High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum

Christiansen, Anders; Kringelum, Jens Vindahl; Hansen, Christian Skjødt; Bøgh, Katrine Lindholm; Sullivan, Eric; Patel, Jigar; Rigby, Neil M.; Eiwegger, Thomas; Szépfalusi, Zsolt; Masi, Federico De; Nielsen, Morten; Lund, Ole; Dufva, Martin

doi:10.1038/srep12913

Cited by 62 publications

(63 citation statements)

References 52 publications

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“…The phage display approach can be tuned to be much more powerful than recent 24,35,36 publications in the field suggest. The phage display approach can be tuned to be much more powerful than recent 24,35,36 publications in the field suggest.…”

Section: Discussionmentioning

confidence: 99%

The immunome of soy bean allergy: Comprehensive identification and characterization of epitopes

Kern

Havenith

Delaroque

et al. 2018

Clin Experimental Allergy

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Summary 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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Section: Discussionmentioning

confidence: 99%

The immunome of soy bean allergy: Comprehensive identification and characterization of epitopes

Kern

Havenith

Delaroque

et al. 2018

Clin Experimental Allergy

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show abstract

“…Second, costly laborious screening is omitted because candidate antibodies are identified in silico . Besides time and cost savings, this feature becomes even more important considering that antibody‐display selections often suffer from screening artefacts or the propagation of false‐positive clones in selections due to a certain growth advantage . Finally, most relevant B‐cell subsets can be comprehensively interrogated by Ig‐seq, which is not the case with hybridomas and other approaches that suffer from low immortalization efficiencies.…”

Section: Sequencing Antibody Repertoiresmentioning

confidence: 99%

Integrating high‐throughput screening and sequencing for monoclonal antibody discovery and engineering

2017

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OTHER ARTICLES PUBLISHED IN THIS SERIES SummaryMonoclonal 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 highthroughput 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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“…Sanger sequencing provides high quality, low error reads of small DNA sequences, aspects which have traditionally been considered necessary for epitope mapping. Recently, NGS has been coupled with random peptide libraries in studies aimed at identifying immunogenic peptides [Heyduk & Heyduk, 2014; Christiansen et al , 2015]. Another utilized NGS with antigenic fragment libraries to map epitopes [Domina et al , 2014].…”

Section: Introductionmentioning

confidence: 99%

Prediction of antibody structural epitopes via random peptide library screening and next generation sequencing

Ibsen

Daugherty

2017

Journal of Immunological Methods

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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 more than 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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High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum

Cited by 62 publications

References 52 publications

The immunome of soy bean allergy: Comprehensive identification and characterization of epitopes

The immunome of soy bean allergy: Comprehensive identification and characterization of epitopes

Integrating high‐throughput screening and sequencing for monoclonal antibody discovery and engineering

Prediction of antibody structural epitopes via random peptide library screening and next generation sequencing

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