Beyond Hot Spots: Biases in Antibody Somatic Hypermutation and Implications for Vaccine Design

Abstract

The evolution of antibodies in an individual during an immune response by somatic hypermutation (SHM) is essential for the ability of the immune system to recognize and remove the diverse spectrum of antigens that may be encountered. These mutations are not produced at random; nucleotide motifs that result in increased or decreased rates of mutation were first reported in 1992. Newer models that estimate the propensity for mutation for every possible 5- or 7-nucleotide motif have emphasized the complexity of SHM targeting and suggested possible new hot spot motifs. Even with these fine-grained approaches, however, non-local context matters, and the mutations observed at a specific nucleotide motif varies between species and even by locus, gene segment, and position along the gene segment within a single species. An alternative method has been provided to further abstract away the molecular mechanisms underpinning SHM, prompted by evidence that certain stereotypical amino acid substitutions are favored at each position of a particular V gene. These "substitution profiles," whether obtained from a single B cell lineage or an entire repertoire, offer a simplified approach to predict which substitutions will be well-tolerated and which will be disfavored, without the need to consider path-dependent effects from neighboring positions. However, this comes at the cost of merging the effects of two distinct biological processes, the generation of mutations, and the selection acting on those mutations. Since selection is contingent on the particular antigens an individual has been exposed to, this suggests that SHM may have evolved to prefer mutations that are most likely to be useful against pathogens that have co-evolved with us. Alternatively, the ability to select favorable mutations may be strongly limited by the biases of SHM targeting. In either scenario, the sequence space explored by SHM is significantly limited and this consequently has profound implications for the rational design of vaccine strategies.

Keywords: affinity maturation; hot spot motifs; somatic hypermutation; substitution profiles; vaccine design.

Figure 1

Substitution profiles and the accumulation of rare mutations. (A) Substitution profile of VH1-69 as calculated by Sheng et al. (33). The germline amino acid sequence is shown below the logo plot. (B) Sequence alignment of VH1-69-derived influenza antibodies capable of neutralizing multiple subtypes. Dots indicate the germline amino acid and extremely rare substitutions [as defined in Ref. (33)] are shown in red. (C) Substitution profile of VH1-2. (D) Sequence alignment of VH1-2-derived broadly neutralizing HIV antibodies targeting the CD4 binding site. Each contains greater than ~20% or more extremely rare substitutions.