Multi Step Selection in Ig H Chains is Initially Focused on CDR3 and Then on Other CDR Regions

Abstract

Affinity maturation occurs through two selection processes: the choice of appropriate clones (clonal selection), and the internal evolution within clones, induced by somatic hyper-mutations, where high affinity mutants are selected for. When a final population of immunoglobulin sequences is observed, the genetic composition of this population is affected by a combination of these two processes. Different immune induced diseases can result from the failure of regulation of clonal selection or of the regulation of the within clone affinity maturation. In order to understand each of these processes separately, we propose a mixed lineage tree/sequence based method to detect within clone selection as defined by the effect of mutations on the average number of offspring. Specifically, we measure the imbalance in the number of leaves in lineage trees branches following synonymous and non-synonymous (NS) mutations. If a mutation is positively selected, we expect the number of leaves in the sub-tree below this mutation to be larger than in the parallel sub-tree without the mutation. The ratio between the number of leaves in such branches following NS mutations can be used to measure selection within a clone. We apply this method to the sampled Ig repertoire from multiple healthy volunteers and show that within clone selection is positive in the CDR2 region and either positive or negative in the CDR3 and FWR3 regions. Selection occurs already at the IgM isotype level mainly in the DH gene region, with a strong negative selection in the join region. This is followed in the later memory stages in the CDR2 region. We have not studied here the FWR1 and CDR1 regions. An important advantage of this method is that it is very weakly affected by the baseline mutation model or by sampling biases, as are most synonymous to NS mutations ratio based methods.

Quantifying evolutionary constraints on B-cell affinity maturation

“…Recent work has offered methods that evaluate selection on a per-sequence basis [38]. There have also been efforts to infer selection based on lineage shape [39][40][41][42][43][44], which has been a common approach in macroevolutionary studies (reviewed in [45]) and more recently in population genetics [46][47][48][49].…”

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire

“…These studies generally monitor global features of the BCR repertoire, such as diversity, mutation levels, isotype subclass usage, and VDJ segment usage frequency as well as identifying specific B cell clones. Identifying B cells arising from the same clonal origin was initially conducted based on identifying common VDJ segment usage ( 15 ), but there is now a move toward incorporating complementarity-determining region (CDR) three amino acid (AA) sequence identity into the definition ( 8 , 17 ), which forms at the junction of VDJ joining and is the most important region for determining antigen-binding properties ( 19 ).…”

Delta Inulin Adjuvant Enhances Plasmablast Generation, Expression of Activation-Induced Cytidine Deaminase and B-Cell Affinity Maturation in Human Subjects Receiving Seasonal Influenza Vaccine

“…BCR antigen specificity is dictated by the complementarity determining regions (CDR), particularly the CDR3 formed by contributions from the V, D, J gene segments during BCR recombination, as depicted in Fig 3A . During B-cell affinity maturation, amino acid substitutions, additions and deletions are introduced into the CDR3 region thereby allowing generation of new non-germline BCR sequences with higher antigen affinity [ 18 ]. We hypothesized that if Advax was enhancing BCR maturation, this should be reflected by an increased frequency of plasmablast BCR amino acid substitutions focused in the antigen-binding CDR3 domain of plasmablasts in the Advax adjuvant groups.…”