Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody
- University of California, San Francisco, United States
- Harvard Medical School, United States
- Harvard University, United States
Abstract
Broadly neutralizing antibodies (bnAbs) that neutralize diverse variants of a particular virus are of considerable therapeutic interest1. Recent advances have enabled us to isolate and engineer these antibodies as therapeutics, but eliciting them through vaccination remains challenging, in part due to our limited understanding of how antibodies evolve breadth2. Here, we analyze the landscape by which an anti-influenza receptor binding site (RBS) bnAb, CH65, evolved broad affinity to diverse H1 influenza strains3,4. We do this by generating an antibody library of all possible evolutionary intermediates between the unmutated common ancestor (UCA) and the affinity-matured CH65 antibody and measure the affinity of each intermediate to three distinct H1 antigens. We find that affinity to each antigen requires a specific set of mutations - distributed across the variable light and heavy chains - that interact non-additively (i.e., epistatically). These sets of mutations form a hierarchical pattern across the antigens, with increasingly divergent antigens requiring additional epistatic mutations beyond those required to bind less divergent antigens. We investigate the underlying biochemical and structural basis for these hierarchical sets of epistatic mutations and find that epistasis between heavy chain mutations and a mutation in the light chain at the VH-VL interface is essential for binding a divergent H1. Collectively, this work is the first to comprehensively characterize epistasis between heavy and light chain mutations and shows that such interactions are both strong and widespread. Together with our previous study analyzing a different class of anti-influenza antibodies5, our results implicate epistasis as a general feature of antibody sequence-affinity landscapes that can potentiate and constrain the evolution of breadth.
Data availability
Data and code used for this study are available at https://github.com/amphilli/CH65-comblib. Antibody affinity and expression data are also available in an interactive data browser at https://ch65-ma90-browser.netlify.app/. FASTQ files from high-throughput sequencing are deposited in the NCBI BioProject database under PRJNA886089. X-ray crystal structures of the Fabs reported here are available at the Protein Data Bank (8EK6 and 8EKH).
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Binding affinity landscape of CH65 to divergent influenza H1 strainsNCBI BioProject, PRJNA886089.
Article and author information
Author details
Funding
Howard Hughes Medical Institute (Hanna H. Gray Postdoctoral Fellowship)
- Angela M Phillips
Human Frontier Science Program (Postdoctoral Fellowship)
- Thomas Dupic
National Institutes of Health (R01AI146779)
- Aaron G Schmidt
National Institutes of Health (P01AI89618-A1)
- Aaron G Schmidt
National Science Foundation (DMS-1764269)
- Michael M Desai
National Science Foundation (DMS-1655960)
- Michael M Desai
National Institutes of Health (GM104239)
- Michael M Desai
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2023, Phillips et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody
eLife 12:e83628.
https://doi.org/10.7554/eLife.83628
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