Predominant structural configuration of natural antibody repertoires enables potent antibody responses against protein antigens

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.

Antibodyomics: bioinformatics technologies for understanding B‐cell immunity to HIV‐1

“…These results suggest that the predominant CDR‐canonical structure in mouse antibody repertoires is a robust framework capable of encoding highly functional antibodies against diverse protein antigens. The results confirm the utility of phage‐displayed synthetic antibody libraries in testing hypotheses concerning natural antibody repertoires and in developing artificial antibody repertoires to discover functional antibodies targeting diverse epitopes 111, 114, 115, 116, 117…”

“…As random searching for functional antibodies to counter the near‐infinite diversity of potential immunogens may be problematic, well‐configured antibody repertoires may be key to protective humoral immunity 111. The human immune system, for example, typically responds to a novel antigen by generating antigen‐specific antibodies within just a few weeks 112…”

“…11). 114, 115, 116, 117 NGS was employed to sample the antibody repertoire, and we used the extracellular domain (ECD) of human epidermal growth factor receptor 2 (HER2) as a model antigen 111. Computational analysis of the NGS data indicated that the antibody repertoires from naïve mice and from vaccinated mice immunized with various immunization protocols were largely skewed toward a CDR‐canonical structure.…”

“…As random searching for functional antibodies to counter the nearinfinite diversity of potential immunogens may be problematic, well-configured antibody repertoires may be key to protective humoral immunity. 111 The human immune system, for example, typically responds to a novel antigen by generating antigen-specific antibodies within just a few weeks. 112 Unfortunately, our understanding of the principles underlying well-configured antibody repertoires has been hindered by two Continued technical advances in NGS and in antibody library synthesis have, however, begun to make headway in addressing these technical barriers [reviewed in (53,113)], and a number of fundamental F I G U R E 9 Antibodyomics8: Free energy perturbation analysis of antibodyantigen interactions.…”

High throughput cytotoxicity screening of anti-HER2 immunotoxins conjugated with antibody fragments from phage-displayed synthetic antibody libraries

“…Candidate scFvs were then screened for soluble scFv binding to HER2-ECD and for binding to Protein A and Protein L (step 3)27. Simultaneous binding to Protein A and Protein L indicates that the scFv with the IGKV1-NL1*01/IGHV3-23*04 framework is well-folded (structure shown in PDB code: 4HKZ)33.…”