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A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile

Antibody discovery by phage display consists of two phases, i.e., the binding phase and the amplification phase. Ideally, the selection process is dominated by the former, and all the retrieved clones are amplified equally during the latter. In reality, the amplification efficiency of antibody fragm...

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Autores principales: Bai, Xuelian, Jang, Moonseon, Lee, Nam Ju, Nguyen, Thi Thu Ha, Jung, Mooyoung, Hwang, Jeong Yeon, Shim, Hyunbo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9181208/
https://www.ncbi.nlm.nih.gov/pubmed/35682935
http://dx.doi.org/10.3390/ijms23116255
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author Bai, Xuelian
Jang, Moonseon
Lee, Nam Ju
Nguyen, Thi Thu Ha
Jung, Mooyoung
Hwang, Jeong Yeon
Shim, Hyunbo
author_facet Bai, Xuelian
Jang, Moonseon
Lee, Nam Ju
Nguyen, Thi Thu Ha
Jung, Mooyoung
Hwang, Jeong Yeon
Shim, Hyunbo
author_sort Bai, Xuelian
collection PubMed
description Antibody discovery by phage display consists of two phases, i.e., the binding phase and the amplification phase. Ideally, the selection process is dominated by the former, and all the retrieved clones are amplified equally during the latter. In reality, the amplification efficiency of antibody fragments varies widely among different sequences and, after a few rounds of phage display panning, the output repertoire often includes rapidly amplified sequences with low or no binding activity, significantly diminishing the efficiency of antibody isolation. In this work, a novel synthetic single-chain variable fragment (scFv) library with complementarity-determining region (CDR) diversities aimed at improved amplification efficiency was designed and constructed. A previously reported synthetic scFv library with low, non-combinatorial CDR diversities was panned against protein A superantigen, and the library repertoires before and after the panning were analyzed by next generation sequencing. The enrichment or depletion patterns of CDR sequences after panning served as the basis for the design of the new library. Especially for CDR-H3 with a higher and more random diversity, a machine learning method was applied to predict potential fast-amplified sequences among a simulated sequence repertoire. In a direct comparison with the previous generation library, the new library performed better against a panel of antigens in terms of the number of binders isolated, the number of unique sequences, and/or the speed of binder enrichment. Our results suggest that the amplification-centric design of sequence diversity is a valid strategy for the construction of highly functional phage display antibody libraries.
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spelling pubmed-91812082022-06-10 A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile Bai, Xuelian Jang, Moonseon Lee, Nam Ju Nguyen, Thi Thu Ha Jung, Mooyoung Hwang, Jeong Yeon Shim, Hyunbo Int J Mol Sci Article Antibody discovery by phage display consists of two phases, i.e., the binding phase and the amplification phase. Ideally, the selection process is dominated by the former, and all the retrieved clones are amplified equally during the latter. In reality, the amplification efficiency of antibody fragments varies widely among different sequences and, after a few rounds of phage display panning, the output repertoire often includes rapidly amplified sequences with low or no binding activity, significantly diminishing the efficiency of antibody isolation. In this work, a novel synthetic single-chain variable fragment (scFv) library with complementarity-determining region (CDR) diversities aimed at improved amplification efficiency was designed and constructed. A previously reported synthetic scFv library with low, non-combinatorial CDR diversities was panned against protein A superantigen, and the library repertoires before and after the panning were analyzed by next generation sequencing. The enrichment or depletion patterns of CDR sequences after panning served as the basis for the design of the new library. Especially for CDR-H3 with a higher and more random diversity, a machine learning method was applied to predict potential fast-amplified sequences among a simulated sequence repertoire. In a direct comparison with the previous generation library, the new library performed better against a panel of antigens in terms of the number of binders isolated, the number of unique sequences, and/or the speed of binder enrichment. Our results suggest that the amplification-centric design of sequence diversity is a valid strategy for the construction of highly functional phage display antibody libraries. MDPI 2022-06-02 /pmc/articles/PMC9181208/ /pubmed/35682935 http://dx.doi.org/10.3390/ijms23116255 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Bai, Xuelian
Jang, Moonseon
Lee, Nam Ju
Nguyen, Thi Thu Ha
Jung, Mooyoung
Hwang, Jeong Yeon
Shim, Hyunbo
A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile
title A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile
title_full A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile
title_fullStr A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile
title_full_unstemmed A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile
title_short A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile
title_sort novel synthetic antibody library with complementarity-determining region diversities designed for an improved amplification profile
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9181208/
https://www.ncbi.nlm.nih.gov/pubmed/35682935
http://dx.doi.org/10.3390/ijms23116255
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