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Front. Immunol. | doi: 10.3389/fimmu.2018.00395

The many routes to an antibody heavy-chain CDR3: necessary, yet insufficient, for specific binding

  • 1Specifica Inc, United States
  • 2Los Alamos National Laboratory (DOE), United States

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 vast 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.

Based on 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.

Keywords: HCDR3, scFv display, Binding Specificity, rearrangement, Inverse PCR

Received: 01 Dec 2017; Accepted: 13 Feb 2018.

Edited by:

Jacob Glanville, Distributed Bio, United States

Reviewed by:

Mepur H. Ravindranath, Terasaki Foundation, United States
Ramya Yarlagadda, Intrexon (United States), United States  

Copyright: © 2018 D'angelo, Ferrara, Naranjo, Erasmus, Hraber and Bradbury. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: MD, PhD. Andrew R. Bradbury, Specifica Inc, Santa Fe, United States,