Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
Katherine R Lawrence
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States; Quantitative Biology Initiative, Harvard University, Cambridge, United States; Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
Alief Moulana
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
Thomas Dupic
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
Jeffrey Chang
Department of Physics, Harvard University, Cambridge, United States
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, United States; Quantitative Biology Initiative, Harvard University, Cambridge, United States; Department of Physics, Harvard University, Cambridge, United States
Over the past two decades, several broadly neutralizing antibodies (bnAbs) that confer protection against diverse influenza strains have been isolated. Structural and biochemical characterization of these bnAbs has provided molecular insight into how they bind distinct antigens. However, our understanding of the evolutionary pathways leading to bnAbs, and thus how best to elicit them, remains limited. Here, we measure equilibrium dissociation constants of combinatorially complete mutational libraries for two naturally isolated influenza bnAbs (CR9114, 16 heavy-chain mutations; CR6261, 11 heavy-chain mutations), reconstructing all possible evolutionary intermediates back to the unmutated germline sequences. We find that these two libraries exhibit strikingly different patterns of breadth: while many variants of CR6261 display moderate affinity to diverse antigens, those of CR9114 display appreciable affinity only in specific, nested combinations. By examining the extensive pairwise and higher order epistasis between mutations, we find key sites with strong synergistic interactions that are highly similar across antigens for CR6261 and different for CR9114. Together, these features of the binding affinity landscapes strongly favor sequential acquisition of affinity to diverse antigens for CR9114, while the acquisition of breadth to more similar antigens for CR6261 is less constrained. These results, if generalizable to other bnAbs, may explain the molecular basis for the widespread observation that sequential exposure favors greater breadth, and such mechanistic insight will be essential for predicting and eliciting broadly protective immune responses.
