A Germinal Center Checkpoint of AIRE in B Cells Limits Antibody Diversification

Reviewer #1 (Public review):

Summary:

The authors provide in vivo and in vitro evidence for an interaction between AIRE and AID. This has implications for the dynamics of the germinal center response and autoimmunity related to the APSI disease.

The manuscript describes an unexpected function of AIRE, which is more well known for its function to regulate negative selection of T cells in the thymus. Here, the gene has also been shown to be expressed by B cells (Immunity 2015: 26070482). They describe that AIRE interacts with AID, and in its absence, B cells acquire more hypermutations and also produce auto-antibodies against IL-17. These autoantibodies have been described previously.

Strengths:

The study is interesting and provides some additional information about how AIRE regulates immune cell function. Several biochemical and in vivo experiments show the interaction and the function of AIREs in the regulation of AID activity in the GC response.

Weaknesses:

Some of the hypothetical consequences of this regulation are not investigated. This includes responses to model antigens and dynamics of the germinal center related to kinetics.

Major Comments:

(1) AID regulates both switch and somatic hypermutation. Switch is easier to achieve, so which of these processes does AIRE influence the most? Also, the switch is thought to occur before the B cell enters the GC. Looking at the histology, is AIRE also expressed at the early proliferative stage that has been described by Ann Haberman?

(2) In experiments determining anti-CD40-dependent upregulation of AIRE, naïve resting B cells were used from mice. A proportion of the B-cells got activated. Are these MZB or FOB cells as MZBs are more easily activated?

(3) In the BM chimeric experiments in Figure 3. Do the AIRE+ and AIRE - populations distribute equally among B cell subpopulations?

(4) Furthermore, in the NP-KLH experiments, one would expect that B cells with increased affinity would leave the GC earlier and become plasma cells. Thus, the kinetics of the AIRE+ vs AIRE- B cells within the GC would be different? Also, would they maybe take over at some point, as the increased affinity would favor help from Tfh cells that are known to be limited?

(5) Given the previous studies on AIRE's function in regulating transcription (PMID: 34518235), how does this interaction fit into this picture?

(6) In the uracil experiments, the readout for AID to induce double-stranded breaks could be tested.

(7) The candida experiments are a nice connection to the situation in patients. However, why is it mostly auto-antibodies against IL-17? How about other immune responses, as well as T cell-independent type I and II responses?

Reviewer #2 (Public review):

Summary:

In this study, Zhou et al investigated the expression and function of AIRE in B cells in peripheral lymphoid tissues. First, they found the expression of AIRE protein in mature B cells in the follicles in human tonsils and spleens from healthy donors. Flow cytometry analyses using human samples as well as Aire-reporter mice demonstrated AIRE expression in germinal center B cells. The expression of Aire in B cells was induced by CD40 signals. Then, to investigate the impact of AIRE deficiency on B-cell function, the authors used a method of transplanting bone marrow cells from Aire-KO and WT mice into B-cell-deficient mice, comparing B-cell development and function reconstituted in the recipient mice. Their results showed that Aire-deficient B cells strongly responded to immunization with antigens, exhibiting enhanced class switching and somatic hypermutation of antibodies compared with WT B cells. The same phenomena were observed in CRISPRed B cell lines lacking Aire. The authors successfully utilized the Aire-deficient B cell line to demonstrate that Aire suppresses antibody class switching and somatic hypermutation via its interaction with AID. Finally, using B cell transfer into B cell-deficient mice demonstrated that mice harboring Aire-deficient B cells produced high levels of autoantibodies against Th17 cytokines and exhibited reduced resistance to Candida infection. This mirrors characteristic symptoms in AIRE-deficient patients. The findings of this study not only reveal an unexpected function of AIRE in B cells but also have the potential to contribute to understanding the pathogenesis of APECED and to offering a new direction for developing therapies.

Strengths:

The strength of this study lies in demonstrating the expression of the function of AIRE in B cells in both mice and humans. It also revealed the direct interaction between AIRE and AID, along with its binding mode (requiring CARD and NLS domains of AIRE), and showed that this interaction is crucial for AIRE function in B cells. It is also significant that the study demonstrated how B-cell-intrinsic dysfunction of AIRE leads to autoantibody production against cytokines.

Weaknesses:

As for loss-of-function analysis of Aire in B cells, in addition to the B cell transfer from Aire-KO mice performed in this study, generating B cell-specific Aire-deficient mice using Aire-flox mice (Dobes et al, Eur J Immunol 2018) would further reinforce the conclusions of this study. Furthermore, the relationship with Aire function in thymic B cells reported by previous studies remains unclear, posing an unresolved challenge. This study also failed to address whether Aire deficiency affects gene expression in GC B cells, in particular, whether it induces the expression of various self-antigens as reported in thymic B cells or mTECs.