Journal Club: Large-scale analysis of somatic hypermutations

This week I presented a paper by Burkovitz et al from Bar Ilan University in Israel.  The study investigates the mutations that occur in B-cell maturation and how the propensity for a change to be selected is affected by where in the antibody structure it is located. It nicely combines analysis of both DNA and amino-acid sequence with structural considerations to inform conclusions about how in vivo affinity maturation occurs.

Before being exposed to an antigen, an antibody has a sequence determined by a combination of genes (V and J for the light chain; V, D and J for the heavy chain). Once exposed, B-cells (the cells that produce antibodies), undergo somatic hyper-mutation (SHM) to optimise the antibody-antigen (ab-ag) interaction. These mutations are commonly thought to be promoted at activation-induced deaminase (AID) hotspots.

The authors’ first finding is that the locations of SHMs do not correlate well with the positions of AID hotspots and that the distribution of their distance to a hotspot is not much different to that of the background distribution. They conclude that although perhaps a mechanism to promote mutation, AID hotspots are not a strong factor that indicate whether a mutation will fix.

Motivated to find other determinants for SHM preferences, the study turns to examining structural features and energetics of the molecules. SHMs are found to be more prevalent on the VH domain of an Fv than the VL. However, when present, the energetic importance of an SHM is not related to the domain it is on. In contrast, the contribution an SHM makes to the binding energy is related to its structural location. As one might perhaps expect, those SHMs in positions that can make contact with the antigen have more affect than those that do not. Consideration of their propensity instead of raw frequency also shows that SHMs are more prevalent in antibody-antigen interfaces than in the rest of the molecule. However, they are also likely to occur in the VH-VL interface suggesting an importance for this region in fine-tuning the geometry and flexibility of the binding site.

figure

Figure taken from Burkovitz et al shows a) the location of different structural regions on the Fv b) the energetic contribution of the SHMs in each region c) the fraction of SHMs in the regions and their relative size d) the propensity for an SHM to occur in each of the five structural regions.

Perhaps the most interesting result of this study is the authors’ conclusions about the propensity of SHMs to mutate germline residues to particular amino-acids. It is found that whilst germline amino-acid usage in binding sites is distinctive from other protein-protein interfaces, the residue profiles of SHMs are less diverged. They therefore act to bring the properties ab-ag interaction towards those seen in normal interactions. This may suggest, as proposed by other studies, that the somatic hyper-mutation process is similar to mutation properties observed in evolution. In addition, it is found that five amino-acids, asparagine, arginine, serine, threonine and aspartic acid are the most common substitutions made in SHM. Finally, positions where SHMs most often have an important effect on binding energy are presented. These positions, and the amino-acid preferences provide promising targets for use in rational antibody design procedures.

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