Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination

Abstract

In order to produce effective antibodies, B cells undergo rapid somatic hypermutation (SHM) and selection for binding affinity to antigen via a process called affinity maturation. The similarities between this process and evolution by natural selection have led many groups to use phylogenetic methods to characterize the development of immunological memory, vaccination, and other processes that depend on affinity maturation. However, these applications are limited by the fact that most phylogenetic models are designed to be applied to individual lineages comprising genetically diverse sequences, while B cell repertoires often consist of hundreds to thousands of separate low-diversity lineages. Further, several features of affinity maturation violate important assumptions in standard phylogenetic models. Here, we introduce a hierarchical phylogenetic framework that integrates information from all lineages in a repertoire to more precisely estimate model parameters while simultaneously incorporating the unique features of SHM. We demonstrate the power of this repertoire-wide approach by characterizing previously undescribed phenomena in affinity maturation. First, we find evidence consistent with age-related changes in SHM hot-spot targeting. Second, we identify a consistent relationship between increased tree length and signs of increased negative selection, apparent in the repertoires of recently vaccinated subjects and those without any known recent infections or vaccinations. This suggests that B cell lineages shift toward negative selection over time as a general feature of affinity maturation. Our study provides a framework for undertaking repertoire-wide phylogenetic testing of SHM hypotheses and provides a means of characterizing dynamics of mutation and selection during affinity maturation.

Distinct clonal evolution of B-cells in HIV controllers with neutralizing antibody breadth

“…The largest lineage trees constructed in TNs and NNs are visualized in Figure 3E and Figure 3F respectively. These results are therefore consistent with prior observations that B cell lineages shift toward negative selection over time as a general feature of affinity maturation (29) and suggest that the dominant clones in the TNs have reached a peak of maximum affinity maturation where further random amino acid changes would rather be detrimental and decrease affinity (30).…”

“…Next, we estimated the evolutionary process of mutation and selection in B cells using phylogenetic models. Selective dynamics have been estimated using ω: dN/dS, the ratio of nonsynonymous (amino acid replacement) and synonymous (silent) mutation rates (28,29). Low ωCDR values indicate fewer amino acid changes in CDRs than expected suggesting negative BCR selection to remove affinitydecreasing variants, while positive selection to introduce new affinity-increasing amino acid variants is associated with higher ωCDR values.…”

Phylogenetic analysis of migration, differentiation, and class switching in B cells

“…The proposed framework provides a principled, flexible, and scalable approach for characterizing migration, class switching, and differentiation in a wide array of contexts. This differs from other phylogenetic tools we developed recently, which used model-based approaches for characterizing somatic hypermutation and clonal selection [4,36]. The methods developed in this paper are available in the R package dowser , available at https://bitbucket.org/kleinstein/dowser as part of the Immcantation suite (http://immcantation.org).…”

“…Sequences were obtained from peripheral blood samples taken from one subject at ten time points, from eight days before to 28 days after influenza vaccination [26] (subject 420IV). Sequence preprocessing and clonal clustering are described in [4]. Sequences were down-sampled by 50%, and only clones with >10 unique sequences were retained.…”

“…The genetic variation within these clonal lineages has been long investigated using phylogenetic methods [2]. When obtained through high throughput sequencing, BCR sequences have shown promise in elucidating information about the adaptive immune response in humans, such as the sequence of mutations that occur during antibody co-evolution with HIV [3], and the process of mutation and selection during affinity maturation generally [4]. Other important biological processes may occur as BCR sequences evolve, such as B-cell migration between tissues [5], differentiation into cellular subsets [6], and antibody isotype class switching [7].…”