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Ivanova A, Kohl F, González-King Garibotti H, Chalupska R, Cvjetkovic A, Firth M, Jennbacken K, Martinsson S, Silva AM, Viken I, Wang QD, Wiseman J, Dekker N. In vivo phage display identifies novel peptides for cardiac targeting. Sci Rep 2024; 14:12177. [PMID: 38806609 PMCID: PMC11133476 DOI: 10.1038/s41598-024-62953-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024] Open
Abstract
Heart failure remains a leading cause of mortality. Therapeutic intervention for heart failure would benefit from targeted delivery to the damaged heart tissue. Here, we applied in vivo peptide phage display coupled with high-throughput Next-Generation Sequencing (NGS) and identified peptides specifically targeting damaged cardiac tissue. We established a bioinformatics pipeline for the identification of cardiac targeting peptides. Hit peptides demonstrated preferential uptake by human induced pluripotent stem cell (iPSC)-derived cardiomyocytes and immortalized mouse HL1 cardiomyocytes, without substantial uptake in human liver HepG2 cells. These novel peptides hold promise for use in targeted drug delivery and regenerative strategies and open new avenues in cardiovascular research and clinical practice.
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Affiliation(s)
- Alena Ivanova
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden.
| | - Franziska Kohl
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, Solna, 171 77, Stockholm, Sweden
| | - Hernán González-King Garibotti
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - Renata Chalupska
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - Aleksander Cvjetkovic
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Karin Jennbacken
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - Sofia Martinsson
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - Andreia M Silva
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - Ida Viken
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - Qing-Dong Wang
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - John Wiseman
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden
| | - Niek Dekker
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50, Gothenburg, Sweden.
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2
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Kim SM, Heo HR, Kim CS, Shin HH. Genetically engineered bacteriophages as novel nanomaterials: applications beyond antimicrobial agents. Front Bioeng Biotechnol 2024; 12:1319830. [PMID: 38725991 PMCID: PMC11079243 DOI: 10.3389/fbioe.2024.1319830] [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: 10/11/2023] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Bacteriophages, also known as phages, are viruses that replicate in bacteria and archaea. Phages were initially discovered as antimicrobial agents, and they have been used as therapeutic agents for bacterial infection in a process known as "phage therapy." Recently, phages have been investigated as functional nanomaterials in a variety of areas, as they can function not only as therapeutic agents but also as biosensors and tissue regenerative materials. Phages are nontoxic to humans, and they possess self-assembled nanostructures and functional properties. Additionally, phages can be easily genetically modified to display specific peptides or to screen for functional peptides via phage display. Here, we demonstrated the application of phage nanomaterials in the context of tissue engineering, sensing, and probing.
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Affiliation(s)
- Seong-Min Kim
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Hye Ryoung Heo
- Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, Republic of Korea
| | - Chang Sup Kim
- Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, Republic of Korea
| | - Hwa Hui Shin
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
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3
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França RKA, Studart IC, Bezerra MRL, Pontes LQ, Barbosa AMA, Brigido MM, Furtado GP, Maranhão AQ. Progress on Phage Display Technology: Tailoring Antibodies for Cancer Immunotherapy. Viruses 2023; 15:1903. [PMID: 37766309 PMCID: PMC10536222 DOI: 10.3390/v15091903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The search for innovative anti-cancer drugs remains a challenge. Over the past three decades, antibodies have emerged as an essential asset in successful cancer therapy. The major obstacle in developing anti-cancer antibodies is the need for non-immunogenic antibodies against human antigens. This unique requirement highlights a disadvantage to using traditional hybridoma technology and thus demands alternative approaches, such as humanizing murine monoclonal antibodies. To overcome these hurdles, human monoclonal antibodies can be obtained directly from Phage Display libraries, a groundbreaking tool for antibody selection. These libraries consist of genetically engineered viruses, or phages, which can exhibit antibody fragments, such as scFv or Fab on their capsid. This innovation allows the in vitro selection of novel molecules directed towards cancer antigens. As foreseen when Phage Display was first described, nowadays, several Phage Display-derived antibodies have entered clinical settings or are undergoing clinical evaluation. This comprehensive review unveils the remarkable progress in this field and the possibilities of using clever strategies for phage selection and tailoring the refinement of antibodies aimed at increasingly specific targets. Moreover, the use of selected antibodies in cutting-edge formats is discussed, such as CAR (chimeric antigen receptor) in CAR T-cell therapy or ADC (antibody drug conjugate), amplifying the spectrum of potential therapeutic avenues.
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Affiliation(s)
- Renato Kaylan Alves França
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.F.); (M.M.B.)
- Graduate Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Igor Cabral Studart
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza 60440-970, Brazil
| | - Marcus Rafael Lobo Bezerra
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza 60440-970, Brazil
| | - Larissa Queiroz Pontes
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza 60440-970, Brazil
| | - Antonio Marcos Aires Barbosa
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Applied Informatics, University of Fortaleza, Fortaleza 60811-905, Brazil
| | - Marcelo Macedo Brigido
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.F.); (M.M.B.)
| | - Gilvan Pessoa Furtado
- Oswaldo Cruz Foundation, Fiocruz Ceará, Eusébio 61773-270, Brazil; (I.C.S.); (M.R.L.B.); (L.Q.P.); (A.M.A.B.); (G.P.F.)
- Graduate Program in Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza 60440-970, Brazil
| | - Andréa Queiroz Maranhão
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.F.); (M.M.B.)
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Rafique A, Hichiwa G, Jatnika MF, Ito Y. A Novel Strategy for Screening Tumor-Specific Variable Domain of Heavy-Chain Antibodies. Int J Mol Sci 2023; 24:10804. [PMID: 37445977 DOI: 10.3390/ijms241310804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
The properties of the variable domain of heavy-chain (VHH) antibodies are particularly relevant in cancer therapy. To isolate tumor cell-specific VHH antibodies, VHH phage libraries were constructed from multiple tumor cells. After enriching the libraries against particular tumor cell lines, a next-generation sequencer was used to screen the pooled phages of each library for potential antibody candidates. Based on high amplification folds, 50 sequences from each library were used to construct phylogenetic trees. Several clusters with identical CDR3 were observed. Groups X, Y, and Z were assigned as common sequences among the different trees. These identical groups over the trees were considered to be cross-reactive antibodies. To obtain monoclonal antibodies, we assembled 200 sequences (top 50 sequences from each library) and rebuilt a combined molecular phylogenetic tree. Groups were categorized as A-G. For each group, we constructed a phagemid and determined its binding specificity with tumor cells. The phage-binding results were consistent with the phylogenetic tree-generated groups, which indicated particular tumor-specific clusters; identical groups showed cross-reactivity. The strategy used in the current study is effective for screening and isolating monoclonal antibodies. Specific antibodies can be identified, even when the target markers of cancer cells are unknown.
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Affiliation(s)
- Abdur Rafique
- Graduate School of Science and Engineering, University of Kagoshima, Kagoshima 890-0065, Japan
| | - Genki Hichiwa
- Graduate School of Medical Sciences, Tottori University, Tottori 680-8550, Japan
| | - Muhammad Feisal Jatnika
- Graduate School of Science and Engineering, University of Kagoshima, Kagoshima 890-0065, Japan
| | - Yuji Ito
- Graduate School of Science and Engineering, University of Kagoshima, Kagoshima 890-0065, Japan
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Depth of Sequencing Plays a Determining Role in the Characterization of Phage Display Peptide Libraries by NGS. Int J Mol Sci 2023; 24:ijms24065396. [PMID: 36982469 PMCID: PMC10049078 DOI: 10.3390/ijms24065396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/27/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Next-generation sequencing (NGS) has raised a growing interest in phage display research. Sequencing depth is a pivotal parameter for using NGS. In the current study, we made a side-by-side comparison of two NGS platforms with different sequencing depths, denoted as lower-throughput (LTP) and higher-throughput (HTP). The capacity of these platforms for characterization of the composition, quality, and diversity of the unselected Ph.D.TM-12 Phage Display Peptide Library was investigated. Our results indicated that HTP sequencing detects a considerably higher number of unique sequences compared to the LTP platform, thus covering a broader diversity of the library. We found a larger percentage of singletons, a smaller percentage of repeated sequences, and a greater percentage of distinct sequences in the LTP datasets. These parameters suggest a higher library quality, resulting in potentially misleading information when using LTP sequencing for such assessment. Our observations showed that HTP reveals a broader distribution of peptide frequencies, thus revealing increased heterogeneity of the library by the HTP approach and offering a comparatively higher capacity for distinguishing peptides from each other. Our analyses suggested that LTP and HTP datasets show discrepancies in their peptide composition and position-specific distribution of amino acids within the library. Taken together, these findings lead us to the conclusion that a higher sequencing depth can yield more in-depth insights into the composition of the library and provide a more complete picture of the quality and diversity of phage display peptide libraries.
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6
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Caballero LR, Treudler R, Delaroque N, Simon JC, Kern K, Szardenings M. Peptide epitopes as biomarkers of soya sensitization in rBet v 1 immunotherapy of birch-related soya allergy. Clin Exp Allergy 2023; 53:316-326. [PMID: 36102274 DOI: 10.1111/cea.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/16/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND There are no diagnostic and/or prognostic markers of the treatment outcome in patients receiving allergen immunotherapy (AIT). Although numerous allergen epitopes are known, their value in this context has not been investigated. This paper deals with re-evaluation of sera from patients who underwent AIT against rBet v 1 for treatment of their soya allergy (BASALIT trial). OBJECTIVE To evaluate the diagnostic and/or prognostic potential of allergen epitopes recognition by antibodies from patients with birch-related soya allergy before and after rBet v 1-immunotherapy. METHODS PR-10 epitope-binding profiles from 34 patients were identified in silico using a statistical peptide phage display at start and at end of AIT. IgE- and IgG-binding to these peptide epitopes was measured in peptide microarrays. Clinical relevance of epitopes was evaluated by comparing these measurements to a number of treatment outcome measures recorded during double-blind placebo-controlled food challenge at start and end of AIT. RESULTS We showed that IgG- and IgE-recognition of peptide epitopes after AIT were surrogate markers of 5 out of 12 analysed treatment outcome measures using this patient cohort. Seven epitopes were identified from multiple PR-10 allergen sequences. Twenty-six peptide epitopes were used for IgG and IgE measurements. IgE-binding to one of the epitopes was associated with stronger intensity of oral tingling/itching after ingesting soya at start of AIT. IgG recognizing two other epitopes at start of AIT could predict decreased Cor a 1-specific IgE concentration (p = .043) and decreased lip swelling intensity (p = .016) after AIT. Tolerance to increasing amounts of soy at food challenge correlated with IgG-binding to another epitope at start of AIT (p = .046). CONCLUSION IgG- and IgE-binding to peptide epitopes in PR-10 is a potential indicator of the outcome and clinical course of AIT of soya-sensitized patients with rBet v 1.
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Affiliation(s)
| | - Regina Treudler
- Leipzig Comprehensive Allergy Center LICA-CAC, Department of Dermatology, Venereology and Allergology, University of Leipzig, Leipzig, Germany
| | - Nicolas Delaroque
- Ligand Development Unit, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
| | - Jan C Simon
- Leipzig Comprehensive Allergy Center LICA-CAC, Department of Dermatology, Venereology and Allergology, University of Leipzig, Leipzig, Germany
| | - Karolin Kern
- Ligand Development Unit, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
| | - Michael Szardenings
- Ligand Development Unit, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
- epitopic GmbH, Leipzig, Germany
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7
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He S, Lim GE. The Application of High-Throughput Approaches in Identifying Novel Therapeutic Targets and Agents to Treat Diabetes. Adv Biol (Weinh) 2023; 7:e2200151. [PMID: 36398493 DOI: 10.1002/adbi.202200151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Indexed: 11/19/2022]
Abstract
During the past decades, unprecedented progress in technologies has revolutionized traditional research methodologies. Among these, advances in high-throughput drug screening approaches have permitted the rapid identification of potential therapeutic agents from drug libraries that contain thousands or millions of molecules. Moreover, high-throughput-based therapeutic target discovery strategies can comprehensively interrogate relationships between biomolecules (e.g., gene, RNA, and protein) and diseases and significantly increase the authors' knowledge of disease mechanisms. Diabetes is a chronic disease primarily characterized by the incapacity of the body to maintain normoglycemia. The prevalence of diabetes in modern society has become a severe public health issue that threatens the well-being of millions of patients. Although a number of pharmacological treatments are available, there is no permanent cure for diabetes, and discovering novel therapeutic targets and agents continues to be an urgent need. The present review discusses the technical details of high-throughput screening approaches in drug discovery, followed by introducing the applications of such approaches to diabetes research. This review aims to provide an example of the applicability of high-throughput technologies in facilitating different aspects of disease research.
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Affiliation(s)
- Siyi He
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
| | - Gareth E Lim
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
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Nagy K, McBride R, Head SR, Ordoukhanian P, Law M. Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes. Methods Mol Biol 2023; 2578:63-81. [PMID: 36152281 DOI: 10.1007/978-1-0716-2732-7_6] [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
Understanding antibody specificity and defining response profiles to antigens continue to be essential to both vaccine research and therapeutic antibody development. Peptide scanning assays enable mapping of continuous epitopes in order to delineate antibody-antigen interactions beyond traditional immunoassay formats. We have developed a relatively low-cost method to generate peptide microarray slides for antibody binding studies that allow for interrogation of up to 1536 overlapping peptides derived from the target antigens on a single microslide. Using an IntavisAG MultiPep RS peptide synthesizer and a Digilab MicroGrid II 600 microarray printer robot, each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface. Interrogation of the surface can then be performed using polyclonal immune sera or monoclonal antibodies, and sensitive detection using an InnoScan 1100 AL scanner with fluorescent-conjugated secondary reagents maximizes conservation of reagents.
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Affiliation(s)
- Kenna Nagy
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan McBride
- Genomics Core, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven R Head
- Genomics Core, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Mansun Law
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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Zhang X, Li S, Luo H, He S, Yang H, Li L, Tian T, Han Q, Ye J, Huang C, Liu A, Jiang Y. Identification of heptapeptides targeting a lethal bacterial strain in septic mice through an integrative approach. Signal Transduct Target Ther 2022; 7:245. [PMID: 35871689 PMCID: PMC9309159 DOI: 10.1038/s41392-022-01035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/06/2022] [Accepted: 05/18/2022] [Indexed: 11/11/2022] Open
Abstract
Effectively killing pathogenic bacteria is key for the treatment of sepsis. Although various anti-infective drugs have been used for the treatment of sepsis, the therapeutic effect is largely limited by the lack of a specific bacterium-targeting delivery system. This study aimed to develop antibacterial peptides that specifically target pathogenic bacteria for the treatment of sepsis. The lethal bacterial strain Escherichia coli MSI001 was isolated from mice of a cecal ligation and puncture (CLP) model and was used as a target to screen bacterial binding heptapeptides through an integrative bioinformatics approach based on phage display technology and high-throughput sequencing (HTS). Heptapeptides binding to E. coli MSI001 with high affinity were acquired after normalization by the heptapeptide frequency of the library. A representative heptapeptide VTKLGSL (VTK) was selected for fusion with the antibacterial peptide LL-37 to construct the specific-targeting antibacterial peptide VTK-LL37. We found that, in comparison with LL37, VTK-LL37 showed prominent bacteriostatic activity and an inhibitive effect on biofilm formation in vitro. In vivo experiments demonstrated that VTK-LL37 significantly inhibited bacterial growth, reduced HMGB1 expression, alleviated lesions of vital organs and improved the survival of mice subjected to CLP modeling. Furthermore, membrane DEGP and DEGQ were identified as VTK-binding proteins by proteomic methods. This study provides a novel strategy for targeted pathogen killing, which is helpful for the treatment of sepsis in the era of precise medicine.
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Weiss Z, DasGupta S. REVERSE: a user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments. Nucleic Acids Res 2022; 50:W639-W650. [PMID: 35699225 PMCID: PMC9252737 DOI: 10.1093/nar/gkac508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/22/2022] [Accepted: 05/27/2022] [Indexed: 11/14/2022] Open
Abstract
Next-generation sequencing (NGS) enables the identification of functional nucleic acid sequences from in vitro selection/evolution experiments and illuminates the evolutionary process at single-nucleotide resolution. However, analyzing the vast output from NGS can be daunting, especially with limited programming skills. We developed REVERSE (Rapid EValuation of Experimental RNA Selection/Evolution) (https://www.reverseserver.org/), a web server that implements an integrated computational pipeline through a graphical user interface, which performs both pre-processing and detailed sequence level analyses within minutes. Raw FASTQ files are quality-filtered, dereplicated, and trimmed before being analyzed by either of two pipelines. The first pipeline counts, sorts, and tracks enrichment of unique sequences and user-defined sequence motifs. It also identifies mutational intermediates present in the sequence data that connect two input sequences. The second pipeline sorts similar sequences into clusters and tracks enrichment of peak sequences. It also performs nucleotide conservation analysis on the cluster of choice and generates a consensus sequence. Both pipelines generate downloadable spreadsheets and high-resolution figures. Collectively, REVERSE is a one-stop solution for the rapid analysis of NGS data obtained from in vitro selection/evolution experiments that obviates the need for computational expertise.
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Affiliation(s)
- Zoe Weiss
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Saurja DasGupta
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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11
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McLure RJ, Radford SE, Brockwell DJ. High-throughput directed evolution: a golden era for protein science. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Kulkarni A, Mochnáčová E, Majerova P, Čurlík J, Bhide K, Mertinková P, Bhide M. Single Domain Antibodies Targeting Receptor Binding Pockets of NadA Restrain Adhesion of Neisseria meningitidis to Human Brain Microvascular Endothelial Cells. Front Mol Biosci 2020; 7:573281. [PMID: 33425985 PMCID: PMC7785856 DOI: 10.3389/fmolb.2020.573281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/03/2020] [Indexed: 01/02/2023] Open
Abstract
Neisseria adhesin A (NadA), one of the surface adhesins of Neisseria meningitides (NM), interacts with several cell types including human brain microvascular endothelial cells (hBMECs) and play important role in the pathogenesis. Receptor binding pockets of NadA are localized on the globular head domain (A33 to K69) and the first coiled-coil domain (L121 to K158). Here, the phage display was used to develop a variable heavy chain domain (VHH) that can block receptor binding sites of recombinant NadA (rec-NadA). A phage library displaying VHH was panned against synthetic peptides (NadA-gdA33−K69 or NadA-ccL121−K158), gene encoding VHH was amplified from bound phages and re-cloned in the expression vector, and the soluble VHHs containing disulfide bonds were overexpressed in the SHuffle E. coli. From the repertoire of 96 clones, two VHHs (VHHF3–binding NadA-gdA33−K69 and VHHG9–binding NadA-ccL121−K158) were finally selected as they abrogated the interaction between rec-NadA and the cell receptor. Preincubation of NM with VHHF3 and VHHG9 significantly reduced the adhesion of NM on hBMECs in situ and hindered the traversal of NM across the in-vitro BBB model. The work presents a phage display pipeline with a single-round of panning to select receptor blocking VHHs. It also demonstrates the production of soluble and functional VHHs, which blocked the interaction between NadA and its receptor, decreased adhesion of NM on hBMECs, and reduced translocation of NM across BBB in-vitro. The selected NadA blocking VHHs could be promising molecules for therapeutic translation.
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Affiliation(s)
- Amod Kulkarni
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.,Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Evelína Mochnáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Ján Čurlík
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Patrícia Mertinková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.,Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
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Üzülmez Ö, Kalic T, Breiteneder H. Advances and novel developments in molecular allergology. Allergy 2020; 75:3027-3038. [PMID: 32882057 PMCID: PMC7756543 DOI: 10.1111/all.14579] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022]
Abstract
The continuous search for new allergens and the design of allergen derivatives improves the understanding of their allergenicity and aids the design of novel diagnostic and immunotherapy approaches. This article discusses the recent developments in allergen and epitope discovery, allergy diagnostics and immunotherapy. Structural information is crucial for the elucidation of cross-reactivity of marker allergens such as the walnut Jug r 6 or that of nonhomologous allergens, as shown for the peanut allergens Ara h 1 and 2. High-throughput sequencing, liposomal nanoallergen display, bead-based assays, and protein chimeras have been used in epitope discovery. The binding of natural ligands by the birch pollen allergen Bet v 1 or the mold allergen Alt a 1 increased the stability of these allergens, which is directly linked to their allergenicity. We also report recent findings on the use of component-resolved approaches, basophil activation test, and novel technologies for improvement of diagnostics. New strategies in allergen-specific immunotherapy have also emerged, such as the use of virus-like particles, biologics or novel adjuvants. The identification of dectin-1 as a key player in allergy to tropomyosins and the formyl peptide receptor 3 in allergy to lipocalins are outstanding examples of research into the mechanism of allergic sensitization.
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Affiliation(s)
- Öykü Üzülmez
- Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
| | - Tanja Kalic
- Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
| | - Heimo Breiteneder
- Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
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von Witting E, Lindbo S, Lundqvist M, Möller M, Wisniewski A, Kanje S, Rockberg J, Tegel H, Åstrand M, Uhlén M, Hober S. Small Bispecific Affinity Proteins for Simultaneous Target Binding and Albumin-Associated Half-Life Extension. Mol Pharm 2020; 18:328-337. [PMID: 33259222 PMCID: PMC9490751 DOI: 10.1021/acs.molpharmaceut.0c00975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Albumin-binding fusion partners are
frequently used as a means
for the in vivo half-life extension of small therapeutic
molecules that would normally be cleared very rapidly from circulation.
However, in applications where small size is key, fusion to an additional
molecule can be disadvantageous. Albumin-derived affinity proteins
(ADAPTs) are a new type of scaffold proteins based on one of the albumin-binding
domains of streptococcal protein G, with engineered binding specificities
against numerous targets. Here, we engineered this scaffold further
and showed that this domain, as small as 6 kDa, can harbor two distinct
binding surfaces and utilize them to interact with two targets simultaneously.
These novel ADAPTs were developed to possess affinity toward both
serum albumin as well as another clinically relevant target, thus
circumventing the need for an albumin-binding fusion partner. To accomplish
this, we designed a phage display library and used it to successfully
select for single-domain bispecific binders toward a panel of targets:
TNFα, prostate-specific antigen (PSA), C-reactive protein (CRP),
renin, angiogenin, myeloid-derived growth factor (MYDGF), and insulin.
Apart from successfully identifying bispecific binders for all targets,
we also demonstrated the formation of the ternary complex consisting
of the ADAPT together with albumin and each of the five targets, TNFα,
PSA, angiogenin, MYDGF, and insulin. This simultaneous binding of
albumin and other targets presents an opportunity to combine the advantages
of small molecules with those of larger ones allowing for lower cost
of goods and noninvasive administration routes while still maintaining
a sufficient in vivo half-life.
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Affiliation(s)
- Emma von Witting
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Sarah Lindbo
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Magnus Lundqvist
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Marit Möller
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Andreas Wisniewski
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Sara Kanje
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Johan Rockberg
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Hanna Tegel
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Mikael Åstrand
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Mathias Uhlén
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Sophia Hober
- Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm 10691, Sweden
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15
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Tyagi A, Daliri EBM, Kwami Ofosu F, Yeon SJ, Oh DH. Food-Derived Opioid Peptides in Human Health: A Review. Int J Mol Sci 2020; 21:E8825. [PMID: 33233481 PMCID: PMC7700510 DOI: 10.3390/ijms21228825] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
World Health Organization data suggest that stress, depression, and anxiety have a noticeable prevalence and are becoming some of the most common causes of disability in the Western world. Stress-related disorders are considered to be a challenge for the healthcare system with their great economic and social impact. The knowledge on these conditions is not very clear among many people, as a high proportion of patients do not respond to the currently available medications for targeting the monoaminergic system. In addition, the use of clinical drugs is also associated with various side effects such as vomiting, dizziness, sedation, nausea, constipation, and many more, which prevents their effective use. Therefore, opioid peptides derived from food sources are becoming one of the safe and natural alternatives because of their production from natural sources such as animals and plant proteins. The requirement for screening and considering dietary proteins as a source of bioactive peptides is highlighted to understand their potential roles in stress-related disorders as a part of a diet or as a drug complementing therapeutic prescription. In this review, we discussed current knowledge on opioid endogenous and exogenous peptides concentrating on their production, purification, and related studies. To fully understand their potential in stress-related conditions, either as a drug or as a therapeutic part of a diet prescription, the need to screen more dietary proteins as a source of novel opioid peptides is emphasized.
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Affiliation(s)
| | | | | | | | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 200-701, Korea; (A.T.); (E.B.-M.D.); (F.K.O.); (S.-J.Y.)
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16
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Chang YC, Kao CY, Tang HC, Huang MS, Mou KY. Direct Antibody Isolation on Cells Using Affinity-Tag-Guided Proximity Selection. Biochemistry 2020; 59:4285-4293. [DOI: 10.1021/acs.biochem.0c00730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- You-Chiun Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Yi Kao
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11529, Taiwan
| | - Hao-Cheng Tang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Meng-Sen Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Kurt Yun Mou
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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17
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Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction. Nat Commun 2020; 11:4414. [PMID: 32887877 PMCID: PMC7473865 DOI: 10.1038/s41467-020-18204-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/12/2020] [Indexed: 02/03/2023] Open
Abstract
CD4+ helper T cells contribute important functions to the immune response during pathogen infection and tumor formation by recognizing antigenic peptides presented by class II major histocompatibility complexes (MHC-II). While many computational algorithms for predicting peptide binding to MHC-II proteins have been reported, their performance varies greatly. Here we present a yeast-display-based platform that allows the identification of over an order of magnitude more unique MHC-II binders than comparable approaches. These peptides contain previously identified motifs, but also reveal new motifs that are validated by in vitro binding assays. Training of prediction algorithms with yeast-display library data improves the prediction of peptide-binding affinity and the identification of pathogen-associated and tumor-associated peptides. In summary, our yeast-display-based platform yields high-quality MHC-II-binding peptide datasets that can be used to improve the accuracy of MHC-II binding prediction algorithms, and potentially enhance our understanding of CD4+ T cell recognition. Identifying peptides that can bind major histocompatibility complex II (MHC-II) is important for our understanding of T cell immunity and specificity. Here the authors present a yeast-display library screening approach that identifies more potential binders than various reported algorithms to help expand our understanding for antigen presentation.
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18
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Ramírez Caballero L, Kny C, Treudler R, Simon JC, Kern K, Jappe U, Szardenings M. Identification of Seasonal Variations of Antibodies against PR-10-Specific Epitopes Can Be Improved Using Peptide-Phage Display. Int Arch Allergy Immunol 2020; 181:919-925. [PMID: 32846424 DOI: 10.1159/000509995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/08/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In pollinosis patients, allergen-specific antibody titers show seasonal variations. Little is known about these variations at the epitope level. OBJECTIVES We aimed at investigating seasonal variations on the level of allergen epitope recognition in patients with Bet v 1-related food allergy using a peptide phage display approach. METHODS Serum samples collected over 1 year from 4 patients of the placebo arm of the birch-associated soya allergy immunotherapy trial were included. To identify epitopes from Bet v 1-related food allergens, patient sera were used in peptide phage display experiments. In silico analysis of enriched allergen-related motifs was performed. RESULTS We identified epitope motifs related to Bet v 1 and its homologs in soya and hazelnut (Gly m 4 and Cor a 1, respectively) that were enriched in accordance with birch and hazel pollen exposure. Within several weeks after the birch pollen season peak, the pattern of identified epitope motifs differed considerably among patients. Data for amino acid preferences in homologous Bet v 1 and Cor a 1 epitope motifs identified for one of the investigated patients suggest changes in concentration or specificity of serum antibodies for the Cor a 1 epitope motif. CONCLUSIONS Peptide phage display data suggest an impact of birch and hazel pollen exposure on the recognition pattern of Bet v 1-like allergen epitopes. Epitope-oriented analyses could provide deeper, personalized details regarding the allergen epitope recognition influenced by pollen exposure beyond the capability of current methods.
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Affiliation(s)
| | - Christoph Kny
- Ligand Development Unit, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
| | - Regina Treudler
- Leipzig Comprehensive Allergy Center LICA-CAC, Department of Dermatology, Venereology and Allergology, University of Leipzig, Leipzig, Germany
| | - Jan C Simon
- Leipzig Comprehensive Allergy Center LICA-CAC, Department of Dermatology, Venereology and Allergology, University of Leipzig, Leipzig, Germany
| | - Karolin Kern
- Ligand Development Unit, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
| | - Uta Jappe
- Division of Clinical and Molecular Allergology, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research, Borstel, Germany.,Interdisciplinary Outpatient Clinic, Department of Pneumology, University of Lübeck, Lübeck, Germany
| | - Michael Szardenings
- Ligand Development Unit, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany,
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19
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Kodama T, Yoshihara A, Goel I, Sekino M, Kuwahata A, Yoshimori A, Murayama Y, Ishihara K, Ekdahl KN, Nilsson B, Teramura Y. Identification of Metal-Binding Peptides and Their Conjugation onto Nanoparticles of Superparamagnetic Iron Oxides and Liposomes. ACS APPLIED MATERIALS & INTERFACES 2020; 12:24623-24634. [PMID: 32375468 DOI: 10.1021/acsami.0c06138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metallic materials are used for clinical medical devices such as vascular stents and coils to treat both ischemic and hemorrhagic vascular diseases. An antiplatelet drug is required to avoid thromboembolic complication until metallic surface is covered with a neo-endothelial cell layer. It is important to identify endothelial cell coverage on the metallic surface. However, it is difficult since there are no selective ligands. Here, we used the phage display method to identify peptide ligands that had high affinity for the metallic surface of Ni-Ti stents, Pt-W coils, and Co-Cr stents. The binding assay using fluorescence labeling revealed that several synthetic peptides could bind onto those surfaces. We also chose some oligopeptides for the conjugation onto superparamagnetic iron oxide (SPIO) nanoparticles and liposome-encapsulating SPIO nanoparticles and studied their ability to bind to the stent and coils. By SEM and fluorophotometry, we found that those modified SPIOs and liposomes were selectively bound onto those surfaces. In addition, both treated stents and coils could be detected by magnetic resonance imaging due to the magnetic artifact through the SPIOs and liposomes that were immobilized onto the surface. Thus, we identified metal-binding peptides which may enable to stop antiplatelet therapy after vascular stenting or coiling.
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Affiliation(s)
- Tomonobu Kodama
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Neurosurgery, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Akifumi Yoshihara
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Isha Goel
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masaki Sekino
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Electrical Engineering and Information Systems, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Akihiro Kuwahata
- Department of Electrical Engineering and Information Systems, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Yuichi Murayama
- Department of Neurosurgery, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Kazuhiko Ishihara
- Department of Material Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kristina N Ekdahl
- Department of Immunology, Genetics and Pathology (IGP), Uppsala University, Dag Hammarskjölds väg 20, SE-751 85 Uppsala, Sweden
- Linnaeus Center of Biomaterials Chemistry, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Bo Nilsson
- Department of Immunology, Genetics and Pathology (IGP), Uppsala University, Dag Hammarskjölds väg 20, SE-751 85 Uppsala, Sweden
| | - Yuji Teramura
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Immunology, Genetics and Pathology (IGP), Uppsala University, Dag Hammarskjölds väg 20, SE-751 85 Uppsala, Sweden
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20
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Comparison of motif-based and whole-unique-sequence-based analyses of phage display library datasets generated by biopanning of anti-Borrelia burgdorferi immune sera. PLoS One 2020; 15:e0226378. [PMID: 31940357 PMCID: PMC6961823 DOI: 10.1371/journal.pone.0226378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/25/2019] [Indexed: 11/19/2022] Open
Abstract
Detection of protection-associated epitopes via reverse vaccinology is the first step for development of subunit vaccines against microbial pathogens. Mapping subunit vaccine targets requires high throughput methods, which would allow delineation of epitopes recognized by protective antibodies on a large scale. Phage displayed random peptide library coupled to Next Generation Sequencing (PDRPL/NGS) is the universal platform that enables high-yield identification of peptides that mimic epitopes (mimotopes). Despite being unsurpassed as a tool for discovery of polyclonal serum mimotopes, the PDRPL/NGS is far inferior as a quantitative method of immune response. Difficult-to-control fluctuations in amounts of antibody-bound phages after rounds of selection and amplification diminish the quantitative capacity of the PDRPL/NGS. In an attempt to improve the accuracy of the PDRPL/NGS method, we compared the discriminating capacity of two approaches for PDRPL/NGS data analysis. The whole-unique-sequence-based analysis (WUSA) involved generation of 7-mer peptide profiles and comparison of the numbers of sequencing reads for unique peptide sequences between serum samples. The motif-based analysis (MA) included identification of 4-mer consensus motifs unifying unique 7-mer sequences and comparison of motifs between serum samples. The motif comparison was based not on the numbers of sequencing reads, but on the numbers of distinct 7-mers constituting the motifs. Our PDRPL/NGS datasets generated from biopanning of protective and non-protective anti-Borrelia burgdorferi sera of New Zealand rabbits were used to contrast the two approaches. As a result, the principle component analyses (PCA) showed that the discriminating powers of the WUSA and MA were similar. In contrast, the unsupervised hierarchical clustering obtained via the MA classified the preimmune, non-protective, and protective sera better than the WUSA-based clustering. Also, a total number of discriminating motifs was higher than that of discriminating 7-mers. In sum, our results indicate that MA approach improves the accuracy and quantitative capacity of the PDRPL/NGS method.
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Canassa-DeLeo T, Campo VL, Rodrigues LC, Marchiori MF, Fuzo C, Brigido MM, Sandomenico A, Ruvo M, Maranhão AQ, Dias-Baruffi M. Multifaceted antibodies development against synthetic α-dystroglycan mucin glycopeptide as promising tools for dystroglycanopathies diagnostic. Glycoconj J 2019; 37:77-93. [PMID: 31823246 DOI: 10.1007/s10719-019-09893-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 01/19/2023]
Abstract
Dystroglycanopathies are diseases characterized by progressive muscular degeneration and impairment of patient's quality of life. They are associated with altered glycosylation of the dystrophin-glycoprotein (DGC) complex components, such as α-dystroglycan (α-DG), fundamental in the structural and functional stability of the muscle fiber. The diagnosis of dystroglycanopathies is currently based on the observation of clinical manifestations, muscle biopsies and enzymatic measures, and the available monoclonal antibodies are not specific for the dystrophic hypoglycosylated muscle condition. Thus, modified α-DG mucins have been considered potential targets for the development of new diagnostic strategies toward these diseases. In this context, this work describes the synthesis of the hypoglycosylated α-DG mimetic glycopeptide NHAc-Gly-Pro-Thr-Val-Thr[αMan]-Ile-Arg-Gly-BSA (1) as a potential tool for the development of novel antibodies applicable to dystroglycanopathies diagnosis. Glycopeptide 1 was used for the development of polyclonal antibodies and recombinant monoclonal antibodies by Phage Display technology. Accordingly, polyclonal antibodies were reactive to glycopeptide 1, which enables the application of anti-glycopeptide 1 antibodies in immune reactive assays targeting hypoglycosylated α-DG. Regarding monoclonal antibodies, for the first time variable heavy (VH) and variable light (VL) immunoglobulin domains were selected by Phage Display, identified by NGS and described by in silico analysis. The best-characterized VH and VL domains were cloned, expressed in E. coli Shuffle T7 cells, and used to construct a single chain fragment variable that recognized the Glycopeptide 1 (GpαDG1 scFv). Molecular modelling of glycopeptide 1 and GpαDG1 scFv suggested that their interaction occurs through hydrogen bonds and hydrophobic contacts involving amino acids from scFv (I51, Y33, S229, Y235, and P233) and R8 and α-mannose from Glycopeptide 1.
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Affiliation(s)
- Thais Canassa-DeLeo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Vanessa Leiria Campo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil.,Centro Universitário Barão de Mauá, Rua Ramos de Azevedo 423, Jardim Paulista, CEP, Ribeirão Preto, 14090-180, SP, Brazil
| | - Lílian Cataldi Rodrigues
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marcelo Fiori Marchiori
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Carlos Fuzo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marcelo Macedo Brigido
- Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, DF, CEP 70910-900, Brazil
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Andrea Queiroz Maranhão
- Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, DF, CEP 70910-900, Brazil
| | - Marcelo Dias-Baruffi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil.
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Xi J, He M, Pi J. Identification of antigenic sites destructed by high hydrostatic pressure (HHP) of the β subunit of β-conglycinin. Int J Biol Macromol 2019; 141:1287-1292. [PMID: 31499107 DOI: 10.1016/j.ijbiomac.2019.09.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 02/02/2023]
Abstract
β-conglycinin is one of the most allergenic proteins, and its constituent subunits α', α, and β are all potential allergens to humans. In the present study, we concentrated on the destructed antigenic sites of β subunit of β-conglycinin after high hydrostatic pressure (HHP) treatment. In this paper, the overlapping gene fragments of the β subunit of β-conglycinin were amplified by polymerase chain reaction (PCR) and cloned into T7 phage vectors. After being packaged in vitro, the recombinant T7 phage was constructed, and the overlapping fragments of the β subunit were displayed on the phage surface. The recombinant phages that expressed the overlapping fragments of the β subunit were used to react with specific antiserum by indirect ELISA to identify the HHP destructed antigenic sites. After three rounds of expression and identification, we used synthetic peptide technology to identify that the obtained fragment was a conformational epitope. We further confirmed that HHP treatment changed the conformational structure of β-conglycinin, which reduced the antigenicity of the protein.
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Affiliation(s)
- Jun Xi
- Engineering Technology Research Center for Grain & Oil Food, State Administration of Grain, School of Food Science and Technology, Henan University of Technology, Zhengzhou 450001, Henan, China.
| | - MengXue He
- Engineering Technology Research Center for Grain & Oil Food, State Administration of Grain, School of Food Science and Technology, Henan University of Technology, Zhengzhou 450001, Henan, China
| | - JiangYi Pi
- Engineering Technology Research Center for Grain & Oil Food, State Administration of Grain, School of Food Science and Technology, Henan University of Technology, Zhengzhou 450001, Henan, China
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23
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Eiwegger T, Hung L, San Diego KE, O'Mahony L, Upton J. Recent developments and highlights in food allergy. Allergy 2019; 74:2355-2367. [PMID: 31593325 DOI: 10.1111/all.14082] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/03/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023]
Abstract
The achievement of long-lasting, safe treatments for food allergy is dependent on the understanding of the immunological basis of food allergy. Accurate diagnosis is essential for management. In recent years, data from oral food challenges have revealed that routine allergy testing is poor at predicting clinical allergy for tree nuts, almonds in particular. More advanced antigen-based tests including component-resolved diagnostics and epitope reactivity may lead to more accurate diagnosis and selection of therapeutic intervention. Additional diagnostic accuracy may come from cellular tests such as the basophil activation test or mast cell approaches. In the context of clinical trials, cellular tests have revealed specific T-cell and B-cell populations that are more abundant in food-allergic individuals with distinct mechanistic features. Awareness of clinical markers, such as the ability to eat baked forms of milk and egg, continues to inform the understanding of natural tolerance development. Mouse models have allowed for investigation into multiple mechanisms of food allergy including modification of epithelial metabolism, and the induction of regulatory cell subsets and the microbiome. Increasing numbers of children who underwent food immunotherapy enlarged the body of evidence on mechanisms and predictors of treatment success. Experimental immunological markers in conjunction with clinical determinants such as lower age and lower initial specific IgE appear to be of benefit. More research on the optimal dose, preparation, and route of application integrating a high-level safety and efficacy is demanded. Alternatively, biologics blocking TSLP, IL-33, IL-4 and IL-13, or IgE may help to achieve that.
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Affiliation(s)
- Thomas Eiwegger
- Translational Medicine Program Research Institute Hospital for Sick Children Toronto ON Canada
- Department of Immunology University of Toronto Toronto ON Canada
- Division of Immunology and Allergy Food Allergy and Anaphylaxis Program Departments of Paediatrics The Hospital for Sick Children University of Toronto Toronto ON Canada
| | - Lisa Hung
- Translational Medicine Program Research Institute Hospital for Sick Children Toronto ON Canada
- Department of Immunology University of Toronto Toronto ON Canada
| | | | - Liam O'Mahony
- Departments of Medicine and Microbiology APC Microbiome Ireland National University of Ireland Cork Ireland
| | - Julia Upton
- Translational Medicine Program Research Institute Hospital for Sick Children Toronto ON Canada
- Division of Immunology and Allergy Food Allergy and Anaphylaxis Program Departments of Paediatrics The Hospital for Sick Children University of Toronto Toronto ON Canada
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Wu FL, Lai DY, Ding HH, Tang YJ, Xu ZW, Ma ML, Guo SJ, Wang JF, Shen N, Zhao XD, Qi H, Li H, Tao SC. Identification of Serum Biomarkers for Systemic Lupus Erythematosus Using a Library of Phage Displayed Random Peptides and Deep Sequencing. Mol Cell Proteomics 2019; 18:1851-1863. [PMID: 31308251 PMCID: PMC6731078 DOI: 10.1074/mcp.ra119.001582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/01/2019] [Indexed: 12/26/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is one of the most serious autoimmune diseases, characterized by highly diverse clinical manifestations. A biomarker is still needed for accurate diagnostics. SLE serum autoantibodies were discovered and validated using serum samples from independent sample cohorts encompassing 306 participants divided into three groups, i.e. healthy, SLE patients, and other autoimmune-related diseases. To discover biomarkers for SLE, a phage displayed random peptide library (Ph.D. 12) and deep sequencing were applied to screen specific autoantibodies in a total of 100 serum samples from 50 SLE patients and 50 healthy controls. A statistical analysis protocol was set up for the identification of peptides as potential biomarkers. For validation, 10 peptides were analyzed using enzyme-linked immunosorbent assays (ELISA). As a result, four peptides (SLE2018Val001, SLE2018Val002, SLE2018Val006, and SLE2018Val008) were discovered with high diagnostic power to differentiate SLE patients from healthy controls. Among them, two peptides, i.e. SLE2018Val001 and SLE2018Val002, were confirmed between SLE with other autoimmune patients. The procedure we established could be easily adopted for the identification of autoantibodies as biomarkers for many other diseases.
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Affiliation(s)
- Fan-Lin Wu
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; ¶School of Agriculture, Ludong University, Yantai 264025, China
| | - Dan-Yun Lai
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Hui-Hua Ding
- ‖Shanghai Institute of Rheumatology, Department of rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shan Dong Road (c), Shanghai 200240, China
| | - Yuan-Jia Tang
- ‖Shanghai Institute of Rheumatology, Department of rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shan Dong Road (c), Shanghai 200240, China
| | - Zhao-Wei Xu
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ming-Liang Ma
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shu-Juan Guo
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jing-Fang Wang
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Nan Shen
- ‖Shanghai Institute of Rheumatology, Department of rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shan Dong Road (c), Shanghai 200240, China; **State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, 2200 Lane 25 Xietu Road, Shanghai 200240, China
| | - Xiao-Dong Zhao
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Huan Qi
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Hua Li
- §Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Sheng-Ce Tao
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; §Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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He B, Chen H, Huang J. PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition. PeerJ 2019; 7:e7131. [PMID: 31245183 PMCID: PMC6585900 DOI: 10.7717/peerj.7131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 05/15/2019] [Indexed: 01/08/2023] Open
Abstract
Selection from phage display libraries empowers isolation of high-affinity ligands for various targets. However, this method also identifies propagation-related target-unrelated peptides (PrTUPs). These false positive hits appear because of their amplification advantages. In this report, we present PhD7Faster 2.0 for predicting fast-propagating clones from the Ph.D.-7 phage display library, which was developed based on the support vector machine. Feature selection was performed against PseAAC and tripeptide composition using the incremental feature selection method. Ten-fold cross-validation results show that PhD7Faster 2.0 succeeds a decent performance with the accuracy of 81.84%, the Matthews correlation coefficient of 0.64 and the area under the ROC curve of 0.90. The permutation test with 1,000 shuffles resulted in p < 0.001. We implemented PhD7Faster 2.0 into a publicly accessible web tool (http://i.uestc.edu.cn/sarotup3/cgi-bin/PhD7Faster.pl) and constructed standalone graphical user interface and command-line versions for different systems. The standalone PhD7Faster 2.0 is able to detect PrTUPs within small datasets as well as large-scale datasets. This makes PhD7Faster 2.0 an enhanced and powerful tool for scanning and reporting faster-growing clones from the Ph.D.-7 phage display library.
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Affiliation(s)
- Bifang He
- School of Medicine, Guizhou University, Guiyang, Guizhou, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Heng Chen
- School of Medicine, Guizhou University, Guiyang, Guizhou, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
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26
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He B, Chen H, Li N, Huang J. SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data. Int J Biol Sci 2019; 15:1452-1459. [PMID: 31337975 PMCID: PMC6643146 DOI: 10.7150/ijbs.31957] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/09/2019] [Indexed: 01/13/2023] Open
Abstract
SAROTUP (Scanner And Reporter Of Target-Unrelated Peptides) 3.1 is a significant upgrade to the widely used SAROTUP web server for the rapid identification of target-unrelated peptides (TUPs) in phage display data. At present, SAROTUP has gathered a suite of tools for finding potential TUPs and other purposes. Besides the TUPScan, the motif-based tool, and three tools based on the BDB database, i.e., MimoScan, MimoSearch, and MimoBlast, three predictors based on support vector machine, i.e., PhD7Faster, SABinder and PSBinder, are integrated into SAROTUP. The current version of SAROTUP contains 27 TUP motifs and 823 TUP sequences. We also developed the standalone SAROTUP application with graphical user interface (GUI) and command line versions for processing deep sequencing phage display data and distributed it as an open source package, which can perform perfectly locally on almost all systems that support C++ with little or no modification. The web interfaces of SAROTUP have also been redesigned to be more self-evident and user-friendly. The latest version of SAROTUP is freely available at http://i.uestc.edu.cn/sarotup3.
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Affiliation(s)
- Bifang He
- School of Medicine, Guizhou University, Guiyang 550025, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Heng Chen
- School of Medicine, Guizhou University, Guiyang 550025, China
| | - Ning Li
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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27
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Cao B, Li Y, Yang T, Bao Q, Yang M, Mao C. Bacteriophage-based biomaterials for tissue regeneration. Adv Drug Deliv Rev 2019; 145:73-95. [PMID: 30452949 PMCID: PMC6522342 DOI: 10.1016/j.addr.2018.11.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 07/24/2018] [Accepted: 11/12/2018] [Indexed: 12/11/2022]
Abstract
Bacteriophage, also called phage, is a human-safe bacteria-specific virus. It is a monodisperse biological nanostructure made of proteins (forming the outside surface) and nucleic acids (encased in the protein capsid). Among different types of phages, filamentous phages have received great attention in tissue regeneration research due to their unique nanofiber-like morphology. They can be produced in an error-free format, self-assemble into ordered scaffolds, display multiple signaling peptides site-specifically, and serve as a platform for identifying novel signaling or homing peptides. They can direct stem cell differentiation into specific cell types when they are organized into proper patterns or display suitable peptides. These unusual features have allowed scientists to employ them to regenerate a variety of tissues, including bone, nerves, cartilage, skin, and heart. This review will summarize the progress in the field of phage-based tissue regeneration and the future directions in this field.
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Affiliation(s)
- Binrui Cao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, Institute for Biomedical Engineering, Science and Technology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States
| | - Yan Li
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, Institute for Biomedical Engineering, Science and Technology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Mingying Yang
- Institute of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Zhejiang, Hangzhou 310058, China.
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, Institute for Biomedical Engineering, Science and Technology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States; School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China.
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28
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Ponce M, Schroeder F, Bannert C, Schmidthaler K, Hansen CS, Lindholm Bøgh K, Soldo R, Tsui SK, Weinhäusel A, Szépfalusi Z, Eiwegger T. Preventive sublingual immunotherapy with House Dust Mite extract modulates epitope diversity in pre-school children. Allergy 2019; 74:780-787. [PMID: 30394551 DOI: 10.1111/all.13658] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/23/2018] [Accepted: 10/10/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND The preventive effect of allergen immunotherapy (AIT) on allergy and asthma development is currently assessed using primary and secondary AIT approaches. Knowledge of the immunological effects of these interventions is limited and the impact on epitope diversity remains to be defined. METHODS We used high-density peptide arrays that included all known Dermatophagoides pteronyssinus (Der p) and Dermatophagoides farinae (Der f) allergens and the whole proteome of Der f to study changes in House Dust Mite (HDM) linear peptide recognition during a 2-year preventive double-blind placebo-controlled sublingual HDM AIT pilot study in 2-5-year-old children with sensitization to HDM but without symptoms. RESULTS Preventive AIT-treated patients showed significantly higher IgG epitope diversity to HDM allergens compared to placebo-treated individuals at 24 months of treatment (P < 0.05), while no increase in IgE diversity was seen. At 24 months of treatment, IgG4 diversity for HDM allergens was significantly higher in the pAIT-treated patients compared to placebo group (P < 0.05). Potentially beneficial changes in epitope recognition throughout the treatment are also seen in peptides derived from Der f proteome. CONCLUSION These data suggest a beneficial immunomodulation of preventive sublingual immunotherapy at a molecular level by favoring a broader blocking repertoire and inhibiting epitope spreading.
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Affiliation(s)
- Marta Ponce
- Department of Paediatrics and Adolescent Medicine Medical University of Vienna Vienna Austria
| | - Fabian Schroeder
- Competence Unit for Molecular Diagnostics AIT, Austrian Institute of Technology Vienna Austria
| | - Christina Bannert
- Department of Paediatrics and Adolescent Medicine Medical University of Vienna Vienna Austria
| | - Klara Schmidthaler
- Department of Paediatrics and Adolescent Medicine Medical University of Vienna Vienna Austria
| | | | | | - Regina Soldo
- Competence Unit for Molecular Diagnostics AIT, Austrian Institute of Technology Vienna Austria
| | - Stephen Kwok‐Wing Tsui
- Hong Kong Bioinformatics Centre Chinese University of Hong Kong Hong Kong China
- School of Biomedical Sciences Chinese University of Hong Kong Hong Kong China
| | - Andreas Weinhäusel
- Competence Unit for Molecular Diagnostics AIT, Austrian Institute of Technology Vienna Austria
| | - Zsolt Szépfalusi
- Department of Paediatrics and Adolescent Medicine Medical University of Vienna Vienna Austria
| | - Thomas Eiwegger
- Department of Paediatrics and Adolescent Medicine Medical University of Vienna Vienna Austria
- Program in Translational Medicine The Hospital for Sick Children Toronto Ontario Canada
- Department of Immunology The University of Toronto Toronto Ontario Canada
- Division of Immunology and Allergy Food allergy and Anaphylaxis Program The Department of Paediatrics The Hospital for Sick Children Toronto Ontario Canada
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29
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Ferreira D, Silva AP, Nobrega FL, Martins IM, Barbosa-Matos C, Granja S, Martins SF, Baltazar F, Rodrigues LR. Rational Identification of a Colorectal Cancer Targeting Peptide through Phage Display. Sci Rep 2019; 9:3958. [PMID: 30850705 PMCID: PMC6408488 DOI: 10.1038/s41598-019-40562-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/19/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer is frequently diagnosed at an advanced stage due to the absence of early clinical indicators. Hence, the identification of new targeting molecules is crucial for an early detection and development of targeted therapies. This study aimed to identify and characterize novel peptides specific for the colorectal cancer cell line RKO using a phage-displayed peptide library. After four rounds of selection plus a negative step with normal colorectal cells, CCD-841-CoN, there was an obvious phage enrichment that specifically bound to RKO cells. Cell-based enzyme-linked immunosorbent assay (ELISA) was performed to assess the most specific peptides leading to the selection of the peptide sequence CPKSNNGVC. Through fluorescence microscopy and cytometry, the synthetic peptide RKOpep was shown to specifically bind to RKO cells, as well as to other human colorectal cancer cells including Caco-2, HCT 116 and HCT-15, but not to the normal non-cancer cells. Moreover, it was shown that RKOpep specifically targeted human colorectal cancer cell tissues. A bioinformatics analysis suggested that the RKOpep targets the monocarboxylate transporter 1, which has been implicated in colorectal cancer progression and prognosis, proven through gene knockdown approaches and shown by immunocytochemistry co-localization studies. The peptide herein identified can be a potential candidate for targeted therapies for colorectal cancer.
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Affiliation(s)
- Débora Ferreira
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal.,MIT-Portugal Program, Lisbon, Portugal
| | - Ana P Silva
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal
| | - Franklin L Nobrega
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Ivone M Martins
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal
| | - Catarina Barbosa-Matos
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Sara Granja
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Sandra F Martins
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Surgery Department, Coloproctology Unit, Braga Hospital, Braga, Portugal
| | - Fátima Baltazar
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ligia R Rodrigues
- Centre of Biological Engineering, University of Minho (CEB), Campus de Gualtar, 4710-057, Braga, Portugal. .,MIT-Portugal Program, Lisbon, Portugal.
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30
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Sannino A, Gabriele E, Bigatti M, Mulatto S, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries. Chembiochem 2019; 20:955-962. [DOI: 10.1002/cbic.201800766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Elena Gabriele
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | | | - Sara Mulatto
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jacopo Piazzi
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | | | - Florent Samain
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
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31
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Kern K, Havenith H, Delaroque N, Rautenberger P, Lehmann J, Fischer M, Spiegel H, Schillberg S, Ehrentreich-Foerster E, Aurich S, Treudler R, Szardenings M. The immunome of soy bean allergy: Comprehensive identification and characterization of epitopes. Clin Exp Allergy 2019; 49:239-251. [PMID: 30267550 DOI: 10.1111/cea.13285] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND The precise mapping of multiple antibody epitopes recognized by patients' sera allows a more detailed and differentiated understanding of immunological diseases. It may lead to the development of novel therapies and diagnostic tools. OBJECTIVE Mapping soy bean specific epitopes relevant for soy bean allergy patients and persons sensitized to soy bean, and analysis of their IgE/IgG binding spectrum. METHODS Identification of epitopes using sera, applying an optimized peptide phage display library followed by next-generation sequencing, specially designed in silico data analysis and subsequent peptide microarray analysis. RESULTS We were able to identify more than 400 potential epitope motifs in soy bean proteins. More than 60% of them have not yet been described as potential epitopes. Eighty-three peptides, representing the 42 most frequently found epitope candidates, were validated by microarray analysis using 50 sera from people who have been tested positive in skin prick test (SPT). Of these peptides, 56 were bound by antibodies, 55 by serum IgE, 43 by serum IgG and 30 by both. Person-specific epitope patterns were found for each individual and protein. CONCLUSIONS For individuals with clinical symptoms, epitope resolved analyses reveal a high prevalence of IgE binding to a few soy bean specific epitopes. Evaluation of individual immune profiles of patients with soy bean sensitization allows the identification of peptides that do facilitate studying individual IgE/IgG epitope binding patterns. This enables discrimination of sensitization from disease, such assay test has the potential to replace SPT assays.
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Affiliation(s)
- Karolin Kern
- Ligand Development Unit, Fraunhofer IZI, Leipzig, Germany
| | - Heide Havenith
- Molecular Biotechnology Division, Fraunhofer IME, Aachen, Germany
| | | | | | - Jörg Lehmann
- Department Therapy Validation, Fraunhofer IZI, Leipzig, Germany
| | | | - Holger Spiegel
- Molecular Biotechnology Division, Fraunhofer IME, Aachen, Germany
| | | | | | - Stefanie Aurich
- Department of Dermatology, Venereology and Allergology, Comprehensive Allergy Centre, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Regina Treudler
- Department of Dermatology, Venereology and Allergology, Comprehensive Allergy Centre, Universitätsklinikum Leipzig, Leipzig, Germany
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Palermo A, Nesterov-Mueller A. Serological Number for Characterization of Circulating Antibodies. Int J Mol Sci 2019; 20:ijms20030604. [PMID: 30704134 PMCID: PMC6387039 DOI: 10.3390/ijms20030604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/11/2019] [Accepted: 01/29/2019] [Indexed: 11/16/2022] Open
Abstract
The dissociation constant of the circulating IgG antibodies is suggested to be proportional to the partial concentrations of these antibodies in blood serum in equilibrium. This coefficient, called serological number, is a dimensionless parameter and may be equal for all antibodies in a serum. Based on the serological number, we derived the equilibrium equation of the humoral immune system which allows estimating the number of different binding motifs in a serum. This equation also allows estimating the number of binding motifs of posttranslational and conformational nature. The feasibility of measuring the serological number via peptide arrays was demonstrated. Fifteen peptides with unique binding motifs were incubated and stained with the blood serum of a healthy adult at different dilutions. From these experiments, the serological number was determined. The serological number may explain the pre-existing antibody response after vaccination.
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Affiliation(s)
- Andrea Palermo
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany.
| | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany.
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33
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Heffron AS, Mohr EL, Baker D, Haj AK, Buechler CR, Bailey A, Dudley DM, Newman CM, Mohns MS, Koenig M, Breitbach ME, Rasheed M, Stewart LM, Eickhoff J, Pinapati RS, Beckman E, Li H, Patel J, Tan JC, O’Connor DH. Antibody responses to Zika virus proteins in pregnant and non-pregnant macaques. PLoS Negl Trop Dis 2018; 12:e0006903. [PMID: 30481182 PMCID: PMC6286021 DOI: 10.1371/journal.pntd.0006903] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/07/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022] Open
Abstract
The specificity of the antibody response against Zika virus (ZIKV) is not well-characterized. This is due, in part, to the antigenic similarity between ZIKV and closely related dengue virus (DENV) serotypes. Since these and other similar viruses co-circulate, are spread by the same mosquito species, and can cause similar acute clinical syndromes, it is difficult to disentangle ZIKV-specific antibody responses from responses to closely-related arboviruses in humans. Here we use high-density peptide microarrays to profile anti-ZIKV antibody reactivity in pregnant and non-pregnant macaque monkeys with known exposure histories and compare these results to reactivity following DENV infection. We also compare cross-reactive binding of ZIKV-immune sera to the full proteomes of 28 arboviruses. We independently confirm a purported ZIKV-specific IgG antibody response targeting ZIKV nonstructural protein 2B (NS2B) that was recently reported in ZIKV-infected people and we show that antibody reactivity in pregnant animals can be detected as late as 127 days post-infection (dpi). However, we also show that these responses wane over time, sometimes rapidly, and in one case the response was elicited following DENV infection in a previously ZIKV-exposed animal. These results suggest epidemiologic studies assessing seroprevalence of ZIKV immunity using linear epitope-based strategies will remain challenging to interpret due to susceptibility to false positive results. However, the method used here demonstrates the potential for rapid profiling of proteome-wide antibody responses to a myriad of neglected diseases simultaneously and may be especially useful for distinguishing antibody reactivity among closely related pathogens.
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Affiliation(s)
- Anna S. Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Emma L. Mohr
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States of America
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Amelia K. Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Connor R. Buechler
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Adam Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mariel S. Mohns
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michelle Koenig
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Meghan E. Breitbach
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mustafa Rasheed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Laurel M. Stewart
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Jens Eickhoff
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Richard S. Pinapati
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - Erica Beckman
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - Hanying Li
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - Jigar Patel
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - John C. Tan
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
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He B, Jiang L, Duan Y, Chai G, Fang Y, Kang J, Yu M, Li N, Tang Z, Yao P, Wu P, Derda R, Huang J. Biopanning data bank 2018: hugging next generation phage display. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4955852. [PMID: 29688378 PMCID: PMC7206649 DOI: 10.1093/database/bay032] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/07/2018] [Indexed: 12/12/2022]
Abstract
The 2018 update of the biopanning data bank (BDB) stores phage display data sequenced by Sanger sequencing and next generation sequencing technologies. In this work, we upgraded the database with more biopanning data sets and several new features, including (i) incorporation of next generation biopanning data and the unselected population where the target is not determined and the round of screening is zero; (ii) addition of sequencing information; (iii) improvement of browsing and searching systems and 3 D chemical structure viewer; (iv) integration of standalone tools for target-unrelated peptides analysis within conventional phage display and next generation phage display (NGPD) data. In the current version of BDB (released on 19 January 2018), the database houses 3291 sets of biopanning data collected from 1540 published articles, including 95 NGPD data sets and 3196 traditional biopanning data sets. The BDB database serves as an important and comprehensive resource for developing peptide ligands. Database URL: The BDB database is available at http://immunet.cn/bdb
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Affiliation(s)
- Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Lixu Jiang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Yaocong Duan
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Guoshi Chai
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Yewei Fang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Juanjuan Kang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Min Yu
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Ning Li
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Zhongjie Tang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Pengcheng Yao
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Pengcheng Wu
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
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Anti-Drug Antibodies: Emerging Approaches to Predict, Reduce or Reverse Biotherapeutic Immunogenicity. Antibodies (Basel) 2018; 7:antib7020019. [PMID: 31544871 PMCID: PMC6698869 DOI: 10.3390/antib7020019] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
The development of anti-drug antibodies (ADAs) following administration of biotherapeutics to patients is a vexing problem that is attracting increasing attention from pharmaceutical and biotechnology companies. This serious clinical problem is also spawning creative research into novel approaches to predict, avoid, and in some cases even reverse such deleterious immune responses. CD4+ T cells are essential players in the development of most ADAs, while memory B-cell and long-lived plasma cells amplify and maintain these responses. This review summarizes methods to predict and experimentally identify T-cell and B-cell epitopes in therapeutic proteins, with a particular focus on blood coagulation factor VIII (FVIII), whose immunogenicity is clinically significant and is the subject of intensive current research. Methods to phenotype ADA responses in humans are described, including T-cell stimulation assays, and both established and novel approaches to determine the titers, epitopes and isotypes of the ADAs themselves. Although rational protein engineering can reduce the immunogenicity of many biotherapeutics, complementary, novel approaches to induce specific tolerance, especially during initial exposures, are expected to play significant roles in future efforts to reduce or reverse these unwanted immune responses.
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Ryvkin A, Ashkenazy H, Weiss-Ottolenghi Y, Piller C, Pupko T, Gershoni JM. Phage display peptide libraries: deviations from randomness and correctives. Nucleic Acids Res 2018; 46:e52. [PMID: 29420788 PMCID: PMC5961013 DOI: 10.1093/nar/gky077] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/25/2017] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study, we demonstrate that the UAG over-representation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by mass spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications.
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Affiliation(s)
- Arie Ryvkin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yael Weiss-Ottolenghi
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Piller
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan M Gershoni
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Sadam H, Pihlak A, Kivil A, Pihelgas S, Jaago M, Adler P, Vilo J, Vapalahti O, Neuman T, Lindholm D, Partinen M, Vaheri A, Palm K. Prostaglandin D2 Receptor DP1 Antibodies Predict Vaccine-induced and Spontaneous Narcolepsy Type 1: Large-scale Study of Antibody Profiling. EBioMedicine 2018; 29:47-59. [PMID: 29449194 PMCID: PMC5925455 DOI: 10.1016/j.ebiom.2018.01.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/23/2018] [Accepted: 01/31/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Neuropathological findings support an autoimmune etiology as an underlying factor for loss of orexin-producing neurons in spontaneous narcolepsy type 1 (narcolepsy with cataplexy; sNT1) as well as in Pandemrix influenza vaccine-induced narcolepsy type 1 (Pdmx-NT1). The precise molecular target or antigens for the immune response have, however, remained elusive. METHODS Here we have performed a comprehensive antigenic repertoire analysis of sera using the next-generation phage display method - mimotope variation analysis (MVA). Samples from 64 children and adolescents were analyzed: 10 with Pdmx-NT1, 6 with sNT1, 16 Pandemrix-vaccinated, 16 H1N1 infected, and 16 unvaccinated healthy individuals. The diagnosis of NT1 was defined by the American Academy of Sleep Medicine international criteria of sleep disorders v3. FINDINGS Our data showed that although the immunoprofiles toward vaccination were generally similar in study groups, there were also striking differences in immunoprofiles between sNT1 and Pdmx-NT1 groups as compared with controls. Prominent immune response was observed to a peptide epitope derived from prostaglandin D2 receptor (DP1), as well as peptides homologous to B cell lymphoma 6 protein. Further validation confirmed that these can act as true antigenic targets in discriminating NT1 diseased along with a novel epitope of hemagglutinin of H1N1 to delineate exposure to H1N1. INTERPRETATION We propose that DP1 is a novel molecular target of autoimmune response and presents a potential diagnostic biomarker for NT1. DP1 is involved in the regulation of non-rapid eye movement (NREM) sleep and thus alterations in its functions could contribute to the disturbed sleep regulation in NT1 that warrants further studies. Together our results also show that MVA is a helpful method for finding novel peptide antigens to classify human autoimmune diseases, possibly facilitating the design of better therapies.
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Affiliation(s)
- Helle Sadam
- Protobios Llc, Mäealuse 4, 12618 Tallinn, Estonia; Department of Gene Technology, Tallinn University of Technology, Akadeemia Tee 15, 12618 Tallinn, Estonia
| | - Arno Pihlak
- Protobios Llc, Mäealuse 4, 12618 Tallinn, Estonia; Department of Gene Technology, Tallinn University of Technology, Akadeemia Tee 15, 12618 Tallinn, Estonia
| | - Anri Kivil
- Protobios Llc, Mäealuse 4, 12618 Tallinn, Estonia
| | | | | | - Priit Adler
- Institute of Computer Science, University of Tartu, Liivi 2-314, 50409 Tartu, Estonia; Quretec LLC, Ülikooli 6a, 51003 Tartu, Estonia
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Liivi 2-314, 50409 Tartu, Estonia; Quretec LLC, Ülikooli 6a, 51003 Tartu, Estonia
| | - Olli Vapalahti
- Department of Virology, Medicum, Haartmaninkatu 3, 00014 University of Helsinki, Finland; Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin Katu 2, 00014 University of Helsinki, Finland; Virology and Immunology, HUSLAB, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Toomas Neuman
- Protobios Llc, Mäealuse 4, 12618 Tallinn, Estonia; IPDx Immunoprofiling Diagnostics GmbH, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Dan Lindholm
- Department of Biochemistry and Developmental Biology, Medicum, Haartmaninkatu 8, 00014 University of Helsinki, Finland; Minerva Foundation Medical Research Institute, Tukholmankatu 8, 00290 Helsinki, Finland
| | - Markku Partinen
- Finnish Narcolepsy Research Center, Helsinki Sleep Clinic, Vitalmed Research Center, Valimotie 21, 00380, Helsinki, Finland
| | - Antti Vaheri
- Department of Virology, Medicum, Haartmaninkatu 3, 00014 University of Helsinki, Finland
| | - Kaia Palm
- Protobios Llc, Mäealuse 4, 12618 Tallinn, Estonia; Department of Gene Technology, Tallinn University of Technology, Akadeemia Tee 15, 12618 Tallinn, Estonia.
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Ibsen KN, Daugherty PS. Prediction of antibody structural epitopes via random peptide library screening and next generation sequencing. J Immunol Methods 2017; 451:28-36. [PMID: 28827189 PMCID: PMC5698135 DOI: 10.1016/j.jim.2017.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
Next generation sequencing (NGS) is widely applied in immunological research, but has yet to become common in antibody epitope mapping. A method utilizing a 12-mer random peptide library expressed in bacteria coupled with magnetic-based cell sorting and NGS correctly identified >75% of epitope residues on the antigens of two monoclonal antibodies (trastuzumab and bevacizumab). PepSurf, a web-based computational method designed for structural epitope mapping was utilized to compare peptides in libraries enriched for monoclonal antibody (mAb) binders to antigen surfaces (HER2 and VEGF-A). Compared to mimotopes recovered from Sanger sequencing of plated colonies from the same sorting protocol, motifs derived from sets of the NGS data improved epitope prediction as defined by sensitivity and precision, from 18% to 82% and 0.27 to 0.51 for trastuzumab and 47% to 76% and 0.19 to 0.27 for bevacizumab. Specificity was similar for Sanger and NGS, 99% and 97% for trastuzumab and 66% and 67% for bevacizumab. These results indicate that combining peptide library screening with NGS yields epitope motifs that can improve prediction of structural epitopes.
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MESH Headings
- Algorithms
- Amino Acid Motifs
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibody Specificity
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/metabolism
- Bevacizumab/immunology
- Bevacizumab/metabolism
- Binding Sites, Antibody
- Computational Biology
- Databases, Genetic
- Epitope Mapping/methods
- Epitopes
- High-Throughput Nucleotide Sequencing
- Immunomagnetic Separation
- Models, Chemical
- Peptide Library
- Protein Binding
- Receptor, ErbB-2/chemistry
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/immunology
- Receptor, ErbB-2/metabolism
- Structure-Activity Relationship
- Trastuzumab/immunology
- Trastuzumab/metabolism
- Vascular Endothelial Growth Factor A/chemistry
- Vascular Endothelial Growth Factor A/genetics
- Vascular Endothelial Growth Factor A/immunology
- Vascular Endothelial Growth Factor A/metabolism
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Affiliation(s)
- Kelly N Ibsen
- Department of Chemical Engineering, University of California Santa Barbara, CA 93106, USA.
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, CA 93106, USA
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Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology 2017; 153:31-41. [PMID: 28898398 DOI: 10.1111/imm.12838] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high-throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high-throughput sequencing has made it possible to obtain large-scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high-throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high-throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Life Science Zurich Graduate School, Systems Biology, ETH Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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Lykkemark S, Mandrup OA, Jensen MB, Just J, Kristensen P. A novel excision selection method for isolation of antibodies binding antigens expressed specifically by rare cells in tissue sections. Nucleic Acids Res 2017; 45:e107. [PMID: 28369551 PMCID: PMC5499801 DOI: 10.1093/nar/gkx207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/21/2017] [Indexed: 12/22/2022] Open
Abstract
There is a growing appreciation of single cell technologies to provide increased biological insight and allow development of improved therapeutics. The central dogma explains why single cell technologies is further advanced in studies targeting nucleic acids compared to proteins, as nucleic acid amplification makes experimental detection possible. Here we describe a novel method for single round phage display selection of antibody fragments from genetic libraries targeting antigens expressed by rare cells in tissue sections. We present and discuss the results of two selections of antibodies recognizing antigens expressed by perivascular cells surrounding capillaries located in a human brain section; with the aim of identifying biomarkers expressed by pericytes. The area targeted for selection was identified by a known biomarker and morphological appearance, however in situ hybridizations to nucleic acids can also be used for the identification of target cells. The antibody selections were performed directly on the tissue sections followed by excision of the target cells using a glass capillary attached to micromanipulation equipment. Antibodies bound to the target cells were characterized using ELISA, immunocytochemistry and immunohistochemistry. The described method will provide a valuable tool for the discovery of novel biomarkers on rare cells in all types of tissues.
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Affiliation(s)
- Simon Lykkemark
- Department of Clinical Medicine, Aarhus University, Nørrebrogade 44, 8000 Aarhus C, Denmark.,Sino-Danish Centre for Education and Research (SDC), Niels Jensens Vej 2, 8000 Aarhus C, Denmark
| | - Ole Aalund Mandrup
- Department of Engineering, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Mads Bjørnkjær Jensen
- Department of Engineering, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Jesper Just
- Department of Molecular Biology and Genetics, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Peter Kristensen
- Department of Engineering, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
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Slocik JM, Naik RR. Sequenced defined biomolecules for nanomaterial synthesis, functionalization, and assembly. Curr Opin Biotechnol 2017; 46:7-13. [DOI: 10.1016/j.copbio.2016.11.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 10/20/2022]
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Abstract
Background For fighting cancer, earlier detection is crucial. Circulating auto-antibodies produced by the patient’s own immune system after exposure to cancer proteins are promising bio-markers for the early detection of cancer. Since an antibody recognizes not the whole antigen but 4–7 critical amino acids within the antigenic determinant (epitope), the whole proteome can be represented by a random peptide phage display library. This opens the possibility to develop an early cancer detection test based on a set of peptide sequences identified by comparing cancer patients’ and healthy donors’ global peptide profiles of antibody specificities. Results Due to the enormously large number of peptide sequences contained in global peptide profiles generated by next generation sequencing, the large number of cancer and control sera is required to identify cancer-specific peptides with high degree of statistical significance. To decrease the number of peptides in profiles generated by nextgen sequencing without losing cancer-specific sequences we used for generation of profiles the phage library enriched by panning on the pool of cancer sera. To further decrease the complexity of profiles we used computational methods for transforming a list of peptides constituting the mimotope profiles to the list motifs formed by similar peptide sequences. Conclusion We have shown that the amino-acid order is meaningful in mimotope motifs since they contain significantly more peptides than motifs among peptides where amino-acids are randomly permuted. Also the single sample motifs significantly differ from motifs in peptides drawn from multiple samples. Finally, multiple cancer-specific motifs have been identified.
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Abstract
Molecular imaging allows for the visualization of changes at the cellular level in diseases such as cancer. A successful molecular imaging agent must rely on disease-selective targets and ligands that specifically interact with those targets. Unfortunately, the translation of novel target-specific ligands into the clinic has been frustratingly slow with limitations including the complex design and screening approaches for ligand identification, as well as their subsequent optimization into useful imaging agents. This review focuses on combinatorial library approaches towards addressing these two challenges, with particular focus on phage display and one-bead one-compound (OBOC) libraries. Both of these peptide-based techniques have proven successful in identifying new ligands for cancer-specific targets and some of the success stories will be highlighted. New developments in screening methodology and sequencing technology have pushed the bounds of phage display and OBOC even further, allowing for even faster and more robust discovery of novel ligands. The combination of multiple high-throughput technologies will not only allow for more accurate identification, but also faster affinity maturation, while overall streamlining the process of translating novel ligands into clinical imaging agents.
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Anany H, Chou Y, Cucic S, Derda R, Evoy S, Griffiths M. From Bits and Pieces to Whole Phage to Nanomachines: Pathogen Detection Using Bacteriophages. Annu Rev Food Sci Technol 2017; 8:305-329. [DOI: 10.1146/annurev-food-041715-033235] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- H. Anany
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt 11566
| | - Y. Chou
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - S. Cucic
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
| | - R. Derda
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - S. Evoy
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - M.W. Griffiths
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
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Mathebula EM, Faber FE, Van Wyngaardt W, Van Schalkwyk A, Pretorius A, Fehrsen J. B-cell epitopes of African horse sickness virus serotype 4 recognised by immune horse sera. ACTA ACUST UNITED AC 2017; 84:e1-e12. [PMID: 28281773 PMCID: PMC6238682 DOI: 10.4102/ojvr.v84i1.1313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 01/07/2023]
Abstract
Identifying antigenic proteins and mapping their epitopes is important for the development of diagnostic reagents and recombinant vaccines. B-cell epitopes of African horse sickness virus (AHSV) have previously been mapped on VP2, VP5, VP7 and NS1, using mouse, rabbit and chicken monoclonal antibodies. A comprehensive study of the humoral immune response of five vaccinated horses to AHSV-4 antigenic peptides was undertaken. A fragmented-genome phage display library expressing a repertoire of AHSV-4 peptides spanning the entire genome was constructed. The library was affinity selected for binders on immobilised polyclonal immunoglobulin G (IgG) isolated from horse sera collected pre- and post-immunisation with an attenuated AHSV-4 monovalent vaccine. The DNA inserts of binding phages were sequenced with Illumina high-throughput sequencing. The data were normalised using pre-immune IgG-selected sequences. More sequences mapped to the genes coding for NS3, VP6 and VP5 than to the other genes. However, VP2 and VP5 each had more antigenic regions than each of the other proteins. This study identified a number of epitopes to which the horse’s humoral immune system responds during immunisation with AHSV-4.
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Affiliation(s)
| | | | | | | | | | - Jeanni Fehrsen
- New Generation Vaccines Programme, Agricultural Research Council - Onderstepoort Veterinary Institute; Department of Veterinary Tropical Diseases, University of Pretoria.
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Havenith H, Kern K, Rautenberger P, Spiegel H, Szardenings M, Ueberham E, Lehmann J, Buntru M, Vogel S, Treudler R, Fischer R, Schillberg S. Combination of two epitope identification techniques enables the rational design of soy allergen Gly m 4 mutants. Biotechnol J 2017; 12. [PMID: 27906504 DOI: 10.1002/biot.201600441] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 11/08/2022]
Abstract
Detailed IgE-binding epitope analysis is a key requirement for the understanding and development of diagnostic and therapeutic agents to address food allergies. An IgE-specific linear peptide microarray with random phage peptide display for the high-resolution mapping of IgE-binding epitopes of the major soybean allergen Gly m 4, which is a homologue to the birch pollen allergen Bet v 1 is combined. Three epitopes are identified and mapped to a resolution of four key amino acids, allowing the rational design and the production of three Gly m 4 mutants with the aim to abolish or reduce the binding of epitope-specific IgE. In ELISA, the binding of the mutant allergens to polyclonal rabbit-anti Gly m 4 serum as well as IgE purified from Gly m 4-reactive soybean allergy patient sera is reduced by up to 63% compared to the wild-type allergen. Basophil stimulation experiments using RBL-SX38 cells loaded with patient IgE are showed a decreased stimulation from 25% for the wild-type Gly m 4 to 13% for one mutant. The presented approach demonstrates the feasibility of precise mapping of allergy-related IgE-binding epitopes, allowing the rational design of less allergenic mutants as potential therapeutic agents.
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Affiliation(s)
- Heide Havenith
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Karolin Kern
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Paul Rautenberger
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | | | - Elke Ueberham
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Jörg Lehmann
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Matthias Buntru
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Simon Vogel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Regina Treudler
- Dermatology, Venereology and Allergology Clinic, University of Leipzig, Leipzig, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- RWTH Aachen University, Institute for Molecular Biotechnology, Aachen, Germany
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Phytopathology and Applied Zoology, Justus-Liebig University Giessen, Gießen, Germany
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48
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Lindau P, Robins HS. Advances and applications of immune receptor sequencing in systems immunology. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2016.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Hansen CS, Østerbye T, Marcatili P, Lund O, Buus S, Nielsen M. ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping. PLoS One 2017; 12:e0168453. [PMID: 28095436 PMCID: PMC5240915 DOI: 10.1371/journal.pone.0168453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 12/01/2016] [Indexed: 11/19/2022] Open
Abstract
Identification of epitopes targeted by antibodies (B cell epitopes) is of critical importance for the development of many diagnostic and therapeutic tools. For clinical usage, such epitopes must be extensively characterized in order to validate specificity and to document potential cross-reactivity. B cell epitopes are typically classified as either linear epitopes, i.e. short consecutive segments from the protein sequence or conformational epitopes adapted through native protein folding. Recent advances in high-density peptide microarrays enable high-throughput, high-resolution identification and characterization of linear B cell epitopes. Using exhaustive amino acid substitution analysis of peptides originating from target antigens, these microarrays can be used to address the specificity of polyclonal antibodies raised against such antigens containing hundreds of epitopes. However, the interpretation of the data provided in such large-scale screenings is far from trivial and in most cases it requires advanced computational and statistical skills. Here, we present an online application for automated identification of linear B cell epitopes, allowing the non-expert user to analyse peptide microarray data. The application takes as input quantitative peptide data of fully or partially substituted overlapping peptides from a given antigen sequence and identifies epitope residues (residues that are significantly affected by substitutions) and visualize the selectivity towards each residue by sequence logo plots. Demonstrating utility, the application was used to identify and address the antibody specificity of 18 linear epitope regions in Human Serum Albumin (HSA), using peptide microarray data consisting of fully substituted peptides spanning the entire sequence of HSA and incubated with polyclonal rabbit anti-HSA (and mouse anti-rabbit-Cy3). The application is made available at: www.cbs.dtu.dk/services/ArrayPitope.
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Affiliation(s)
- Christian Skjødt Hansen
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Thomas Østerbye
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paolo Marcatili
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Søren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Nielsen
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
- * E-mail:
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Luzar J, Štrukelj B, Lunder M. Phage display peptide libraries in molecular allergology: from epitope mapping to mimotope-based immunotherapy. Allergy 2016; 71:1526-1532. [PMID: 27341497 DOI: 10.1111/all.12965] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 01/07/2023]
Abstract
Identification of allergen epitopes is a key component in proper understanding of the pathogenesis of type I allergies, for understanding cross-reactivity and for the development of mimotope immunotherapeutics. Phage particles have garnered recognition in the field of molecular allergology due to their value not only in competitive immunoscreening of peptide libraries but also as immunogenic carriers of allergen mimotopes. They integrate epitope discovery technology and immunization functions into a single platform. This article provides an overview of allergen mimotopes identified through the phage display technique. We discuss the contribution of phage display peptide libraries in determining dominant B-cell epitopes of allergens, in developing mimotope immunotherapy, in understanding cross-reactivity, and in determining IgE epitope profiles of individual patients to improve diagnostics and individualize immunotherapy. We also discuss the advantages and pitfalls of the methodology used to identify and validate the mimotopes.
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Affiliation(s)
- J. Luzar
- Chair of Pharmaceutical Biology; Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - B. Štrukelj
- Chair of Pharmaceutical Biology; Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - M. Lunder
- Chair of Pharmaceutical Biology; Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
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