Special Issue "Antibody Repertoire Mining for Immune Profiling, Antibody Discovery and Vaccine Design"

A special issue of Antibodies (ISSN 2073-4468).

Deadline for manuscript submissions: closed (28 February 2019)

Special Issue Editors

Guest Editor
Dr. Prabakaran Ponraj

Sanofi Genzyme, 49 New York Ave, Framingham, MA 01701, USA
E-Mail
Interests: next-generation sequencing of iImmune repertoires for biologics/vaccine discovery; protein/antibody design and engineering; structural biology; bioinformatics; immunology
Guest Editor
Dr. Brandon J Dekosky

The University of Kansas, 2095 Simons Biosciences Research Labs, Rm 136B, Lawrence, KS 66044
E-Mail
Interests: next-generation sequencing of immune repertoires for biologics/vaccine discovery; infectious disease prevention, vaccine design, protein/antibody design and engineering; bioinformatics; immunology

Special Issue Information

Dear Colleagues,

Immunogenetic mechanisms underlying the complex processes of antibody V(D)J gene rearrangement, junctional modification, and somatic mutation, which appear to randomly create repertoires of vast diversity. However, detailed analyses of antibody repertories in different stages of ontogeny, development, immunological condition and responses have demonstrated that normal and immune repertoires can be constrained and shaped by natural selection, immune checkpoints, and exposure to autoantigens, microbes and vaccines. Recently, comparative deep sequencing studies of antibody repertoires between individuals have revealed the existence of public and private repertoires. Exploring genetic diversity of these repertoires and their impacts on the humoral immune response is the subject of active investigations that have tremendous applications, such as antibody discovery, immune profiling in disease conditions (ex., autoimmunity, cancer and viral infection) and following vaccination, and B-cell lineage-based approach to vaccine design.

This Special Issue of Antibodies focuses on recent advances in antibody repertoire mining from human and other organisms, including, high-throughput single B cell technologies for antibody discovery, NGS data mining pipeline and in silico analysis for clone selection and improved antibody library generation, evolutionary and developmental aspects of B-cell receptor repertoires, maturation pathway analysis for vaccine design, and understanding immunogenetic and molecular basis of antibody responses at the repertoire level to pathogens, vaccines and autoantigens.

Dr. Prabakaran Ponraj
Dr. Brandon J Dekosky
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibodies is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 350 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Next-generation sequencing of antibodies
  • B-cell receptor repertoire
  • Antibodyome

Published Papers (2 papers)

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Research

Open AccessArticle
Preferential Identification of Agonistic OX40 Antibodies by Using Cell Lysate to Pan Natively Paired, Humanized Mouse-Derived Yeast Surface Display Libraries
Antibodies 2019, 8(1), 17; https://doi.org/10.3390/antib8010017
Received: 5 January 2019 / Revised: 12 February 2019 / Accepted: 14 February 2019 / Published: 19 February 2019
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Abstract
To discover therapeutically relevant antibody candidates, many groups use mouse immunization followed by hybridoma generation or B cell screening. One modern approach is to screen B cells by generating natively paired single chain variable fragment (scFv) display libraries in yeast. Such methods typically [...] Read more.
To discover therapeutically relevant antibody candidates, many groups use mouse immunization followed by hybridoma generation or B cell screening. One modern approach is to screen B cells by generating natively paired single chain variable fragment (scFv) display libraries in yeast. Such methods typically rely on soluble antigens for scFv library screening. However, many therapeutically relevant cell-surface targets are difficult to express in a soluble protein format, complicating discovery. In this study, we developed methods to screen humanized mouse-derived yeast scFv libraries using recombinant OX40 protein in cell lysate. We used deep sequencing to compare screening with cell lysate to screening with soluble OX40 protein, in the context of mouse immunizations using either soluble OX40 or OX40-expressing cells and OX40-encoding DNA vector. We found that all tested methods produce a unique diversity of scFv binders. However, when we reformatted forty-one of these scFv as full-length monoclonal antibodies (mAbs), we observed that mAbs identified using soluble antigen immunization with cell lysate sorting always bound cell surface OX40, whereas other methods had significant false positive rates. Antibodies identified using soluble antigen immunization and cell lysate sorting were also significantly more likely to activate OX40 in a cellular assay. Our data suggest that sorting with OX40 protein in cell lysate is more likely than other methods to retain the epitopes required for antibody-mediated OX40 agonism. Full article
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Open AccessFeature PaperArticle
Rapid Generation of Monoclonal Antibodies from Single B Cells by Ecobody Technology
Antibodies 2018, 7(4), 38; https://doi.org/10.3390/antib7040038
Received: 25 September 2018 / Revised: 25 October 2018 / Accepted: 31 October 2018 / Published: 7 November 2018
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Abstract
Single B cell sampling following to direct gene amplification and transient expression in animal cells has been recognized as powerful monoclonal antibodies (mAbs) screening strategies. Here we report Ecobody technology which allows mAbs screening from single B cells in two days This technology [...] Read more.
Single B cell sampling following to direct gene amplification and transient expression in animal cells has been recognized as powerful monoclonal antibodies (mAbs) screening strategies. Here we report Ecobody technology which allows mAbs screening from single B cells in two days This technology uses Escherichia coli cell-free protein synthesis (CFPS) for mAb expression. In the CFPS step, we employed our original techniques: (1) ‘Zipbody’ as a modified Fab (fragment of antigen binding) format, in which the active Fab formation is facilitated by adhesive leucine zipper peptides fused at the C-termini of the light and heavy chains; and (2) an N-terminal SKIK peptide tag that can markedly increase protein production. By the Ecobody technology, we demonstrated rapid screening of antigen specific mAbs from immunized rabbits and Epstein-Barr Virus infected human B cells. We further obtained rabbit mAbs in E. coli expression system yielding to 8.5 mg of purified proteins from 1 L bacterial culture. Full article
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