In addition to somatic recombination and junctional imprecision, antigen-activated B cells can undergo an additional diversity-generating process called somatic hypermutation. Upon exposure to antigen and receipt of the proper additional signals, most of which are provided by T cells, expression of activation-induced deaminase (AID) is turned on. This enzyme deaminates cytosine residues, converting them to uracil. When a B cell that carries this lesion replicates, it may place an adenine on the complementary strand, thus generating a G-to-A transition (see Figure 5-34). Alternatively, the uracil may be excised by DNA glycosylase to yield an abasic site. Such abasic sites, when copied, give rise to possible transitions as well as a transversion, unless the nucleotide opposite the gap is the original G that paired with the cytosine target. Mutations thus accumulate with every successive round of B-cell division, yielding numerous mutations in the rearranged VJ and VDJ segments. Error-prone filling by DNA polymerase of gaps created by nucleotide excision repair also contributes to somatic hypermutation.

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The process of somatic hypermutation occurs when lymphocytes reside in specialized microanatomic structures known as germinal centers. These structures, which arise within the follicles of secondary lymphoid organs upon immunization, consist of foci of thousands of rapidly proliferating and hypermutating B cells. In addition to B cells, germinal centers contain follicular dendritic cells, a cell type that serves as a depot for antigen that can be retrieved by B cells, and a small number of helper T cells specialized in providing selective signals that control B cells. Many of the somatic mutations induced by AID are deleterious in that they reduce the affinity of the encoded antibody for an antigen, but some improve the encoded antibody’s affinity for an antigen. In a process analogous to Darwinian evolution, B cells carrying affinity-increasing mutations have a selective advantage in picking up antigen from follicular dendritic cells, which allows them to successfully compete for signals from the limiting number of helper T cells residing in the germinal center, as described in Section 23.6. These signals thus trigger the clonal selection of higher-affinity B cells for further proliferation and additional mutations, as well as for differentiation into antibody-secreting plasma cells or memory B cells. The net result is generation of a B-cell population whose antibodies, as a rule, show a higher affinity for the antigen.

In the course of an immune response, or upon repeated immunization, the adaptive immune response exhibits affinity maturation—an increase in the average affinity of antibodies for an antigen as a function of time after antigen exposure—as the result of somatic hypermutation and selection. Antibodies produced following this phase of the adaptive immune response display affinities for antigen in the nanomolar (or better) range. For reasons that are not understood, the activity of AID is focused mainly on rearranged VJ and VDJ segments, and this targeting may therefore require active transcription. The entire process of somatic hypermutation is strictly antigen-dependent and shows an absolute requirement for interactions between the B cells and certain T-cell types.