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Title: Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding

Abstract

Because of its great potential for diversity, the immunoglobulin heavy-chain complementarity-determining region 3 (HCDR3) is taken as an antibody molecule’s most important component in conferring binding activity and specificity. For this reason, HCDR3s have been used as unique identifiers to investigate adaptive immune responses in vivo and to characterize in vitro selection outputs where display systems were employed. Here, we show that many different HCDR3s can be identified within a target-specific antibody population after in vitro selection. For each identified HCDR3, a number of different antibodies bearing differences elsewhere can be found. In such selected populations, all antibodies with the same HCDR3 recognize the target, albeit at different affinities. In contrast, within unselected populations, the majority of antibodies with the same HCDR3 sequence do not bind the target. In one HCDR3 examined in depth, all target-specific antibodies were derived from the same VDJ rearrangement, while non-binding antibodies with the same HCDR3 were derived from many different V and D gene rearrangements. Careful examination of previously published in vivo datasets reveals that HCDR3s shared between, and within, different individuals can also originate from rearrangements of different V and D genes, with up to 26 different rearrangements yielding the same identical HCDR3more » sequence. On the basis of these observations, we conclude that the same HCDR3 can be generated by many different rearrangements, but that specific target binding is an outcome of unique rearrangements and VL pairing: the HCDR3 is necessary, albeit insufficient, for specific antibody binding.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [1]
  1. Specifica Inc., Santa Fe, NM (United States)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE; National Inst. of Health (NIH) (United States)
OSTI Identifier:
1430019
Report Number(s):
LA-UR-17-30898
Journal ID: ISSN 1664-3224
Grant/Contract Number:  
AC52-06NA25396; 1-U54-DK093500-01
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Immunology
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1664-3224
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science

Citation Formats

D'Angelo, Sara, Ferrara, Fortunato, Naranjo, Leslie, Erasmus, M. Frank, Hraber, Peter, and Bradbury, Andrew R. M. Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding. United States: N. p., 2018. Web. doi:10.3389/fimmu.2018.00395.
D'Angelo, Sara, Ferrara, Fortunato, Naranjo, Leslie, Erasmus, M. Frank, Hraber, Peter, & Bradbury, Andrew R. M. Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding. United States. https://doi.org/10.3389/fimmu.2018.00395
D'Angelo, Sara, Ferrara, Fortunato, Naranjo, Leslie, Erasmus, M. Frank, Hraber, Peter, and Bradbury, Andrew R. M. 2018. "Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding". United States. https://doi.org/10.3389/fimmu.2018.00395. https://www.osti.gov/servlets/purl/1430019.
@article{osti_1430019,
title = {Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding},
author = {D'Angelo, Sara and Ferrara, Fortunato and Naranjo, Leslie and Erasmus, M. Frank and Hraber, Peter and Bradbury, Andrew R. M.},
abstractNote = {Because of its great potential for diversity, the immunoglobulin heavy-chain complementarity-determining region 3 (HCDR3) is taken as an antibody molecule’s most important component in conferring binding activity and specificity. For this reason, HCDR3s have been used as unique identifiers to investigate adaptive immune responses in vivo and to characterize in vitro selection outputs where display systems were employed. Here, we show that many different HCDR3s can be identified within a target-specific antibody population after in vitro selection. For each identified HCDR3, a number of different antibodies bearing differences elsewhere can be found. In such selected populations, all antibodies with the same HCDR3 recognize the target, albeit at different affinities. In contrast, within unselected populations, the majority of antibodies with the same HCDR3 sequence do not bind the target. In one HCDR3 examined in depth, all target-specific antibodies were derived from the same VDJ rearrangement, while non-binding antibodies with the same HCDR3 were derived from many different V and D gene rearrangements. Careful examination of previously published in vivo datasets reveals that HCDR3s shared between, and within, different individuals can also originate from rearrangements of different V and D genes, with up to 26 different rearrangements yielding the same identical HCDR3 sequence. On the basis of these observations, we conclude that the same HCDR3 can be generated by many different rearrangements, but that specific target binding is an outcome of unique rearrangements and VL pairing: the HCDR3 is necessary, albeit insufficient, for specific antibody binding.},
doi = {10.3389/fimmu.2018.00395},
url = {https://www.osti.gov/biblio/1430019}, journal = {Frontiers in Immunology},
issn = {1664-3224},
number = ,
volume = 9,
place = {United States},
year = {Thu Mar 08 00:00:00 EST 2018},
month = {Thu Mar 08 00:00:00 EST 2018}
}

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Cited by: 36 works
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Works referenced in this record:

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Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting
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Comprehensive Interrogation of a Minimalist Synthetic CDR-H3 Library and Its Ability to Generate Antibodies with Therapeutic Potential
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Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells
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Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire
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In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire
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From deep sequencing to actual clones
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Inferring processes underlying B-cell repertoire diversity
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IgBLAST: an immunoglobulin variable domain sequence analysis tool
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Insertion of N regions into heavy-chain genes is correlated with expression of terminal deoxytransferase in B cells
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Next generation sequencing of all variable loops of synthetic single framework scFv—Application in anti-HDL antibody selections
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Structural repertoire of the human VH segments
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Theoretical studies of clonal selection: Minimal antibody repertoire size and reliability of self-non-self discrimination
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The Mechanism and Regulation of Chromosomal V(D)J Recombination
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Terminal deoxynucleotidyl transferase and repertoire development
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Using Phage Display to Select Antibodies Recognizing Post-translational Modifications Independently of Sequence Context
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Antibodies in haystacks: how selection strategy influences the outcome of selection from molecular diversity libraries
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In vivo recombination as a tool to generate molecular diversity in phage antibody libraries
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journal, December 1991


Assessment of antibody library diversity through next generation sequencing and technical error compensation
text, January 2017


Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting
text, January 2016


Isolation of high affinity human antibodies directly from large synthetic repertoires.
journal, July 1994


Influence of the V(D)J recombination mechanism on the formation of the primary T and B cell repertoires
journal, June 1994


Canonical structures for the hypervariable regions of immunoglobulins
journal, August 1987


Structural repertoire of the human VH segments
journal, October 1992


Theoretical studies of clonal selection: Minimal antibody repertoire size and reliability of self-non-self discrimination
journal, December 1979


Convergent Antibody Signatures in Human Dengue
journal, June 2013


Identifying functional anti-Staphylococcus aureus antibodies by sequencing antibody repertoires of patient plasmablasts
journal, May 2014


Specific binder for Lightning-Link® biotinylated proteins from an antibody phage library
journal, September 2013


The Remarkable Flexibility of the Human Antibody Repertoire; Isolation of Over One Thousand Different Antibodies to a Single Protein, BLyS
journal, November 2003


Comprehensive Interrogation of a Minimalist Synthetic CDR-H3 Library and Its Ability to Generate Antibodies with Therapeutic Potential
journal, May 2013


Deep sequencing in library selection projects: what insight does it bring?
journal, August 2015


Deep sequencing of phage display libraries to support antibody discovery
journal, March 2013


High-Throughput Screening of Single-Chain Antibodies Using Multiplexed Flow Cytometry
journal, March 2007


Insertion of N regions into heavy-chain genes is correlated with expression of terminal deoxytransferase in B cells
journal, October 1984


Conformations of immunoglobulin hypervariable regions
journal, December 1989


Exploiting recombination in single bacteria to make large phage antibody libraries
journal, January 2000


Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples
journal, June 2016


In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire
journal, December 2014


Endothelial Unc5B controls blood-brain barrier integrity
journal, March 2022


Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing
journal, January 2015


Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire
journal, October 2009


Identification and characterization of the constituent human serum antibodies elicited by vaccination
journal, January 2014


Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells
journal, June 2014


Semisynthetic combinatorial antibody libraries: a chemical solution to the diversity problem.
journal, May 1992


In vitro selection and affinity maturation of antibodies from a naive combinatorial immunoglobulin library.
journal, April 1992


A complementarity-determining region synthetic peptide acts as a miniantibody and neutralizes human immunodeficiency virus type 1 in vitro.
journal, May 1993


Structural diversity in a human antibody germline library
journal, May 2016


Receptor Revision of Immunoglobulin Heavy Chain Variable Region Genes in Normal Human B Lymphocytes
journal, May 2000


Construction of a semisynthetic antibody library using trinucleotide oligos
journal, November 1997


Antibody binding loop insertions as diversity elements
journal, October 2006


IMGT(R), the international ImMunoGeneTics information system(R)
journal, January 2009


Using T7 phage display to select GFP-based binders
journal, May 2008


From deep sequencing to actual clones
journal, September 2014


Affinity transfer by CDR grafting on a nonimmunoglobulin scaffold
journal, July 2004


Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting
journal, March 2016


Antibody Multispecificity Mediated by Conformational Diversity
journal, February 2003


Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination
journal, February 2013


Mechanism and Control of V(D)J Recombination at the Immunoglobulin Heavy Chain Locus
journal, April 2006


Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes
journal, January 2013


A Public Database of Memory and Naive B-Cell Receptor Sequences
journal, August 2016


Assembly of IgH CDR3: Mechanism, Regulation, and Influence on Antibody Diversity
journal, January 1992


The Application of Next Generation Sequencing to the Understanding of Antibody Repertoires
journal, January 2013


The Restricted D H Gene Reading Frame Usage in the Expressed Human Antibody Repertoire Is Selected Based upon its Amino Acid Content
journal, April 2013


Large scale production of phage antibody libraries using a bioreactor
journal, January 2015


Inferring processes underlying B-cell repertoire diversity
text, January 2015


Works referencing / citing this record:

Recombinant Antibodies against Mycolactone
journal, June 2019


Adaption of human antibody λ and κ light chain architectures to CDR repertoires
journal, March 2019


Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences
journal, December 2019


Exploiting next-generation sequencing in antibody selections – a simple PCR method to recover binders
journal, January 2020


Stability and uniqueness of clonal immunoglobulin CDR3 sequences for MRD tracking in multiple myeloma
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Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences
text, January 2020


Exploiting next-generation sequencing in antibody selections – a simple PCR method to recover binders
journal, January 2020


Immunosenescence and human vaccine immune responses
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ASAP - A Webserver for Immunoglobulin-Sequencing Analysis Pipeline
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Recombinant Antibodies against Mycolactone
journal, June 2019