of the biosynthetic pathways for natural products, synthetic biology and the development of biosensors to detect target molecules, are now providing new opportunities to directly harness evolutionary pressure to identify and optimize compounds with desired bioactivities. Here, we describe innovations in the key components of such strategies and highlight pioneering examples that indicate the potential of the directed-evolution concept. We also discuss the scientific gaps and challenges that remain to be addressed to realize this potential more broadly in drug discovery.
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Affiliation(s)
- Andrew M Davis
- AstraZeneca R&D Gothenburg, Pepparedsleden 1, Mölndal, 43150, Sweden
| | - Alleyn T Plowright
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Eric Valeur
- AstraZeneca R&D Gothenburg, Pepparedsleden 1, Mölndal, 43150, Sweden
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Yun S, Ryu H, Lee E. Immunomagnetic separation of human myeloperoxidase using an antibody-mimicking peptide identified by phage display. J Biotechnol 2017; 257:118-121. [DOI: 10.1016/j.jbiotec.2016.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/06/2016] [Accepted: 12/11/2016] [Indexed: 10/20/2022]
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Cavallari M. Rapid and Direct VHH and Target Identification by Staphylococcal Surface Display Libraries. Int J Mol Sci 2017; 18:ijms18071507. [PMID: 28704956 PMCID: PMC5535997 DOI: 10.3390/ijms18071507] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/07/2017] [Accepted: 07/10/2017] [Indexed: 01/01/2023] Open
Abstract
Unbiased and simultaneous identification of a specific antibody and its target antigen has been difficult without prior knowledge of at least one interaction partner. Immunization with complex mixtures of antigens such as whole organisms and tissue extracts including tumoral ones evokes a highly diverse immune response. During such a response, antibodies are generated against a variety of epitopes in the mixture. Here, we propose a surface display design that is suited to simultaneously identify camelid single domain antibodies and their targets. Immune libraries of single-domain antigen recognition fragments from camelid heavy chain-only antibodies (VHH) were attached to the peptidoglycan of Gram-positive Staphylococcus aureus employing its endogenous housekeeping sortase enzyme. The sortase transpeptidation reaction covalently attached the VHH to the bacterial peptidoglycan. The reversible nature of the reaction allowed the recovery of the VHH from the bacterial surface and the use of the VHH in downstream applications. These staphylococcal surface display libraries were used to rapidly identify VHH as well as their targets by immunoprecipitation (IP). Our novel bacterial surface display platform was stable under harsh screening conditions, allowed fast target identification, and readily permitted the recovery of the displayed VHH for downstream analysis.
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Affiliation(s)
- Marco Cavallari
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestrasse 18, 79104 Freiburg, Germany.
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49
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Xiao X, Douthwaite JA, Chen Y, Kemp B, Kidd S, Percival-Alwyn J, Smith A, Goode K, Swerdlow B, Lowe D, Wu H, Dall'Acqua WF, Chowdhury PS. A high-throughput platform for population reformatting and mammalian expression of phage display libraries to enable functional screening as full-length IgG. MAbs 2017; 9:996-1006. [PMID: 28613102 DOI: 10.1080/19420862.2017.1337617] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Phage display antibody libraries are a rich resource for discovery of potential therapeutic antibodies. Single-chain variable fragment (scFv) libraries are the most common format due to the efficient display of scFv by phage particles and the ease by which soluble scFv antibodies can be expressed for high-throughput screening. Typically, a cascade of screening and triaging activities are performed, beginning with the assessment of large numbers of E. coli-expressed scFv, and progressing through additional assays with individual reformatting of the most promising scFv to full-length IgG. However, use of high-throughput screening of scFv for the discovery of full-length IgG is not ideal because of the differences between these molecules. Furthermore, the reformatting step represents a bottle neck in the process because each antibody has to be handled individually to preserve the unique VH and VL pairing. These problems could be resolved if populations of scFv could be reformatted to full-length IgG before screening without disrupting the variable region pairing. Here, we describe a novel strategy that allows the reformatting of diverse populations of scFv from phage selections to full-length IgG in a batch format. The reformatting process maintains the diversity and variable region pairing with high fidelity, and the resulted IgG pool enables high-throughput expression of IgG in mammalian cells and cell-based functional screening. The improved process led to the discovery of potent candidates that are comparable or better than those obtained by traditional methods. This strategy should also be readily applicable to Fab-based phage libraries. Our approach, Screening in Product Format (SiPF), represents a substantial improvement in the field of antibody discovery using phage display.
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Affiliation(s)
- Xiaodong Xiao
- a Department of Antibody Discovery and Protein Engineering , Gaithersburg , MD , USA
| | - Julie A Douthwaite
- b Department of Antibody Discovery and Protein Engineering , Cambridge , UK
| | - Yan Chen
- a Department of Antibody Discovery and Protein Engineering , Gaithersburg , MD , USA
| | - Ben Kemp
- b Department of Antibody Discovery and Protein Engineering , Cambridge , UK
| | - Sara Kidd
- b Department of Antibody Discovery and Protein Engineering , Cambridge , UK
| | | | - Alison Smith
- b Department of Antibody Discovery and Protein Engineering , Cambridge , UK
| | - Kate Goode
- b Department of Antibody Discovery and Protein Engineering , Cambridge , UK
| | - Bonnie Swerdlow
- c Department of Respiratory, Inflammation and Autoimmune Diseases , Gaithersburg , MD , USA
| | - David Lowe
- b Department of Antibody Discovery and Protein Engineering , Cambridge , UK
| | - Herren Wu
- a Department of Antibody Discovery and Protein Engineering , Gaithersburg , MD , USA
| | - William F Dall'Acqua
- a Department of Antibody Discovery and Protein Engineering , Gaithersburg , MD , USA
| | - Partha S Chowdhury
- a Department of Antibody Discovery and Protein Engineering , Gaithersburg , MD , USA
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50
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Saeed AFUH, Wang R, Ling S, Wang S. Antibody Engineering for Pursuing a Healthier Future. Front Microbiol 2017; 8:495. [PMID: 28400756 PMCID: PMC5368232 DOI: 10.3389/fmicb.2017.00495] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/09/2017] [Indexed: 12/21/2022] Open
Abstract
Since the development of antibody-production techniques, a number of immunoglobulins have been developed on a large scale using conventional methods. Hybridoma technology opened a new horizon in the production of antibodies against target antigens of infectious pathogens, malignant diseases including autoimmune disorders, and numerous potent toxins. However, these clinical humanized or chimeric murine antibodies have several limitations and complexities. Therefore, to overcome these difficulties, recent advances in genetic engineering techniques and phage display technique have allowed the production of highly specific recombinant antibodies. These engineered antibodies have been constructed in the hunt for novel therapeutic drugs equipped with enhanced immunoprotective abilities, such as engaging immune effector functions, effective development of fusion proteins, efficient tumor and tissue penetration, and high-affinity antibodies directed against conserved targets. Advanced antibody engineering techniques have extensive applications in the fields of immunology, biotechnology, diagnostics, and therapeutic medicines. However, there is limited knowledge regarding dynamic antibody development approaches. Therefore, this review extends beyond our understanding of conventional polyclonal and monoclonal antibodies. Furthermore, recent advances in antibody engineering techniques together with antibody fragments, display technologies, immunomodulation, and broad applications of antibodies are discussed to enhance innovative antibody production in pursuit of a healthier future for humans.
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Affiliation(s)
- Abdullah F U H Saeed
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China
| | - Rongzhi Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China
| | - Sumei Ling
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China
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