Dynamics of heavy chain junctional length biases in antibody repertoires

Kannan Sankar,Isidro Hötzel,Kam Hon Hoi

doi:10.1038/s42003-020-0931-3

Abstract

Antibody variable domain sequence diversity is generated by recombination of germline segments. The third complementarity-determining region of the heavy chain (CDR H3) is the region of highest sequence diversity and is formed by the joining of heavy chain VH, DH and JH germline segments combined with random nucleotide trimming and additions between these segments. We show that CDR H3 and junctional segment length distributions are biased in human antibody repertoires as a function of VH, VL and JH germline segment utilization. Most length biases are apparent in the naive and antigen experienced B cell compartments but not in nonproductive recombination products, indicating B cell selection as a major driver of these biases. Our findings reveal biases in the antibody CDR H3 diversity landscape shaped by VH, VL, and JH germline segment use during naive and antigen-experienced repertoire selection.

Highlights

Antibody variable domain sequence diversity is generated by recombination of germline segments
Understanding antibody complementarity-determining region (CDR) H3 diversity generation, a process critical for the availability of immune receptors binding a wide range of antigens, has long been a goal in the immunology and antibody engineering fields
CDR H3 and junctional segments lengths in the B cell repertoire have been assumed to be independent of value thresholds of 10−4 (VH) and JH germline segments except for their lengths prior to recombination[17,19,20]

Summary

Introduction

Antibody variable domain sequence diversity is generated by recombination of germline segments. A bias towards shorter average CDR H3 lengths is observed in mature relative to immature B cells and in isotype-switched memory B cells relative to naive to B cells[9,10,14] This is accompanied by a reduction of positively charged residue content and hydrophobicity within CDR H3 associated with negative selection of self-reactive clones in the repertoire[9,11,15,16]. A recent analysis of a large dataset of isotypeswitched human antibody sequences with paired chain information revealed an unexpected preferential pairing of IGHV3-7 (VH3-7) and Vκ2-30 germline segments[21] This was determined upon further analysis to be linked with short CDR H3 length biases associated with both germline segments. Our results show several biases in CDR H3 and junctional length distributions associated with VH, VL, and JH germline segment utilization that shape naive and antigen-experienced antibody repertoires in unexpected and unpredictable patterns

Methods

Results

Conclusion