Abstract
Humoral immunity against diverse pathogens is rapidly elicited from natural antibody repertoires of limited complexity. But the organizing principles underlying the antibody repertoires that facilitate this immunity are not well-understood. We used HER2 as a model immunogen and reverse-engineered murine antibody response through constructing an artificial antibody library encoded with rudimentary sequence and structural characteristics learned from high throughput sequencing of antibody variable domains. Antibodies selected in vitro from the phage-displayed synthetic antibody library bound to the model immunogen with high affinity and specificities, which reproduced the specificities of natural antibody responses. We conclude that natural antibody structural repertoires are shaped to allow functional antibodies to be encoded efficiently, within the complexity limit of an individual antibody repertoire, to bind to diverse protein antigens with high specificity and affinity. Phage-displayed synthetic antibody libraries, in conjunction with high-throughput sequencing, can thus be designed to replicate natural antibody responses and to generate novel antibodies against diverse antigens.
Highlights
Only a few predominant epitopes[3]
The GH2 artificial antibody repertoire was constructed to encode minimal but essential characteristics key to the competence of the natural antibody repertoires: all GH2 antibody variants were derived from a single variable domain template with all six complementarity determining regions (CDRs) structures resembling the most prevalent CDR structures respectively as revealed by the next generation sequencing (NGS) data of the mouse antibody repertoires; the amino acid type diversity and preference at each residue position of the 6 CDRs in the artificial repertoire were encoded with the rudimentary principles in (a) conserving amino acid types at structurally critical residue positions, (b) mimicking the aromatic amino acid distributions in position and magnitude over the CDRs in natural antibodies, and (c) distributing short chain hydrophilic residues among the aromatic residues
Synthetic antibodies derived from phage display selection and screening of the GH2 antibody library bound to the human epidermal growth factor receptor 2 (HER2)/extracellular domain (ECD) with affinities approaching to those of the affinity-matured antibodies elicited from HER2/ECD-immunized mice, indicating that the combination of canonical structure (CS) configuration and proper CDR amino acid distribution are sufficient conditions to reach affinity-matured antibodies
Summary
Only a few predominant epitopes[3]. The natural antibody responses can be partially understood by the large number of B cells (on the order of 1011 in a human body6), each of which expresses a unique B cell receptor (BCR) through antibody gene segment recombination and segment junction diversification[7]. The remarkable functionality of the natural antibody repertoires must reside in the repertoire composition, where nature solves the intractable sequence space search problem, after billions of years of evolution, by shaping the antibody repertoires as such that adequate antibodies are readily available in the repertoire to respond to almost any immunogen challenges without extensively relying on SHM to explore the vast sequence space This expectation has been supported by the evidence where antibodies selected in vitro from phage-displayed human antibody libraries[15] or phage-displayed synthetic antibody libraries mimicking natural antibody repertoires[16] are able to recognize random protein antigens with high affinity and specificity without affinity maturation in vivo. Once the antibody library is synthesized and displayed on phage particles[31,32,33], the characteristics of the natural antibody repertoires can be queried with the phage display system
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