Functional Relevance of Improbable Antibody Mutations for HIV Broadly Neutralizing Antibody Development

Abstract

HIV-1 broadly neutralizing antibodies (bnAbs) require high levels of activation-induced cytidine deaminase (AID)-catalyzed somatic mutations for optimal neutralization potency. Probable mutations occur at sites of frequent AID activity, while improbable mutations occur where AID activity is infrequent. One bottleneck for induction of bnAbs is the evolution of viral envelopes (Envs) that can select bnAb B cell receptors (BCR) with improbable mutations. Here we define the probability of bnAb mutations and demonstrate the functional significance of key improbable mutations in three bnAb B cell lineages. We show that bnAbs are enriched for improbable mutations, which implies that their elicitation will be critical for successful vaccine induction of potent bnAb B cell lineages. We discuss a mutation-guided vaccine strategy for identification of Envs that can select B cells with BCRs that have key improbable mutations required for bnAb development.

Graphical abstract

Figure 1

Improbable Mutations Confer Heterologous Neutralization in bnAb Development (A–C) BnAbs (A) CH235, (B) VRC01, and (C) BF520.1 and their corresponding mutants with reverted improbable mutations were tested for neutralization against heterologous viruses. The reversion of improbable mutations in all three bnAbs diminished neutralization potency. The chain in which the mutation was made is listed in parentheses. The estimated probabilities of the mutations, as well as the neutralization capacities of the antibody mutants against additional viruses, are included in Table S1.

Figure 2

BnAbs Are Enriched For Improbable Antibody Mutations (A) Table of improbable mutations (at the < 2% cutoff level) for a representative set of bnAbs. (B) Distributions of the number of improbable mutations from antibody heavy-chain sequences from three groups: (1) “RV144-induced” antibodies were isolated from RV144 vaccinated subjects by antigenically sorting with RV144 immunogens (red shaded area); (2) “uninfected” antibodies correspond to duplicated NGS reads from IgG antibodies isolated from PBMC samples from 8 HIV-uninfected individuals (blue shaded area; see methods for details on sampling); and (3) a representative set of published bnAbs are shown labeled above dotted lines that correspond to their number of improbable mutations. Green labels indicate bnAbs with high potency (< 1 ug/mL) and breadth (> 90%).