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Garzon V, Salvador JP, Marco MP, G.-Pinacho D, Bustos RH. Development and ELISA Characterization of Antibodies against the Colistin, Vancomycin, Daptomycin, and Meropenem: A Therapeutic Drug Monitoring Approach. Antibiotics (Basel) 2024; 13:600. [PMID: 39061282 PMCID: PMC11273741 DOI: 10.3390/antibiotics13070600] [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: 05/02/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
More than 70% of bacteria are resistant to all or nearly all known antimicrobials, creating the need for the development of new types of antimicrobials or the use of "last-line" antimicrobial therapies for the treatment of multi-resistant bacteria. These antibiotics include Glycopeptide (Vancomycin), Polymyxin (Colistin), Lipopeptide (Daptomycin), and Carbapenem (Meropenem). However, due to the toxicity of these types of molecules, it is necessary to develop new rapid methodologies to be used in Therapeutic Drug Monitoring (TDM). TDM could improve patient outcomes and reduce healthcare costs by enabling a favorable clinical outcome. In this way, personalized antibiotic therapy emerges as a viable option, offering optimal dosing for each patient according to pharmacokinetic (PK) and pharmacodynamic (PD) parameters. Various techniques are used for this monitoring, including high-performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS), and immunoassays. The objective of this study is the development and characterization by ELISA of specific polyclonal antibodies for the recognition of the antibiotics Vancomycin (glycopeptide), Colistin (polymyxin), Daptomycin (lipopeptide), and Meropenem (carbapenem) for future applications in the monitoring of these antibiotics in different fluids, such as human plasma. The developed antibodies are capable of recognizing the antibiotic molecules with good detectability, showing an IC50 of 0.05 nM for Vancomycin, 7.56 nM for Colistin, 183.6 nM for Meropenem, and 13.82 nM for Daptomycin. These antibodies offer a promising tool for the precise and effective therapeutic monitoring of these critical antibiotics, potentially enhancing treatment efficacy and patient safety.
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Affiliation(s)
- Vivian Garzon
- Doctoral Programme of Biosciences, Universidad de La Sabana, Chía 140013, Colombia;
- Therapeutic Evidence Group, Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia;
| | - J.-Pablo Salvador
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08034 Barcelona, Spain; (J.-P.S.); (M.-P.M.)
- Nanobiotechnology for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
| | - M.-Pilar Marco
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08034 Barcelona, Spain; (J.-P.S.); (M.-P.M.)
- Nanobiotechnology for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
| | - Daniel G.-Pinacho
- Therapeutic Evidence Group, Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia;
| | - Rosa-Helena Bustos
- Therapeutic Evidence Group, Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia;
- Clínica Universidad de La Sabana, Chía 140013, Colombia
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2
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Liu L, Xu B, Chen L, Liu J, Liu W, Xue F, Feng S, Jiang E, Han M, Shao W, Zhang L, Pei X. An investigation of the immune epitopes of adeno-associated virus capsid-derived peptides among hemophilia patients. Mol Ther Methods Clin Dev 2024; 32:101245. [PMID: 38660620 PMCID: PMC11039395 DOI: 10.1016/j.omtm.2024.101245] [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: 05/25/2023] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
Adeno-associated virus (AAV) is an optimal gene vector for monogenic disorders. However, neutralizing antibodies (Nabs) against AAV hinder its widespread application in gene therapy. In this study, we biosynthesized peptides recognized by the binding antibodies (Babs) from the sera containing high Nab titers against AAV2. We established four immunological methods to detect immune epitopes of the AAV2-derived peptides, including a Bab assay, Nab assay, B cell receptor (BCR) detecting assay, and immunoglobin-producing B cell enzyme-linked immunosorbent spot (B cell ELISpot) assay. Correlations among the epitopes determined by these four methods were analyzed using the serum samples and peripheral blood mononuclear cells (PBMC) from 89 patients with hemophilia A/B. As decoys, the peptides' ability to block the Nab of AAV2 particles was assessed using AAV transduction models both in vitro and in vivo. Overall, we provide insights into AAV2-capsid-derived peptide immune epitopes, involving the Nab, Bab, BCR, and B cell ELISpot assays, offering alternative immunological evaluation approaches and strategies to overcome Nab barriers in AAV-mediated gene therapy.
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Affiliation(s)
- Li Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Bingqi Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Lingling Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Jia Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Wei Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Feng Xue
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Sizhou Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Mingzhe Han
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Wenwei Shao
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, P.R. China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
| | - Xiaolei Pei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, P.R. China
- Tianjin Institutes of Health Science, Tianjin 300020, P.R. China
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3
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Houen G. Peptide Antibodies: Current Status. Methods Mol Biol 2024; 2821:1-8. [PMID: 38997476 DOI: 10.1007/978-1-0716-3914-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Peptide antibodies have become one of the most important classes of reagents in molecular biology and clinical diagnostics. For this reason, methods for their production and characterization continue to be developed, including basic peptide synthesis protocols, peptide-conjugate production and characterization, conformationally restricted peptides, immunization procedures, etc. Detailed mapping of peptide antibody epitopes has yielded important information on antibody-antigen interaction in general and specifically in relation to antibody cross-reactivity and theories of molecular mimicry. This information is essential for detailed understanding of paratope-epitope dynamics, design of antibodies for research, design of peptide-based vaccines, development of therapeutic peptide antibodies, and de novo design of antibodies with predetermined specificity.
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Affiliation(s)
- Gunnar Houen
- Department of Neurology and Translational Research Center, Rigshospitalet, Glostrup, Denmark.
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4
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Hansen PR, Oddo A. Fmoc Solid-Phase Peptide Synthesis. Methods Mol Biol 2024; 2821:33-55. [PMID: 38997478 DOI: 10.1007/978-1-0716-3914-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Synthetic peptides are important as drugs and in research. Currently, the method of choice for producing these compounds is solid-phase peptide synthesis. Here, we describe the scope and limitations of Fmoc solid-phase peptide synthesis. Furthermore, we provide a detailed protocol for Fmoc peptide synthesis.
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Affiliation(s)
- Paul Robert Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Alberto Oddo
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- , Måløv, Denmark
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5
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Trier NH, Friis T. Production of Antibodies to Peptide Targets Using Hybridoma Technology. Methods Mol Biol 2024; 2821:135-156. [PMID: 38997486 DOI: 10.1007/978-1-0716-3914-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Hybridoma technology is a well-established and indispensable tool for generating high-quality monoclonal antibodies and has become one of the most common methods for monoclonal antibody production. In this process, antibody-producing B cells are isolated from mice following immunization of mice with a specific immunogen and fused with an immortal myeloma cell line to form antibody-producing hybridoma cell lines. Hybridoma-derived monoclonal antibodies not only serve as powerful research and diagnostic reagents but have also emerged as the most rapidly expanding class of therapeutic biologicals. In spite of the development of new high-throughput monoclonal antibody generation technologies, hybridoma technology still is applied for antibody production due to its ability to preserve innate functions of immune cells and to preserve natural cognate antibody paring information. In this chapter, an overview of hybridoma technology and the laboratory procedures used for hybridoma production and antibody screening of peptide-specific antibodies are presented.
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Affiliation(s)
| | - Tina Friis
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen S, Denmark
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6
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Acharya S, Lee A, Kim H, Kim HJ, Choi Y. Requirements for anti-aquaporin 5 autoantibody production in a mouse model. Mol Oral Microbiol 2023; 38:442-453. [PMID: 37718989 DOI: 10.1111/omi.12430] [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: 06/17/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 09/19/2023]
Abstract
Several oral bacteria, including Prevotella melaninogenica (Pm), have aquaporin (AQP) proteins homologous to human AQP5, a major water channel protein targeted in Sjogren's syndrome. This study aimed to understand the antigenic characteristics that induce autoantibodies against an AQP5 "E" epitope (AQP5E) in a mouse model using C57BL/6 mice. Immunization with a PmE-L peptide derived from Pm AQP, which contains amino acid mismatches both at the B- and T-cell epitopes, efficiently induced anti-AQP5E autoantibodies accompanied by increased germinal center (GC) B and follicular helper T cells in the draining lymph nodes. However, PmE, a peptide lacking a T-cell epitope, and AQP5E-L, an AQP5-derived self-peptide, hardly induced either anti-AQP5E autoantibodies or GC responses. Surprisingly, OTII-AQP5E, a peptide that replaced the self T-cell epitope of AQP5E-L with an ovalbumin-derived foreign T-cell epitope, was not any better than AQP5E-L in the induction of anti-AQP5E autoantibodies and GC response, despite the substantial expansion of CD4+ T cells and production of anti-OTII-AQP5E antibodies. The complex of biotinylated PmE-L peptide and highly immunogenic streptavidin (SA) induced a strong extrafollicular B-cell response skewed toward the expansion of SA-specific B cells. However, the expansion of AQP5E-specific GC B cells was limited, resulting in the inefficient induction of anti-AQP5E autoantibodies. Collectively, our results have demonstrated that anti-AQP5E autoantibody production is only allowed when foreign B- and T-cell epitopes drive a strong GC response of AQP5E-specific B cells for affinity maturation. This study helps explain why cross-reactive anti-AQP5 autoantibodies are not produced during the immune response to Pm in most healthy people.
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Affiliation(s)
- Sabin Acharya
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Ahreum Lee
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Hyunjin Kim
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Hyeong-Jin Kim
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Youngnim Choi
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
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7
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Zhang H, Lv P, Jiang J, Liu Y, Yan R, Shu S, Hu B, Xiao H, Cai K, Yuan S, Li Y. Advances in developing ACE2 derivatives against SARS-CoV-2. THE LANCET. MICROBE 2023; 4:e369-e378. [PMID: 36934742 PMCID: PMC10019897 DOI: 10.1016/s2666-5247(23)00011-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 03/17/2023]
Abstract
Extensive immune evasion of SARS-CoV-2 rendered therapeutic antibodies ineffective in the COVID-19 pandemic. Propagating SARS-CoV-2 variants are characterised by immune evasion capacity through key amino acid mutations, but can still bind human angiotensin-converting enzyme 2 (ACE2) through the spike protein and are, thus, sensitive to ACE2-mimicking decoys as inhibitors. In this Review, we examine advances in the development of ACE2 derivatives from the past 3 years, including the recombinant ACE2 proteins, ACE2-loaded extracellular vesicles, ACE2-mimicking antibodies, and peptide or mini-protein mimetics of ACE2. Several ACE2 derivatives are granted potent neutralisation efficacy against SARS-CoV-2 variants that rival or surpass endogenous antibodies by various auxiliary techniques such as chemical modification and practical recombinant design. The derivatives also represent enhanced production efficiency and improved bioavailability. In addition to these derivatives of ACE2, new effective therapeutics against SARS-CoV-2 variants are expected to be developed.
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Affiliation(s)
- Haoran Zhang
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Panjing Lv
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Jingrui Jiang
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Yahui Liu
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Ruixi Yan
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Sainan Shu
- Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Bing Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Han Xiao
- Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Cai
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Shuai Yuan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China; Hubei Jiangxia Laboratory, Wuhan, China.
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China; Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.
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8
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Design, Production, Characterization, and Use of Peptide Antibodies. Antibodies (Basel) 2023; 12:antib12010006. [PMID: 36648890 PMCID: PMC9844468 DOI: 10.3390/antib12010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/10/2022] [Accepted: 12/26/2022] [Indexed: 01/15/2023] Open
Abstract
Antibodies are key reagents in diagnostics, therapeutics, and experimental biology, capable of detecting numerous targets [...].
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9
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Liew OW, Ling SSM, Lilyanna S, Chong JPC, Ng JYX, Richards AM. One-Shot Generation of Epitope-Directed Monoclonal Antibodies to Multiple Nonoverlapping Targets: Peptide Selection, Antigen Preparation, and Epitope Mapping. Methods Mol Biol 2023; 2578:121-141. [PMID: 36152284 DOI: 10.1007/978-1-0716-2732-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This chapter describes an epitope-directed approach to generate antipeptide monoclonal antibodies to multiple nonoverlapping protein sites using a cocktail of fusion peptides as immunogen. It provides a step-by-step protocol on how antigenic peptides on a target protein can be identified by in silico prediction and discusses considerations for final peptide selection. Each antigenic peptide (10-20 amino acids long) is displayed as three-copy inserts on the surface exposed loop of a thioredoxin scaffold protein. The corresponding DNA coding sequence specifying the tripeptide insert flanked by Gly-Ser-Gly-Ser-Gly linkers is cloned in-frame into the Rsr II site of the thioredoxin gene in the pET-32a vector. The presence of a C-terminal polyhistidine tag (His6-tag) allows the soluble fusion proteins to be purified by one-step native immobilized metal affinity chromatography (IMAC) to greater than 95% purity. Multiple thioredoxin fusion proteins are mixed in equimolar concentrations and used as an immunogen cocktail for animal immunization. The use of short antigenic peptides of known sequence facilitates direct epitope mapping requiring only small mutagenesis scan peptide libraries in the multipin peptide format.
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Affiliation(s)
- Oi Wah Liew
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore.
| | - Samantha Shi Min Ling
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Shera Lilyanna
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Jenny Pek Ching Chong
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Jessica Yan Xia Ng
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Arthur Mark Richards
- Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
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10
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Rodríguez-Mera IB, Carrasco-Yépez MM, Vásquez-Moctezuma I, Correa-Basurto J, Salinas GR, Castillo-Ramírez DA, Rosales-Cruz É, Rojas-Hernández S. Role of cathepsin B of Naegleria fowleri during primary amebic meningoencephalitis. Parasitol Res 2022; 121:3287-3303. [PMID: 36125528 PMCID: PMC9485797 DOI: 10.1007/s00436-022-07660-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022]
Abstract
Naegleria fowleri causes primary amoebic meningoencephalitis in humans and experimental animals. It has been suggested that cysteine proteases of parasites play key roles in metabolism, nutrient uptake, host tissue invasion, and immune evasion. The aim of this work was to evaluate the presence, expression, and role of cathepsin B from N. fowleri in vitro and during PAM. Rabbit-specific polyclonal antibodies against cathepsin B were obtained from rabbit immunization with a synthetic peptide obtained by bioinformatic design. In addition, a probe was designed from mRNA for N. fowleri cathepsin B. Both protein and messenger were detected in fixed trophozoites, trophozoites interacted with polymorphonuclear and histological sections of infected mice. The main cathepsin B distribution was observed in cytoplasm or membrane mainly pseudopods and food-cups while messenger was in nucleus and cytoplasm. Surprisingly, both the messenger and enzyme were observed in extracellular medium. To determine cathepsin B release, we used trophozoites supernatant recovered from nasal passages or brain of infected mice. We observed the highest release in supernatant from recovered brain amoebae, and when we analyzed molecular weight of secreted proteins by immunoblot, we found 30 and 37 kDa bands which were highly immunogenic. Finally, role of cathepsin B during N. fowleri infection was determined; we preincubated trophozoites with E-64, pHMB or antibodies with which we obtained 60%, 100%, and 60% of survival, respectively, in infected mice. These results suggest that cathepsin B plays a role during pathogenesis caused by N. fowleri mainly in adhesion and contributes to nervous tissue damage.
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Affiliation(s)
- Itzel Berenice Rodríguez-Mera
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México
| | - María Maricela Carrasco-Yépez
- Laboratorio de Microbiología Ambiental, Estado de México, Universidad Nacional Autónoma de México, Grupo CyMA, UIICSE, FES Iztacala, Tlalnepantla de Baz, México
| | - Ismael Vásquez-Moctezuma
- Laboratorio de Bioquímica, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - Gema Ramírez- Salinas
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - Diego Arturo Castillo-Ramírez
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México
| | - Érika Rosales-Cruz
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Ciudad de Mexico, México
| | - Saúl Rojas-Hernández
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México.
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11
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Jirapongpairoj W, Nozaki R, Koiwai K, Hirono I, Kondo H. Identification of a rabbit Ig light chain recombinant protein bound to serum immunoglobulins from different marine fish species. FISH & SHELLFISH IMMUNOLOGY 2022; 127:939-947. [PMID: 35868474 DOI: 10.1016/j.fsi.2022.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The structures of fish serum immunoglobulin differ among different fish species. In this study, we accidently isolated a rabbit immunoglobulin (Ig) light chain bound to serum immunoglobulin from different marine fish species using phage display. Fish Ig was separated using a protein A column. The phage library was generated from variable regions of rabbit spleen B cells immunized with bluefin tuna Thunnus orientalis Ig. Fish Ig-specific phages were enriched using two rounds of bio-panning with yellowtail Seriola quinqueradiata serum Ig, followed by two rounds of bio-panning with red seabream Pagrus major serum Ig. The enriched phages demonstrated an increase in binding specificity to the tuna, yellowtail, and red seabream Igs compared to the phages listed in the unpanned library. A recombinant protein of a single clonal phage, which encodes the rabbit Ig light chain, was produced, and the binding specificities to fish Igs were analyzed using enzyme-linked immunosorbent assay (ELISA) and western blotting. The recombinant protein exhibited binding properties to fish Igs in the ELISA. However, the recombinant protein that bound to serum protein(s), but not IgM, was detected via western blotting. The recombinant protein may provide a novel information on the common structural feature in the fish immunoglobulins.
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Affiliation(s)
- Walissara Jirapongpairoj
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Keiichiro Koiwai
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan.
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12
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Krut' VG, Chuvpilo SA, Astrakhantseva IV, Kozlovskaya LI, Efimov GA, Kruglov AA, Drutskaya MS, Nedospasov SA. Will Peptides Help to Stop COVID-19? BIOCHEMISTRY (MOSCOW) 2022; 87:590-604. [PMID: 36154880 PMCID: PMC9282900 DOI: 10.1134/s0006297922070021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Peptides are widely used for the diagnostics, prevention, and therapy of certain human diseases. How useful can they be for the disease caused by the SARS-CoV-2 coronavirus? In this review, we discuss the possibility of using synthetic and recombinant peptides and polypeptides for prevention of COVID-19 via blocking the interaction between the virus and its main receptor ACE2, as well as components of antiviral vaccines, in particular, against new emerging virus variants.
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Affiliation(s)
- Viktoriya G Krut'
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Sergei A Chuvpilo
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Irina V Astrakhantseva
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Liubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia
| | - Grigory A Efimov
- National Medical Research Center of Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Andrei A Kruglov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- German Rheumatism Research Center (DRFZ), Leibniz Institute, Berlin, 10117, Germany
| | - Marina S Drutskaya
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Sergei A Nedospasov
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
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13
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Production and Characterization of Peptide Antibodies to the C-Terminal of Frameshifted Calreticulin Associated with Myeloproliferative Diseases. Int J Mol Sci 2022; 23:ijms23126803. [PMID: 35743246 PMCID: PMC9223637 DOI: 10.3390/ijms23126803] [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: 04/07/2022] [Revised: 06/04/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022] Open
Abstract
Myeloproliferative Neoplasms (MPNs) constitute a group of rare blood cancers that are characterized by mutations in bone marrow stem cells leading to the overproduction of erythrocytes, leukocytes, and thrombocytes. Mutations in calreticulin (CRT) genes may initiate MPNs, causing a novel variable polybasic stretch terminating in a common C-terminal sequence in the frameshifted CRT (CRTfs) proteins. Peptide antibodies to the mutated C-terminal are important reagents for research in the molecular mechanisms of MPNs and for the development of new diagnostic assays and therapies. In this study, eight peptide antibodies targeting the C-terminal of CRTfs were produced and characterised by modified enzyme-linked immunosorbent assays using resin-bound peptides. The antibodies reacted to two epitopes: CREACLQGWTE for SSI-HYB 385-01, 385-02, 385-03, 385-04, 385-07, 385-08, and 385-09 and CLQGWT for SSI-HYB 385-06. For the majority of antibodies, the residues Cys1, Trp9, and Glu11 were essential for reactivity. SSI-HYB 385-06, with the highest affinity, recognised recombinant CRTfs produced in yeast and the MARIMO cell line expressing CRTfs when examined in Western immunoblotting. Moreover, SSI-HYB 385-06 occasionally reacted to CRTfs from MPN patients when analysed by flow cytometry. The characterized antibodies may be used to understand the role of CRTfs in the pathogenesis of MPNs and to design and develop new diagnostic assays and therapeutic targets.
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Trier NH, Valdarnini N, Fanelli I, Rovero P, Hansen PR, Schafer-Nielsen C, Ciplys E, Slibinskas R, Pociot F, Friis T, Houen G. Peptide Antibody Reactivity to Homologous Regions in Glutamate Decarboxylase Isoforms and Coxsackievirus B4 P2C. Int J Mol Sci 2022; 23:ijms23084424. [PMID: 35457242 PMCID: PMC9028130 DOI: 10.3390/ijms23084424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Two isoforms of the glutamate decarboxylase (GAD) enzyme exist, GAD65 and GAD67, which are associated with type 1 diabetes (T1D) and stiff-person syndrome (SPS), respectively. Interestingly, it has been reported that T1D patients seldom develop SPS, whereas patients with SPS occasionally develop T1D. In addition, coxsackievirus B4 (CVB4) has previously been proposed to be involved in the onset of T1D through molecular mimicry. On this basis, we aimed to examine antibody cross-reactivity between a specific region of GAD65 and GAD67, which has high sequence homology to the nonstructural P2C protein of CVB4 to determine potential correlations at antibody level. Monoclonal peptide antibodies generated in mice specific for a region with high similarity in all three proteins were screened for reactivity along with human sera in immunoassays. In total, six antibodies were generated. Two of the antibodies reacted to both GAD isoforms. However, none of the antibodies were cross-reactive to CVB, suggesting that antibody cross-reactivity between GAD65 and CVB, and GAD67 and CVB may not contribute to the onset of T1D and SPS, respectively.
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Affiliation(s)
- Nicole Hartwig Trier
- Department of Neurology, Rigshospitalet Glostrup, Valdemar Hansens vej 13, 2600 Glostrup, Denmark
- Correspondence: (N.H.T.); (G.H.)
| | - Niccolo Valdarnini
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Via Ugo Schiff 6, I-50019 Sesto Fiorentino, Italy; (N.V.); (I.F.); (P.R.)
| | - Ilaria Fanelli
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Via Ugo Schiff 6, I-50019 Sesto Fiorentino, Italy; (N.V.); (I.F.); (P.R.)
| | - Paolo Rovero
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Via Ugo Schiff 6, I-50019 Sesto Fiorentino, Italy; (N.V.); (I.F.); (P.R.)
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark;
| | | | - Evaldas Ciplys
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (E.C.); (R.S.)
| | - Rimantas Slibinskas
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (E.C.); (R.S.)
| | - Flemming Pociot
- Steno Diabetes Center, Borgmester Ib Juuls Vej 83, 2730 Hellerup, Denmark;
| | - Tina Friis
- Department of Autoimmunity and Biomarkers, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark;
| | - Gunnar Houen
- Department of Neurology, Rigshospitalet Glostrup, Valdemar Hansens vej 13, 2600 Glostrup, Denmark
- Department Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
- Correspondence: (N.H.T.); (G.H.)
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15
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Van Fossen EM, Grutzius S, Ruby CE, Mourich DV, Cebra C, Bracha S, Karplus PA, Cooley RB, Mehl RA. Creating a Selective Nanobody Against 3-Nitrotyrosine Containing Proteins. Front Chem 2022; 10:835229. [PMID: 35265586 PMCID: PMC8899190 DOI: 10.3389/fchem.2022.835229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
A critical step in developing therapeutics for oxidative stress-related pathologies is the ability to determine which specific modified protein species are innocuous by-products of pathology and which are causative agents. To achieve this goal, technologies are needed that can identify, characterize and quantify oxidative post translational modifications (oxPTMs). Nanobodies (Nbs) represent exquisite tools for intracellular tracking of molecules due to their small size, stability and engineerability. Here, we demonstrate that it is possible to develop a selective Nb against an oxPTM protein, with the key advance being the use of genetic code expansion (GCE) to provide an efficient source of the large quantities of high-quality, homogenous and site-specific oxPTM-containing protein needed for the Nb selection process. In this proof-of-concept study, we produce a Nb selective for a 3-nitrotyrosine (nitroTyr) modified form of the 14-3-3 signaling protein with a lesser recognition of nitroTyr in other protein contexts. This advance opens the door to the GCE-facilitated development of other anti-PTM Nbs.
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Affiliation(s)
- Elise M. Van Fossen
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Sonia Grutzius
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Carl E. Ruby
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Dan V. Mourich
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Chris Cebra
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Shay Bracha
- Department of Small Animal Clinical Sciences (VSCS), Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, United States
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
- *Correspondence: Ryan A. Mehl,
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16
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Liu W, Zhang Q, Xing H, Gao G, Liu J, Huang Y, Yang H. Characterization of a Novel Monoclonal Antibody for Serine-129 Phosphorylated α-Synuclein: A Potential Application for Clinical and Basic Research. Front Neurol 2022; 13:821792. [PMID: 35250825 PMCID: PMC8893957 DOI: 10.3389/fneur.2022.821792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
The Lewy bodies (LBs) are the pathological hallmark of Parkinson's disease (PD). More than 90% of α-synuclein (α-syn) within LBs is phosphorylated at the serine-129 residue [pSer129 α-syn (p-α-syn)]. Although various studies have revealed that this abnormally elevated p-α-syn acts as a pathological biomarker and is involved in the pathogenic process of PD, the exact pathophysiological mechanisms of p-α-syn are still not fully understood. Therefore, the development of specific and reliable tools for p-α-syn detection is important. In this study, we generated a novel p-α-syn mouse monoclonal antibody (C140S) using hybridoma technology. To further identify the characteristics of C140S, we performed several in vitro assays using recombinant proteins, along with ex vivo assays utilizing the brains of Thy1-SNCA transgenic (Tg) mice, the preformed fibril (PFF)-treated neurons, and the brain sections of patients with PD. Our C140S specifically recognized human and mouse p-α-syn proteins both in vitro and ex vivo, and similar to commercial p-α-syn antibodies, the C140S detected higher levels of p-α-syn in the midbrain of the Tg mice. Using immunogold electron microscopy, these p-α-syn particles were partly deposited in the cytoplasm and colocalized with the outer mitochondrial membrane. In addition, the C140S recognized p-α-syn pathologies in the PFF-treated neurons and the amygdala of patients with PD. Overall, the C140S antibody was a specific and potential research tool in the detection and mechanistic studies of pathogenic p-α-syn in PD and related synucleinopathies.
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Affiliation(s)
- Weijin Liu
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Beijing, China
| | - Qidi Zhang
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Beijing, China
| | - Hao Xing
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Beijing, China
| | - Ge Gao
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Beijing, China
| | - Jia Liu
- Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
| | - Yue Huang
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Beijing, China
| | - Hui Yang
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Beijing, China
- *Correspondence: Hui Yang
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17
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Poirier D, Théolier J, Marega R, Delahaut P, Gillard N, Godefroy SB. Evaluation of the discriminatory potential of antibodies created from synthetic peptides derived from wheat, barley, rye and oat gluten. PLoS One 2021; 16:e0257466. [PMID: 34555094 PMCID: PMC8459967 DOI: 10.1371/journal.pone.0257466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/01/2021] [Indexed: 11/18/2022] Open
Abstract
Celiac disease (CD) is triggered by ingestion of gluten-containing cereals such as wheat, barley, rye and in some cases oat. The only way for affected individuals to avoid symptoms of this condition is to adopt a gluten-free diet. Thus, gluten-free foodstuffs need to be monitored in order to ensure their innocuity. For this purpose, commercial immunoassays based on recognition of defined linear gluten sequences are currently used. These immunoassays are designed to detect or quantify total gluten regardless of the cereal, and often result in over or underestimation of the exact gluten content. In addition, Canadian regulations require a declaration of the source of gluten on the label of prepackaged foods, which cannot be done due to the limitations of existing methods. In this study, the development of new antibodies targeting discrimination of gluten sources was conducted using synthetic peptides as immunization strategy. Fourteen synthetic peptides selected from unique linear amino acid sequences of gluten were bioconjugated to Concholepas concholepas hemocyanin (CCH) as protein carrier, to elicit antibodies in rabbit. The resulting polyclonal antibodies (pAbs) successfully discriminated wheat, barley and oat prolamins during indirect ELISA assessments. pAbs raised against rye synthetic peptides cross-reacted evenly with wheat and rye prolamins but could still be useful to successfully discriminate gluten sources in combination with the other pAbs. Discrimination of gluten sources can be further refined and enhanced by raising monoclonal antibodies using a similar immunization strategy. A methodology capable of discriminating gluten sources, such as the one proposed in this study, could facilitate compliance with Canadian regulations on this matter. This type of discrimination could also complement current immunoassays by settling the issue of over and underestimation of gluten content, thus improving the safety of food intended to CD and wheat-allergic patients.
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Affiliation(s)
- David Poirier
- Department of Food Science and Nutrition, Pavillon Paul-Comtois, Université Laval, Québec, Québec, Canada
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Québec, Canada
| | - Jérémie Théolier
- Department of Food Science and Nutrition, Pavillon Paul-Comtois, Université Laval, Québec, Québec, Canada
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Québec, Canada
| | | | | | | | - Samuel Benrejeb Godefroy
- Department of Food Science and Nutrition, Pavillon Paul-Comtois, Université Laval, Québec, Québec, Canada
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Québec, Canada
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18
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Mier A, Maffucci I, Merlier F, Prost E, Montagna V, Ruiz‐Esparza GU, Bonventre JV, Dhal PK, Tse Sum Bui B, Sakhaii P, Haupt K. Molecularly Imprinted Polymer Nanogels for Protein Recognition: Direct Proof of Specific Binding Sites by Solution STD and WaterLOGSY NMR Spectroscopies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alejandra Mier
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Irene Maffucci
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Elise Prost
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Valentina Montagna
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Guillermo U. Ruiz‐Esparza
- Divisions of Engineering in Medicine and Renal Medicine Department of Medicine Harvard Medical School, Brigham and Women's Hospital Boston MA 02115 USA
- Division of Health Science and Technology Harvard University—Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Joseph V. Bonventre
- Divisions of Engineering in Medicine and Renal Medicine Department of Medicine Harvard Medical School, Brigham and Women's Hospital Boston MA 02115 USA
- Division of Health Science and Technology Harvard University—Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Pradeep K. Dhal
- US Early Development Sanofi Global R&D 153 Second Avenue Waltham MA 02451 USA
| | - Bernadette Tse Sum Bui
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Peyman Sakhaii
- R&D Global CMC Development—Synthetics—Early Development Frankfurt Sanofi-Aventis (Deutschland) GmbH Industriepark Hoechst Frankfurt am Main Germany
| | - Karsten Haupt
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
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19
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Mier A, Maffucci I, Merlier F, Prost E, Montagna V, Ruiz-Esparza GU, Bonventre JV, Dhal PK, Tse Sum Bui B, Sakhaii P, Haupt K. Molecularly Imprinted Polymer Nanogels for Protein Recognition: Direct Proof of Specific Binding Sites by Solution STD and WaterLOGSY NMR Spectroscopies. Angew Chem Int Ed Engl 2021; 60:20849-20857. [PMID: 34296498 PMCID: PMC8562893 DOI: 10.1002/anie.202106507] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/15/2021] [Indexed: 11/07/2022]
Abstract
Molecularly imprinted polymers (MIPs) are tailor-made synthetic antibodies possessing specific binding cavities designed for a target molecule. Currently, MIPs for protein targets are synthesized by imprinting a short surface-exposed fragment of the protein, called epitope or antigenic determinant. However, finding the epitope par excellence that will yield a peptide "synthetic antibody" cross-reacting exclusively with the protein from which it is derived, is not easy. We propose a computer-based rational approach to unambiguously identify the "best" epitope candidate. Then, using Saturation Transfer Difference (STD) and WaterLOGSY NMR spectroscopies, we prove the existence of specific binding sites created by the imprinting of this peptide epitope in the MIP nanogel. The optimized MIP nanogel could bind the epitope and cognate protein with a high affinity and selectivity. The study was performed on Hepatitis A Virus Cell Receptor-1 protein, also known as KIM-1 and TIM-1, for its ubiquitous implication in numerous pathologies.
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Affiliation(s)
- Alejandra Mier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Irene Maffucci
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Elise Prost
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Valentina Montagna
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Guillermo U Ruiz-Esparza
- Divisions of Engineering in Medicine and Renal Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Health Science and Technology, Harvard University-Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Joseph V Bonventre
- Divisions of Engineering in Medicine and Renal Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Health Science and Technology, Harvard University-Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Pradeep K Dhal
- US Early Development, Sanofi Global R&D, 153 Second Avenue, Waltham, MA, 02451, USA
| | - Bernadette Tse Sum Bui
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Peyman Sakhaii
- R&D Global CMC Development-Synthetics-Early Development Frankfurt, Sanofi-Aventis (Deutschland) GmbH, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Karsten Haupt
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
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20
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Generation of a Polyclonal Antibody against the Mouse Metal Transporter ZIP8. Antibodies (Basel) 2021; 10:antib10020016. [PMID: 33919173 PMCID: PMC8167614 DOI: 10.3390/antib10020016] [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: 01/23/2021] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 11/25/2022] Open
Abstract
ZIP8 is a newly identified metal transporter. In human patients, mutations in ZIP8 result in severe manganese deficiency, suggesting a critical role for ZIP8 in regulating systemic manganese homeostasis. In mice, the deletion of ZIP8 recapitulates the symptoms of patients with ZIP8 mutations. However, further studies using mouse models to examine ZIP8′s function were hindered by the lack of suitable antibodies to detect endogenous ZIP8 protein. In this study, we report the design, generation, and validation of a polyclonal antibody against mouse ZIP8. We have demonstrated that the newly generated antibody can be reliably used in immunoblotting analysis to detect endogenous ZIP8 protein in mouse tissues. The successful generation and validation of anti-mouse ZIP8 antibody provide opportunities to further examine the function and regulation of this metal transporter. In addition, our study may provide valuable insights into the future development of antibodies targeting polytopic membrane proteins.
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21
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Epitope-directed monoclonal antibody production using a mixed antigen cocktail facilitates antibody characterization and validation. Commun Biol 2021; 4:441. [PMID: 33824395 PMCID: PMC8024308 DOI: 10.1038/s42003-021-01965-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/08/2021] [Indexed: 02/01/2023] Open
Abstract
High quality, well-validated antibodies are needed to mitigate irreproducibility and clarify conflicting data in science. We describe an epitope-directed monoclonal antibody (mAb) production method that addresses issues of antibody quality, validation and utility. The workflow is illustrated by generating mAbs against multiple in silico-predicted epitopes on human ankyrin repeat domain 1 (hANKRD1) in a single hybridoma production cycle. Antigenic peptides (13-24 residues long) presented as three-copy inserts on the surface exposed loop of a thioredoxin carrier produced high affinity mAbs that are reactive to native and denatured hANKRD1. ELISA assay miniaturization afforded by novel DEXT microplates allowed rapid hybridoma screening with concomitant epitope identification. Antibodies against spatially distant sites on hANKRD1 facilitated validation schemes applicable to two-site ELISA, western blotting and immunocytochemistry. The use of short antigenic peptides of known sequence facilitated direct epitope mapping crucial for antibody characterization. This robust method motivates its ready adoption for other protein targets.
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22
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Velázquez J, Rodríguez A, Aragón H, Haidar A, González M, Valdés R, Garay HE, Abreu DD, Ramos Y, Cabrales A, Morales A, González O, Herrera F, Estrada MP, Carpio Y. Monoclonal antibody against Nile tilapia (Oreochromis niloticus) IgM heavy chain: A valuable tool for detection and quantification of IgM and IgM + cells. FISH & SHELLFISH IMMUNOLOGY 2021; 110:44-54. [PMID: 33348037 DOI: 10.1016/j.fsi.2020.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/26/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Nile tilapia (Oreochromis niloticus) is a freshwater fish, which is extensively cultivated worldwide and constitutes one of the model species for the study of fish immunology. Monoclonal antibodies are very advantageous molecular tools for studying teleost immune system. Specifically, monoclonal antibodies that react with immunoglobulins are used successfully in the study of the humoral immune response of several fish species. In the present study, we produced and characterized a monoclonal antibody against tilapia IgM heavy chain using a peptide-based strategy. The peptide sequence was selected from the surface-exposed region between CH3-CH4 domains. The specificity of the polyclonal serum and the hybridoma culture supernatant obtained by immunization with the peptide conjugated to keyhole limpet hemocyanin were evaluated by western blotting, both showing reactivity against tilapia serum IgM. The purified mAb was able to recognize secreted IgM by western blotting and ELISA and membrane IgM by flow cytometry. We also demonstrated that the antibody doesn't cross-react with a recombinant IgT fragment. This tool allowed us to study for the first time the stimulation of mucosal immunity after Pituitary Adenylate Cyclase Activating Polypeptide administration. Overall, the results demonstrated the utility of this mAb to characterize humoral immune response in O. niloticus.
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Affiliation(s)
- Janet Velázquez
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Alianet Rodríguez
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Hasel Aragón
- Monoclonal Antibodies Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Arlette Haidar
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Marcos González
- Monoclonal Antibodies Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Rodolfo Valdés
- Monoclonal Antibodies Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Hilda Elsa Garay
- Peptides Synthesis Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - David Diago Abreu
- Peptides Synthesis Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Yassel Ramos
- Proteomics Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Ania Cabrales
- Analytic and Purification Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Antonio Morales
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Osmany González
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Fidel Herrera
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba
| | - Mario Pablo Estrada
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba.
| | - Yamila Carpio
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), P.O. Box 6162, Havana, 10600, Cuba.
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Guru Vishnu P, Bhattacharya TK, Divya D, Rajendra Prasad A, Govardhan Sagar N. Establishment of primary chicken embryo myoblast cell culture, antigenic epitopes prediction and production of anti activin receptor type IIB polyclonal antibody in chicken. Anim Biotechnol 2021; 33:1095-1108. [PMID: 33491546 DOI: 10.1080/10495398.2020.1870483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The detection of activin receptor typeIIB (ACTRIIB) protein, a prominent negative muscle growth regulator has paramount value in augmenting growth traits through molecular breeding schemes in chicken. The study was formulated to establish primary chicken embryo myoblast culture (CEM) using 9th and 18th day chick embryos and to develop antibodies for immunodetection of ACTRIIB protein. The physicochemical and structural attributes of the ACTRIIB sequence were evaluated to identify substantial antigenic regions. The ACTRIIB sequence was transfected into CEM and expressed protein was injected subcutaneously into rats to produce hyperimmune serum. The average propensity of protein sequence for beta turns, surface accessibility, chain flexibility, antigenicity, hydrophilicity and linear epitopes was 0.978, 1.000, 0.991, 1.038, 1.258 and 0.512, respectively. The 9th day CEM exhibited confluency (80-90%) earlier than the 18th day. The expression of myogenic regulatory factors in 9th day myoblasts was higher than the 18th day by 7.28, 5.16, 6.28 and 6.93 folds for MYF5, MRF4, MYOG and MYOD, respectively. The ACTRIIB mRNA was downregulated by 2.54 folds on the 9th day compared to the 18th day myoblasts and protein varied significantly between 9th and 18th day myoblasts. The CEM culture can be harnessed unequivocally to investigate molecular mechanisms underlying muscle growth besides raising antibodies.
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Affiliation(s)
| | - T K Bhattacharya
- Molecular Genetics and Breeding, ICAR-Directorate of Poultry Research, Hyderabad, India
| | - Devara Divya
- ICAR-Directorate of Poultry Research, Hyderabad, India
| | - Athe Rajendra Prasad
- Division of Animal Genetics and Breeding, Indian Veterinary Research Institute, Izatnagar, India
| | - N Govardhan Sagar
- Division of Animal Genetics and Breeding, Indian Veterinary Research Institute, Izatnagar, India
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24
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Piccinni MZ, Guille MJ. Purifying Antibodies Raised against Xenopus Peptides. Cold Spring Harb Protoc 2020; 2020:105619. [PMID: 31900322 DOI: 10.1101/pdb.prot105619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Antibody production for work in Xenopus involves the immunization of a host with an antigen, usually a Xenopus protein or peptide alien to the host. The antibody-containing serum, normally returned to the investigator by the company/bioresource unit where it was raised, is comprised of all proteins not used in blood clotting (coagulation) and all the electrolytes, antibodies, antigens, hormones, and any exogenous substances, such as drugs and microorganisms, that were in the blood. It is often necessary to separate the target antibody from the rest of the serum components to minimize nonspecific protein-antibody interactions in downstream applications (e.g., when performing western blotting). Most antibody production companies provide a column containing the peptide coupled to glass beads. A purification procedure for using this type of column (i.e., one that is based on controlled-pore glass beads) is described here.
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Affiliation(s)
- Maya Z Piccinni
- European Xenopus Resource Centre, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, United Kingdom
| | - Matthew J Guille
- European Xenopus Resource Centre, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, United Kingdom
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25
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Abstract
For work in Xenopus, frog-specific antibodies must usually be raised, although a few antibodies against mammalian proteins cross-react. To produce an immunogen for antibody production, human embryonic kidney (HEK) expression systems can be used as described here. For most laboratories, the actual method of raising the antibody is determined by local ethical regulations controlling the adjuvant and injection protocols used. Because these steps are often outsourced, they are not included in this protocol.
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Affiliation(s)
- Maya Z Piccinni
- European Xenopus Resource Centre, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, United Kingdom
| | - Matthew J Guille
- European Xenopus Resource Centre, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, United Kingdom
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26
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Pérez de la Lastra JM, Baca-González V, Asensio-Calavia P, González-Acosta S, Morales-delaNuez A. Can Immunization of Hens Provide Oral-Based Therapeutics against COVID-19? Vaccines (Basel) 2020; 8:E486. [PMID: 32872186 PMCID: PMC7565424 DOI: 10.3390/vaccines8030486] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
In the current worldwide pandemic situation caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and the newest coronavirus disease (COVID-19), therapeutics and prophylactics are urgently needed for a large population. Some of the prophylaxis strategies are based on the development of antibodies targeting viral proteins. IgY antibodies are a type of immunoglobulin present in birds, amphibians, and reptiles. They are usually obtained from egg yolk of hyper-immunized hens and represent a relatively inexpensive source of antibodies. Specific IgY can be produced by immunizing chickens with the target antigen and then purifying from the egg yolk. Chicken IgY has been widely explored as a clinical anti-infective material for prophylaxis, preventive medicine, and therapy of infectious diseases. Administered non-systemically, IgY antibodies are safe and effective drugs. Moreover, passive immunization with avian antibodies could become an effective alternative therapy, as these can be obtained relatively simply, cost-efficiently, and produced on a large scale. Here, we highlight the potential use of polyclonal avian IgY antibodies as an oral prophylactic treatment for respiratory viral diseases, such as COVID-19, for which no vaccine is yet available.
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Affiliation(s)
- José M. Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain; (V.B.-G.); (S.G.-A.); (A.M.-d.)
| | - Victoria Baca-González
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain; (V.B.-G.); (S.G.-A.); (A.M.-d.)
| | - Patricia Asensio-Calavia
- Biological Activity Service, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain;
| | - Sergio González-Acosta
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain; (V.B.-G.); (S.G.-A.); (A.M.-d.)
| | - Antonio Morales-delaNuez
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain; (V.B.-G.); (S.G.-A.); (A.M.-d.)
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27
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Xing J, Tian HF, Tang XQ, Sheng XZ, Zhan WB. Kinetics of T lymphocyte subsets and B lymphocytes in response to immunostimulants in flounder (Paralichthys olivaceus): implications for CD4 + T lymphocyte differentiation. Sci Rep 2020; 10:13827. [PMID: 32796864 PMCID: PMC7429840 DOI: 10.1038/s41598-020-69542-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/12/2020] [Indexed: 01/22/2023] Open
Abstract
CD4+ T lymphocytes play crucial roles in the adaptive immune system. CD4, as the most effective marker to delineate the T-helper subsets, was identified in many fish species. Two CD4 homologs, CD4-1 and CD4-2, have been reported in flounder (Paralichthys olivaceus). In this study, monoclonal antibodies (mAbs) against CD4-1 and CD4-2 of flounder were produced, CD4+ T lymphocytes were isolated and identified, and the variations in CD4+ and CD8+ T lymphocytes and IgM+ B lymphocytes after Poly I:C, PMA or β-glucan stimulation were investigated. Then, the expression of transcription factors and cytokines in sorted CD4+ T lymphocytes was analyzed. The results showed that the mAbs were specific to flounder CD4-1+ and CD4-2+ T cells. CD4-1+ and CD4-2+ cells responded to all three stimulants, while CD8+ T lymphocytes only give a strong response to Poly I:C, and the percentages of IgM+ B lymphocytes showed a tendency to increase. After stimulation, the expression of transcription factors and cytokines of Th1, Th2 and Th17 cells varied in CD4+ T cells. These results will provide crucial foundations for the differentiation and function of teleost CD4+ T lymphocytes.
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Affiliation(s)
- Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, People's Republic of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Aoshanwei Town, Qingdao, People's Republic of China
| | - Hong-Fei Tian
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Xiao-Qian Tang
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Xiu-Zhen Sheng
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Wen-Bin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, People's Republic of China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Aoshanwei Town, Qingdao, People's Republic of China.
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28
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Bourdeaux F, Kopp Y, Lautenschläger J, Gößner I, Besir H, Vabulas RM, Grininger M. Dodecin as carrier protein for immunizations and bioengineering applications. Sci Rep 2020; 10:13297. [PMID: 32764653 PMCID: PMC7414021 DOI: 10.1038/s41598-020-69990-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022] Open
Abstract
In bioengineering, scaffold proteins have been increasingly used to recruit molecules to parts of a cell, or to enhance the efficacy of biosynthetic or signalling pathways. For example, scaffolds can be used to make weak or non-immunogenic small molecules immunogenic by attaching them to the scaffold, in this role called carrier. Here, we present the dodecin from Mycobacterium tuberculosis (mtDod) as a new scaffold protein. MtDod is a homododecameric complex of spherical shape, high stability and robust assembly, which allows the attachment of cargo at its surface. We show that mtDod, either directly loaded with cargo or equipped with domains for non-covalent and covalent loading of cargo, can be produced recombinantly in high quantity and quality in Escherichia coli. Fusions of mtDod with proteins of up to four times the size of mtDod, e.g. with monomeric superfolder green fluorescent protein creating a 437 kDa large dodecamer, were successfully purified, showing mtDod's ability to function as recruitment hub. Further, mtDod equipped with SYNZIP and SpyCatcher domains for post-translational recruitment of cargo was prepared of which the mtDod/SpyCatcher system proved to be particularly useful. In a case study, we finally show that mtDod-peptide fusions allow producing antibodies against human heat shock proteins and the C-terminus of heat shock cognate 70 interacting protein (CHIP).
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Affiliation(s)
- Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Yannick Kopp
- Institute of Biophysical Chemistry, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Lauer Str. 15, 60438, Frankfurt am Main, Germany
| | - Julia Lautenschläger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Ines Gößner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Hüseyin Besir
- European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- PROGEN Biotechnik GmbH, 69123, Heidelberg, Germany
| | - R Martin Vabulas
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
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29
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Mohsin AZ, Sukor R, Selamat J, Meor Hussin AS, Ismail IH, Jambari NN, Mustaffa-Kamal F. Generation of High Affinity Anti-Peptide Polyclonal Antibodies Recognizing Goat α s1-Casein. Molecules 2020; 25:E2622. [PMID: 32516919 PMCID: PMC7321099 DOI: 10.3390/molecules25112622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 12/02/2022] Open
Abstract
The chemical, technological and allergy properties of goat's milk are significantly affected by the level of αs1-casein. Detection and quantification of αs1-casein requires high-specificity methods to overcome high-sequence similarity between this protein and others in the casein family. Unavailability of antibodies with high affinity and specificity towards goat αs1-casein hinders the development of immuno-based analytical methods such as enzyme-linked immunosorbent assay (ELISA) and biosensors. Here, we report the generation of polyclonal antibodies (or immunoglobulins, IgGs) raised towards goat αs1-casein N- (Nter) and C-terminal (Cter) peptide sequences. The Nter and Cter peptides of goat αs1-casein were immunized in rabbits for the generation of antisera, which were purified using protein G affinity chromatography. The binding affinity of the antisera and purified IgGs were tested and compared using indirect ELISA, where peptide-BSA conjugates and goat αs1-casein were used as the coating antigens. The Nter antiserum displayed higher titer than Cter antiserum, at 1/64,000 and 1/32,000 dilutions, respectively. The purification step further yielded 0.5 mg/mL of purified IgGs from 3 mL of antisera. The purified Nter IgG showed a significantly (p < 0.05) higher binding affinity towards peptide-BSA and goat αs1-casein, with lower Kd value at 5.063 × 10-3 μM compared to 9.046 × 10-3 μM for the Cter IgG. A cross-reactivity test showed that there was no binding in neither Nter nor Cter IgGs towards protein extracts from the milk of cow, buffalo, horse and camel. High-quality antibodies generated will allow further development of immuno-based analytical methods and future in vitro studies to be conducted on goat αs1-casein.
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Affiliation(s)
- Aliah Zannierah Mohsin
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia; (A.Z.M.); (J.S.); (N.N.J.)
| | - Rashidah Sukor
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia; (A.Z.M.); (J.S.); (N.N.J.)
- Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Jinap Selamat
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia; (A.Z.M.); (J.S.); (N.N.J.)
- Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | | | | | - Nuzul Noorahya Jambari
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia; (A.Z.M.); (J.S.); (N.N.J.)
- Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia;
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30
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Naghi Vishteh M, Javadi Mamaghani A, Rashidi S, Seyyed Tabaei SJ, Jeddi-Tehrani M. Peptide-Based Monoclonal Antibody Production Against SAG1 (P30) Protein of Toxoplasma gondii. Monoclon Antib Immunodiagn Immunother 2020; 39:51-56. [DOI: 10.1089/mab.2019.0041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Mohadeseh Naghi Vishteh
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amirreza Javadi Mamaghani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Parasitology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sama Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Javad Seyyed Tabaei
- Department of Parasitology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahmood Jeddi-Tehrani
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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31
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Shu C, Sun P, Xie H, Huang W, Qi J, Ma Y. Virus-Like Particles Presenting the FGF-2 Protein or Identified Antigenic Peptides Promoted Antitumor Immune Responses in Mice. Int J Nanomedicine 2020; 15:1983-1996. [PMID: 32308382 PMCID: PMC7146011 DOI: 10.2147/ijn.s237182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/25/2020] [Indexed: 01/29/2023] Open
Abstract
Background Fibroblast growth factor (FGF)-2 is overexpressed in various tumor tissues. It affects tumor cell proliferation, invasion and survival, promotes tumor angiogenesis and is tightly involved in the development of systemic and local immunosuppressive tumor mechanisms. Purpose This study aimed to develop an effective vaccine against FGF-2 and to investigate the effects of anti-FGF-2 immunization on tumor growth and antitumor immune responses. Methods A set of thirteen synthesized overlapping peptides covering all possible linear B-cell epitopes of murine FGF-2 and a recombinant FGF-2 protein were conjugated to virus-like particles (VLPs) of recombinant hepatitis B core antigen (HBcAg). The VLPs were immunized through a preventive or therapeutic strategy in a TC-1 or 4T1 grafted tumor model. Results Immunization with FGF-2 peptides or full-length protein-coupled VLPs produced FGF-2-specific antibodies with a high titer. Peptide 12, which is located in the heparin-binding site of FGF-2, or protein-conjugated VLPs presented the most significant effects on the suppression of TC-1 tumor growth. The levels of IFN-γ-expressing splenocytes and serum IFN-γ were significantly elevated; further, the immune effector cells CD8+ IFN-γ+ cytotoxic T lymphocytes (CTLs) and CD4+ IFN-γ+ Th1 cells were significantly increased, whereas the immunosuppressive cells CD4+ CD25+ FOXP3+ Treg cells and Gr-1+ CD11b+ myeloid-derived suppressor cells (MDSCs) were decreased in the immunized mice. In addition, VLP immunization significantly suppressed tumor vascularization and promoted tumor cell apoptosis. In mice bearing 4T1 breast tumor, preventive immunization with FGF-2-conjugated VLPs suppressed tumor growth and lung metastasis, and increased effector cell responses. Conclusion Active immunization against FGF-2 is a new possible strategy for tumor immunotherapy.
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Affiliation(s)
- Congyan Shu
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming 650118, People's Republic of China.,Sichuan Institute for Food and Drug Control, Chengdu 611731, People's Republic of China
| | - Pengyan Sun
- Yunnan Center for Disease Control and Prevention, Kunming 650022, People's Republic of China
| | - Hanghang Xie
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming 650118, People's Republic of China
| | - Weiwei Huang
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming 650118, People's Republic of China
| | - Jialong Qi
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming 650118, People's Republic of China
| | - Yanbing Ma
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming 650118, People's Republic of China
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32
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Peptides, Antibodies, Peptide Antibodies and More. Int J Mol Sci 2019; 20:ijms20246289. [PMID: 31847088 PMCID: PMC6941022 DOI: 10.3390/ijms20246289] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
The applications of peptides and antibodies to multiple targets have emerged as powerful tools in research, diagnostics, vaccine development, and therapeutics. Antibodies are unique since they, in theory, can be directed to any desired target, which illustrates their versatile nature and broad spectrum of use as illustrated by numerous applications of peptide antibodies. In recent years, due to the inherent limitations such as size and physical properties of antibodies, it has been attempted to generate new molecular compounds with equally high specificity and affinity, albeit with relatively low success. Based on this, peptides, antibodies, and peptide antibodies have established their importance and remain crucial reagents in molecular biology.
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33
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Valdarnini N, Holm B, Hansen P, Rovero P, Houen G, Trier N. Fine Mapping of Glutamate Decarboxylase 65 Epitopes Reveals Dependency on Hydrophobic Amino Acids for Specific Interactions. Int J Mol Sci 2019; 20:ijms20122909. [PMID: 31207885 PMCID: PMC6627456 DOI: 10.3390/ijms20122909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 01/10/2023] Open
Abstract
Characterization of multiple antibody epitopes has revealed the necessity of specific groups of amino acid residues for reactivity. This applies to the majority of antibody-antigen interactions, where especially charged and hydrophilic amino acids have been reported to be essential for antibody reactivity. This study describes thorough characterization of glutamic acid decarboxylase (GAD) 65 antigenic epitopes, an immunodominant autoantigen in type 1 diabetes (T1D). As linear epitopes are sparsely described for GAD65 in T1D, we aimed to identify and thoroughly characterize two GAD65 antibodies using immunoassays. A monoclonal antibody recognized an epitope in the N-terminal domain of GAD65, 8FWSFGSE14, whereas a polyclonal antibody recognized two continuous epitopes in the C-terminal domain, corresponding to amino acids 514RTLED518 and 549PLGDKVNF556. Hydrophobic amino acids were essential for antibody reactivity, which was verified by competitive inhibition assays. Moreover, the epitopes were located in flexible linker regions and turn structures. These findings confirm the versatile nature of antibody-antigen interactions and describe potential continuous epitopes related to T1D, which predominantly have been proposed to be of discontinuous nature.
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Affiliation(s)
- Niccolò Valdarnini
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Via Ugo Schiff, 6, 50019 Sesto Fiorentino, Italy.
| | - Bettina Holm
- Department of Clinical Immunology, Rigshospitalet, Ole Maaløes vej 26, 2200 Copenhagen N, Denmark.
| | - Paul Hansen
- Department of Drug Design and Pharmacology, Universitetsparken 2, 2100 Copenhagen Ø, Denmark.
| | - Paolo Rovero
- Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Via Ugo Schiff, 6, 50019 Sesto Fiorentino, Italy.
| | - Gunnar Houen
- Department of Neurology, Rigshospitalet Glostrup, Nordre Ringvej 57, 2600 Glostrup, Denmark.
| | - Nicole Trier
- Department of Neurology, Rigshospitalet Glostrup, Nordre Ringvej 57, 2600 Glostrup, Denmark.
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Yan L, Nan X, Zhang C, Wang H, Huang X, Hu J, Liu Y. Development of an enzyme‑linked immunosorbent assay for camptothecin. Mol Med Rep 2019; 20:959-966. [PMID: 31173229 PMCID: PMC6625201 DOI: 10.3892/mmr.2019.10342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/10/2019] [Indexed: 11/06/2022] Open
Abstract
The use of camptothecin and its analogues has increased in clinical settings and in agriculture. Therefore, camptothecins and their derivatives, metabolites and degradation products are frequently found in the environment. Therefore, it is important to develop an ELISA for the quantification of camptothecins in human plasma, plants, animal tissues and other matrices. The present study developed a novel competitive indirect ELISA for camptothecin using a monoclonal antibody (MAb). In total, two haptens and various carrier proteins were tested to select the most suitable immunogen for the production of MAbs against camptothecin. Hapten 1 conjugated with keyhole limpet hemocyanin was selected for the preparation of MAb 5A3, and was used to establish a competitive indirect ELISA for camptothecin. A total of three derivatives of camptothecin used in clinical practice were examined. Topotecan showed an IC50 value of 0.68 µg/ml with a detection limit of 0.19 µg/ml, belotecan showed an IC50 value of 0.87 µg/ml with a detection limit of 0.22 µg/ml and irinotecan showed an IC50 value of 2.85 µg/ml with a detection limit of 0.47 µg/ml. The cross-reactivity results suggested that the assay developed in the present study possessed a high sensitivity to camptothecin. Therefore, this immunoassay technique may be suitable for monitoring the levels of camptothecin in compound analysis, clinical applications, and analyses of food and environmental samples.
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Affiliation(s)
- Liting Yan
- Central Laboratory, Shaanxi Provincial People's Hospital, Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi 710068, P.R. China
| | - Xiang Nan
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Cunzheng Zhang
- Institute of Food Quality and Safety Inspection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, P.R. China
| | - Haifang Wang
- Institute of Integrated Medicine, Shaanxi University of Traditional Chinese Medicine, Xi'an, Shaanxi 712046, P.R. China
| | - Xiaoyan Huang
- Central Laboratory, Shaanxi Provincial People's Hospital, Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi 710068, P.R. China
| | - Jun Hu
- Central Laboratory, Shaanxi Provincial People's Hospital, Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi 710068, P.R. China
| | - Yingqian Liu
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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Targeting Tumor Markers with Antisense Peptides: An Example of Human Prostate Specific Antigen. Int J Mol Sci 2019; 20:ijms20092090. [PMID: 31035335 PMCID: PMC6540241 DOI: 10.3390/ijms20092090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/05/2019] [Accepted: 04/25/2019] [Indexed: 12/20/2022] Open
Abstract
The purpose of this paper was to outline the development of short peptide targeting of the human prostate specific antigen (hPSA), and to evaluate its effectiveness in staining PSA in human prostate cancer tissue. The targeting of the hPSA antigen by means of antisense peptide AVRDKVG was designed according to a three-step method involving: 1. The selection of the molecular target (hPSA epitope), 2. the modeling of an antisense peptide (paratope) based on the epitope sequence, and 3. the spectroscopic evaluation of sense–antisense peptide binding. We then modified standard hPSA immunohistochemical staining practice by using a biotinylated antisense peptide instead of the standard monoclonal antibody and compared the results of both procedures. Immunochemical testing on human tissue showed the applicability of the antisense peptide technology to human molecular targets. This methodology represents a new approach to deriving peptide ligands and potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.
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Yan J, Yang Q, Li W, Yu J, Xie J, Xiang J, Wang H. Two desired epitopes of cTnI benefit for preparation of standardized monoclonal antibodies. Chirality 2019; 31:321-327. [PMID: 30801797 DOI: 10.1002/chir.23058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/01/2019] [Accepted: 01/02/2019] [Indexed: 11/07/2022]
Abstract
Acute myocardial infarction (AMI) is one of the most severe cardiovascular diseases in humans, often resulting in unexpected death. Early detection is critical for patient survival. Sandwich ELISA is a common method for the detection of AMI. However, ELISA kits from different manufacturers can give different results, in part because of the lack of standardized epitopes. Therefore, the purpose of this study was to find two standardized epitopes. We predicted two antigen epitopes and respectively immunize mice to manufacture standardized monoclonal antibodies. Eight monoclonal antibodies were prepared. Monoclonal antibodies 7D2 and 2C3 were selected with high affinity, and their characteristics were explored. The results show that monoclonal antibodies 7D2 and 2C3 can both bind to various modified forms and complexes of cardiac troponin I (cTnI), were not cross-reaction with related antigens of normal human serum and can be paired. Therefore, we deem epitopes 30 to 42 and 77 to 89 standardized epitopes.
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Affiliation(s)
- JunJie Yan
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Department of Bioengineering, Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Jinan University, Guangzhou, China
| | - QiLing Yang
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Department of Bioengineering, Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Jinan University, Guangzhou, China
| | - WenLi Li
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Department of Bioengineering, Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Jinan University, Guangzhou, China
| | - Juan Yu
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Department of Bioengineering, Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Jinan University, Guangzhou, China
| | - Jun Xie
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Department of Bioengineering, Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Jinan University, Guangzhou, China
| | - JunJian Xiang
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Department of Bioengineering, Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Jinan University, Guangzhou, China
| | - Hong Wang
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Department of Bioengineering, Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Jinan University, Guangzhou, China
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37
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Fan C, Long R, You Y, Wang J, Yang X, Huang S, Sheng Y, Peng X, Liu H, Wang Z, Liu K. A novel PADRE-Kv1.3 vaccine effectively induces therapeutic antibodies and ameliorates experimental autoimmune encephalomyelitis in rats. Clin Immunol 2018; 193:98-109. [DOI: 10.1016/j.clim.2018.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 02/23/2018] [Accepted: 02/24/2018] [Indexed: 01/24/2023]
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38
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Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K. Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody. J Biochem 2018; 164:65-76. [PMID: 29924367 DOI: 10.1093/jb/mvy032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/06/2018] [Indexed: 02/06/2023] Open
Abstract
Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity and high affinity. Although equally abundant, the role of intramolecular H-bonds is far less clear and not universally acknowledged. Herein, we have carried out a molecular-level study to dissect the contribution of intramolecular H-bonds in a flexible peptide for the recognition by an antibody. We show that intramolecular H-bonds may have a profound, multifaceted and favorable effect on the binding affinity by up to 2 kcal mol-1 of free energy. Collectively, our results suggest that antibodies are fine tuned to recognize transiently stabilized structures of flexible peptides in solution, for which intramolecular H-bonds play a key role.
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Affiliation(s)
- Kazuhiro Miyanabe
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroki Akiba
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Laboratory of Pharmacokinetic Optimization, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Osamu Kusano-Arai
- Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroko Iwanari
- Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Takao Hamakubo
- Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Laboratory of Pharmacokinetic Optimization, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan.,Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Leferink AM, Reis DS, van Blitterswijk CA, Moroni L. An antibody based approach for multi-coloring osteogenic and chondrogenic proteins in tissue engineered constructs. ACTA ACUST UNITED AC 2018. [PMID: 29516869 DOI: 10.1088/1748-605x/aab51e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
When tissue engineering strategies rely on the combination of three-dimensional (3D) polymeric or ceramic scaffolds with cells to culture implantable tissue constructs in vitro, it is desirable to monitor tissue growth and cell fate to be able to more rationally predict the quality and success of the construct upon implantation. Such a 3D construct is often referred to as a 'black-box' since the properties of the scaffolds material limit the applicability of most imaging modalities to assess important construct parameters. These parameters include the number of cells, the amount and type of tissue formed and the distribution of cells and tissue throughout the construct. Immunolabeling enables the spatial and temporal identification of multiple tissue types within one scaffold without the need to sacrifice the construct. In this report, we concisely review the applicability of antibodies (Abs) and their conjugation chemistries in tissue engineered constructs. With some preliminary experiments, we show an efficient conjugation strategy to couple extracellular matrix Abs to fluorophores. The conjugated probes proved to be effective in determining the presence of collagen type I and type II on electrospun and additive manufactured 3D scaffolds seeded with adult human bone marrow derived mesenchymal stromal cells. The conjugation chemistry applied in our proof of concept study is expected to be applicable in the coupling of any other fluorophore or particle to the Abs. This could ultimately lead to a library of probes to permit high-contrast imaging by several imaging modalities.
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Affiliation(s)
- Anne M Leferink
- Department of Tissue Regeneration, MIRA institute, University of Twente, The Netherlands. BIOS-Lab on a chip group, MIRA institute, University of Twente, The Netherlands
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40
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A harmonized immunoassay with liquid chromatography-mass spectrometry analysis in egg allergen determination. Anal Bioanal Chem 2017; 410:325-335. [PMID: 29138881 DOI: 10.1007/s00216-017-0721-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/08/2017] [Accepted: 10/23/2017] [Indexed: 01/26/2023]
Abstract
Food allergy is a serious health issue worldwide. Implementing allergen labeling regulations is extremely challenging for regulators, food manufacturers, and analytical kit manufacturers. Here we have developed an "amino acid sequence immunoassay" approach to ELISA. The new ELISA comprises of a monoclonal antibody generated via an analyte specific peptide antigen and sodium lauryl sulfate/sulfite solution. This combination enables the antibody to access the epitope site in unfolded analyte protein. The newly developed ELISA recovered 87.1%-106.4% ovalbumin from ovalbumin-incurred model processed foods, thereby demonstrating its applicability as practical egg allergen determination. Furthermore, the comparison of LC-MS/MS and the new ELISA, which targets the amino acid sequence conforming to the LC-MS/MS detection peptide, showed a good agreement. Consequently the harmonization of two methods was demonstrated. The complementary use of the new ELISA and LC-MS analysis can offer a wide range of practical benefits in terms of easiness, cost, accuracy, and efficiency in food allergen analysis. In addition, the new assay is attractive in respect to its easy antigen preparation and predetermined specificity. Graphical abstract The ELISA composing of the monoclonal antibody targeting the amino acid sequence conformed to LC-MS detection peptide, and the protein conformation unfolding reagent was developed. In ovalbumin determination, the developed ELISA showed a good agreement with LC-MS analysis. Consequently the harmonization of immunoassay with LC-MS analysis by using common target amino acid sequence was demonstrated.
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41
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Abbas IM, Schwaar T, Bienwald F, Weller MG. Predictable Peptide Conjugation Ratios by Activation of Proteins with Succinimidyl Iodoacetate (SIA). Methods Protoc 2017; 1:mps1010002. [PMID: 31164550 PMCID: PMC6526413 DOI: 10.3390/mps1010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 12/30/2022] Open
Abstract
The small heterobifunctional linker succinimidyl iodoacetate (SIA) was examined for the preparation of peptide–protein bioconjugates with predicable conjugation ratios. For many conjugation protocols, the protein is either treated with a reductant to cleave disulfide bonds or is reacted with thiolation chemicals, such as Traut’s reagent. Both approaches are difficult to control, need individual optimization and often lead to unsatisfactory results. In another popular approach, a heterobifunctional linker with a N-hydroxysuccinimide (NHS) and a maleimide functionality is applied to the protein. After the activation of some lysine ε-amino groups with the NHS ester functionality, a cysteine-containing peptide is attached to the activated carrier protein via maleimide. Particularly, the maleimide reaction leads to some unwanted byproducts or even cleavage of the linker. Many protocols end up with conjugates with unpredictable and irreproducible conjugation ratios. In addition, the maleimide-thiol addition product should be assumed immunogenic in vivo. To avoid these and other disadvantages of the maleimide approach, we examined the known linker succinimidyl iodoacetate (SIA) in more detail and developed two protocols, which lead to peptide–protein conjugates with predefined average conjugation ratios. This holds potential to eliminate tedious and expensive optimization steps for the synthesis of a bioconjugate of optimal composition.
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Affiliation(s)
- Ioana M Abbas
- Federal Institute for Materials Research and Testing (BAM), Division 1.5 Protein Analysis, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany.
- Humboldt-Universität zu Berlin, School of Analytical Sciences Adlershof, Unter den Linden 6, 10099 Berlin, Germany.
| | - Timm Schwaar
- Federal Institute for Materials Research and Testing (BAM), Division 1.5 Protein Analysis, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany.
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Frank Bienwald
- Federal Institute for Materials Research and Testing (BAM), Division 1.5 Protein Analysis, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany.
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Michael G Weller
- Federal Institute for Materials Research and Testing (BAM), Division 1.5 Protein Analysis, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany.
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42
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Jirapongpairoj W, Hirono I, Kondo H. Development and evaluation of polyclonal antisera for detection of the IgM heavy chain of multiple fish species. J Immunol Methods 2017; 449:71-75. [PMID: 28652011 DOI: 10.1016/j.jim.2017.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 01/06/2023]
Abstract
Antibodies are widely considered to be essential tools for detection of immune responses in various fish species. Here we produced the peptide polyclonal antisera (anti-fish IgH-1 and anti-fish IgH-2) to detect IgM of various fish species. The peptides were designed based on the conserved sequence of the fish immunoglobulin heavy chains of seven fish species (Japanese flounder, seabream, yellowtail, carp, rainbow trout, hybrid sturgeon and banded houndshark). By Western blotting, anti-fish IgH-1 antiserum detected the IgMs of all fish species except banded houndshark. Anti-fish IgH-2 antiserum clearly reacted with the IgMs of only three of the fish species (seabream, yellowtail and rainbow trout). Attempts to use the antisera to measure fish antibody titer by ELISA were unsuccessful. These results demonstrate that anti-fish IgH-1 peptide polyclonal antiserum is a potentially applicable tool for detecting immunoglobulins in various fish species by Western blotting.
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Affiliation(s)
- Walissara Jirapongpairoj
- Laboratory of Genome Science, Graduate School, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan.
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43
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Park SY, Choi J. Molecular Characterization and Expression Analysis of P38 MAPK Gene and Protein in Aquatic Midge, Chironomus riparius (Diptera: Chironomidae), Exposed to Environmental Contaminants. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 72:428-438. [PMID: 28144697 DOI: 10.1007/s00244-017-0366-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
P38 Mitogen-activated protein kinase (MAPK), an important signaling protein involved in various cellular processes, including stress responses, has been well characterized in model organisms. P38 has been identified in a number of insects, including the genus Drosophila; however, its homologue in Chironomus riparius has not yet been identified. In this study, we identified and characterized p38 MAPK (Crp38) gene in C. riparius using a transcriptome database that was previously generated 454 GS-FLX pyrosequencing. Comparative and phylogenetic analyses were performed using the p38 homologue of other species, such as Drosophila melanogaster, Aedes aegypti, Bombyx mori, Caenorhabditis elegans, Homo sapiens, etc. Furthermore, to test its potential as a biomarker of environmental contamination, Crp38 gene expression was analyzed upon exposure to nonylphenol (NP), silver nanoparticles (AgNPs), and cadmium (Cd). Crp38 gene expression was up- or down-regulated depending on the concentration and exposure duration of chemicals. These results show the role of Crp38 gene in defense against environmental stresses, as well as its potential use as a biomarker for various environmental pollutants. We further synthesized p38 antibody based on the predicted amino acid sequence deduced from Crp38 cDNA and, using this customized antibody, examined p38 protein expression in Cd exposed C. riparius. Although transcriptional alteration was not translated to the protein level, this result showed the possible application of a protein level functional study using cDNA sequence information from next-generation sequencing database in nonmodel organisms.
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Affiliation(s)
- Sun-Young Park
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, 02504, Republic of Korea
- Risk Assessment Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
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Abstract
Peptide antibodies, with their high specificities and affinities, are invaluable reagents for peptide and protein recognition in biological specimens. Depending on the application and the assay, in which the peptide antibody is to used, several factors influence successful antibody production, including peptide selection and antibody screening. Peptide antibodies have been used in clinical laboratory diagnostics with great success for decades, primarily because they can be produced to multiple targets, recognizing native wildtype proteins, denatured proteins, and newly generated epitopes. Especially mutation-specific peptide antibodies have become important as diagnostic tools in the detection of various cancers. In addition to their use as diagnostic tools in malignant and premalignant conditions, peptide antibodies are applied in all other areas of clinical laboratory diagnostics, including endocrinology, hematology, neurodegenerative diseases, cardiovascular diseases, infectious diseases, and amyloidoses.
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45
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Jadhav PD, Shim YY, Reaney MJT. Synthesis and Characterization of Site-Selective Orbitide-BSA Conjugate to Produce Antibodies. Bioconjug Chem 2016; 27:2346-2358. [PMID: 27626291 DOI: 10.1021/acs.bioconjchem.6b00357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bioactive flax cyclic peptides (orbitides and linusorbs) were site-specifically ligated through methionine with bovine serum albumin (BSA) to produce immunogenic compounds. In this study, modified flaxseed immunosuppressant orbitides (linusorbs or LOs) containing hydroxyl (OH) groups were synthesized for use as haptens. These compounds were extensively characterized by 1H nuclear magnetic resonance (NMR), 13C NMR, high-performance liquid chromatography-tandem mass spectrometry, and Fourier transform infrared spectroscopy. The haptens were conjugated to BSA, and the extent of hapten incorporation was determined by matrix-assisted laser desorption and ionization, liquid chromatography-electrospray ionization-mass spectrometry, and sodium dodecyl sulfate polyacrylamide gel electrophoresis. The BSA hapten complexes were used to elicit polyclonal antibody (pAbs) production in rabbits. A competitive indirect enzyme-linked immunosorbent assay (CI-ELISA) was developed that used orbitide-specific pAbs and horseradish peroxidase (HRP) conjugates. The LO assay detection limit was approximately 0.01 μg/mL (ppm), and thus, ELISA can be used for the detection of LOs in tissue and plant samples. The pAbs can be used to detect and quantify LOs in flax and flaxseed samples, to verify the presence of LOs in flaxseed containing foods, and for the detection of LOs in tissue samples, wastes, and body fluids of animals fed flaxseed.
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Affiliation(s)
- Pramodkumar D Jadhav
- Department of Plant Sciences, University of Saskatchewan , 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Youn Young Shim
- Department of Plant Sciences, University of Saskatchewan , 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada.,Prairie Tide Chemicals Inc. , 102 Melville Street, Saskatoon, Saskatchewan S7J 0R1, Canada
| | - Martin J T Reaney
- Department of Plant Sciences, University of Saskatchewan , 51 Campus Drive, Saskatoon, Saskatchewan S7N 5A8, Canada.,Prairie Tide Chemicals Inc. , 102 Melville Street, Saskatoon, Saskatchewan S7J 0R1, Canada.,Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
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Challenges for the in vivo quantification of brain neuropeptides using microdialysis sampling and LC-MS. Bioanalysis 2016; 8:1965-85. [PMID: 27554986 DOI: 10.4155/bio-2016-0119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In recent years, neuropeptides and their receptors have received an increased interest in neuropharmacological research. Although these molecules are considered relatively small compared with proteins, their in vivo quantification using microdialysis is more challenging than for small molecules. Low microdialysis recoveries, aspecific adsorption and the presence of various multiply charged precursor ions during ESI-MS/MS detection hampers the in vivo quantification of these low abundant biomolecules. Every step in the workflow, from sampling until analysis, has to be optimized to enable the sensitive analysis of these compounds in microdialysates.
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Lichtmannegger J, Leitzinger C, Wimmer R, Schmitt S, Schulz S, Kabiri Y, Eberhagen C, Rieder T, Janik D, Neff F, Straub BK, Schirmacher P, DiSpirito AA, Bandow N, Baral BS, Flatley A, Kremmer E, Denk G, Reiter FP, Hohenester S, Eckardt-Schupp F, Dencher NA, Adamski J, Sauer V, Niemietz C, Schmidt HHJ, Merle U, Gotthardt DN, Kroemer G, Weiss KH, Zischka H. Methanobactin reverses acute liver failure in a rat model of Wilson disease. J Clin Invest 2016; 126:2721-35. [PMID: 27322060 DOI: 10.1172/jci85226] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/12/2016] [Indexed: 12/15/2022] Open
Abstract
In Wilson disease (WD), functional loss of ATPase copper-transporting β (ATP7B) impairs biliary copper excretion, leading to excessive copper accumulation in the liver and fulminant hepatitis. Current US Food and Drug Administration- and European Medicines Agency-approved pharmacological treatments usually fail to restore copper homeostasis in patients with WD who have progressed to acute liver failure, leaving liver transplantation as the only viable treatment option. Here, we investigated the therapeutic utility of methanobactin (MB), a peptide produced by Methylosinus trichosporium OB3b, which has an exceptionally high affinity for copper. We demonstrated that ATP7B-deficient rats recapitulate WD-associated phenotypes, including hepatic copper accumulation, liver damage, and mitochondrial impairment. Short-term treatment of these rats with MB efficiently reversed mitochondrial impairment and liver damage in the acute stages of liver copper accumulation compared with that seen in untreated ATP7B-deficient rats. This beneficial effect was associated with depletion of copper from hepatocyte mitochondria. Moreover, MB treatment prevented hepatocyte death, subsequent liver failure, and death in the rodent model. These results suggest that MB has potential as a therapeutic agent for the treatment of acute WD.
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Devabhaktuni A, Elias JE. Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets. J Proteome Res 2016; 15:732-42. [PMID: 26743026 DOI: 10.1021/acs.jproteome.5b00861] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dependent on concise, predefined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference databases. However, such algorithms have been difficult to apply to complex protein mixtures, in part due to a lack of methods for automatically validating de novo sequencing results. Here, we present novel metrics for benchmarking de novo sequencing algorithm performance on large-scale proteomics data sets and present a method for accurately calibrating false discovery rates on de novo results. We also present a novel algorithm (LADS) that leverages experimentally disambiguated fragmentation spectra to boost sequencing accuracy and sensitivity. LADS improves sequencing accuracy on longer peptides relative to that of other algorithms and improves discriminability of correct and incorrect sequences. Using these advancements, we demonstrate accurate de novo identification of peptide sequences not identifiable using database search-based approaches.
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Affiliation(s)
- Arun Devabhaktuni
- Department of Chemical & Systems Biology, Stanford University , Stanford, California 94035, United States
| | - Joshua E Elias
- Department of Chemical & Systems Biology, Stanford University , Stanford, California 94035, United States
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Rational design of a low-affinity peptide for the detection of cystatin C in a fast homogeneous immunoassay. Amino Acids 2015; 48:479-86. [PMID: 26403846 DOI: 10.1007/s00726-015-2101-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/14/2015] [Indexed: 01/11/2023]
Abstract
Immunoassays play an essential role in current research and diagnostics resulting in a variety of detection principles. Thereby, homogeneous assays are often used for a fast signal response as demanded for example in point-of-care diagnostics. These systems often rely on a competitive assay design where the sample analyte and the corresponding dye-labeled substance are competing for binding sites on an antibody present in limited amounts. Due to the similar affinities of the antibody towards the sample analyte and the competitor, both sensitivity and assay time are limited. As a consequence, a competitor with a slightly reduced affinity towards the antibody can potentially overcome these drawbacks. Here, we present the rational design of a low-affinity peptide (donor peptide) as a specific analyte competitor for a FRET-based homogeneous immunoassay for the analysis of the protein cystatin C. Thereby, the strategy of peptide-induced antibody generation was combined with the selective variation of the immunization sequence in order to achieve a lower affinity towards the antibody. We could show that shortened donor peptides improved the resulting quenching efficiency in the immunoassay. In addition, the substitution of small hydrophobic amino acids by those with a higher steric demand appeared to be the most promising strategy providing a fast assay response for cystatin C of only 90 s.
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Fan W, Tang Q, Shen C, Qin D, Lu C, Yan Q. Preparation and characterization of polyclonal antibody against Kaposi's sarcoma-associated herpesvirus lytic gene encoding RTA. Folia Microbiol (Praha) 2015; 60:473-81. [PMID: 25832009 DOI: 10.1007/s12223-015-0387-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 03/15/2015] [Indexed: 12/30/2022]
Abstract
Replication and transcription activator (RTA) is a critical lytic protein encoded by Kaposi's sarcoma-associated herpesvirus (KSHV). To prepare rabbit polyclonal antibody against RTA, three antigenic polypeptides of KSHV RTA were initially synthesized. The fragment of RTA was cloned into p3FlagBsd to construct the recombinant plasmid, pRTA-Flag. 293 T and EA.hy926 cells were transfected with pRTA-Flag to obtain RTA-Flag fusion protein, which was detected using anti-Flag antibody. Next, New Zealand white rabbits were immunized with keyhole limpet hemocyanin-conjugated peptides to generate polyclonal antibodies against RTA. Enzyme-linked immunosorbent assays were performed to characterize the polyclonal antibodies, and the titers of the polyclonal antibodies against RTA were greater than 1:11,000. Western blotting and immunofluorescence assay revealed that the prepared antibody reacted specifically with the RTA-Flag fusion protein as well as the native viral protein in KSHV-infected primary effusion lymphoma cells. Collectively, our work successfully constructed the recombinant expression vector, pRTA-Flag, and prepared the polyclonal antibody against RTA, which was valuable for investigating the biochemical and biological functions of the critical KSHV lytic gene.
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Affiliation(s)
- Weifei Fan
- Department of Oncology, Jiangsu Province Official Hospital, 65 Jiangsu Road, Nanjing, 210024, People's Republic of China
| | - Qiao Tang
- Department of Clinical Laboratory, The Affiliated Nanjing First Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Chenyou Shen
- Department of Microbiology, Nanjing Medical University, Nanjing, Jiangsu, 210029, People's Republic of China
| | - Di Qin
- Department of Microbiology, Nanjing Medical University, Nanjing, Jiangsu, 210029, People's Republic of China
| | - Chun Lu
- Department of Microbiology, Nanjing Medical University, Nanjing, Jiangsu, 210029, People's Republic of China
| | - Qin Yan
- Department of Microbiology, Nanjing Medical University, Nanjing, Jiangsu, 210029, People's Republic of China.
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