Research Article

The microanatomic segregation of selection by apoptosis in the germinal center

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Science  13 Oct 2017:
Vol. 358, Issue 6360, eaao2602
DOI: 10.1126/science.aao2602

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Light- and dark-zone death dynamics

Germinal centers (GCs) are areas within lymphoid organs where mature B cells expand and differentiate during normal immune responses. GCs are separated into two anatomic compartments: the dark zone, where B cells divide and undergo somatic hypermutation, and the light zone, where they are selected for affinity-enhancing mutations after interacting with T follicular helper cells. Mayer et al. studied apoptosis reporter mice and found that both GC zones experience very high rates of apoptosis (see the Perspective by Bryant and Hodgkin). However, the underlying mechanisms were distinct and microanatomically segregated. Light-zo ne B cells underwent apoptosis by default unless they were rescued by positive selection. In contrast, apoptotic dark-zone B cells were highly enriched among cells with genes damaged by random antibody-gene mutations.

Science, this issue p. eaao2602; see also p. 171

Structured Abstract


Germinal centers (GCs) are transient microanatomic structures that form in lymphoid organs during an immune response. They are the sites of B cell clonal expansion and affinity maturation, a process that leads to the production of high-affinity antibodies. GCs are highly dynamic and contain activated B cells, specialized T follicular helper (TFH) cells, and antigen-trapping follicular dendritic cells. GCs are organized into two functionally distinct compartments: a dark zone (DZ) and a light zone (LZ). The DZ is the site of rapid cell division and random antibody-gene mutation, which is initiated by activation-induced cytidine deaminase (AID). The mutation process leads to the accumulation of a large number of closely related B cells that carry receptors with distinct antigen-binding properties. Once they stop dividing, DZ B cells migrate to the LZ, where their newly generated B cell receptors (BCRs) are tested: GC B cells with relatively higher-affinity receptors capture and process more antigen, leading to positive selection by interaction with TFH cells. The positively selected LZ B cells return to the DZ, where they undergo further cycles of division and mutation. Concomitantly, small numbers of memory B cells and antibody-secreting plasma cells exit the GC. Together, these processes provide the mechanistic basis for affinity maturation, which is essential for effective vaccination and protection from infections.


In addition to producing antibody variants, AID expression is also a threat to the genome. AID can produce double-strand breaks that are substrates for chromosome translocations. It can also produce immunoglobulin (Ig) gene missense mutations and deletions or create self-reactive antibodies. These deleterious mutations need to be selected against. Indeed, histologists have long appreciated large numbers of apoptotic nuclei in the specialized tingible body macrophages found in GCs. However, beyond histology, little is known about the exact rate of GC B cell apoptosis and whether it differs in the DZ and LZ of the GC. Moreover, the mechanisms that cause apoptosis, their relative importance in each GC compartment, and their role in GC B cell selection have not been defined. To examine these questions, we created fluorescent apoptosis-indicator mice and used them to enumerate, isolate, and characterize dying cells in the GC.


We found that apoptosis is prevalent in both the DZ and LZ compartments of GCs throughout the immune response: up to 50% of GC B cells undergo programmed cell death every 6 hours. Single dying GC B cells were isolated, and their antibody genes were cloned, expressed by transient transfection, and tested for antigen binding and other properties. Apoptotic DZ cells were highly enriched for Ig genes damaged by AID, including missense mutations and deletions. By contrast, dying LZ cells primarily expressed intact antibodies with a range of affinities indistinguishable from GC B cells in the live LZ compartment. By experimentally blocking positive selection and by using reporter mice for Myc, a proto-oncogene, as an indicator of positive selection, we found that apoptosis is the default fate for LZ GC B cells that are not actively positively selected. Thus, LZ GC B cells carrying low-affinity BCRs do not preferentially undergo apoptosis. Instead, apoptosis occurs irrespective of BCR-affinity, and LZ B cells carrying high-affinity BCRs are simply more likely to be positively selected.


Apoptosis is a major feature of GC B cell biology and is required to counterbalance the high rate of proliferation and purge B cells that carry deleterious mutations. Although apoptosis occurs in both the DZ and LZ, the underlying mechanisms of apoptosis in each zone are distinct and microanatomically segregated. These insights into GC B biology are relevant for vaccine design, particularly for pathogens that normally evade effective antibody responses.

Germinal center B cells expressing an apoptosis indicator.

Intravital two-photon microscopy of GC B cells in popliteal lymph nodes of immunized mice (GC B cells, yellow and green; follicular dendritic cell networks, red). The fluorescence resonance energy transfer–based INDIA reporter was used to visualize and purify dying GC B cells.


B cells undergo rapid cell division and affinity maturation in anatomically distinct sites in lymphoid organs called germinal centers (GCs). Homeostasis is maintained in part by B cell apoptosis. However, the precise contribution of apoptosis to GC biology and selection is not well defined. We developed apoptosis-indicator mice and used them to visualize, purify, and characterize dying GC B cells. Apoptosis is prevalent in the GC, with up to half of all GC B cells dying every 6 hours. Moreover, programmed cell death is differentially regulated in the light zone and the dark zone: Light-zone B cells die by default if they are not positively selected, whereas dark-zone cells die when their antigen receptors are damaged by activation-induced cytidine deaminase.

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