SUMMARYBAFF, an activator of the noncanonical NFκB pathway, provides critical survival signals during B cell maturation and contributes to B cell proliferation. We found that the NFκB family member RelB is required ex vivo for B cell maturation, but cRel is required for proliferation. Combined molecular network modeling and experimentation revealed Nfkb2 p100 as a pathway switch; at moderate p100 synthesis rates in maturing B cells, BAFF fully utilizes p100 to generate the RelB:p52 dimer, whereas at high synthesis rates, p100 assembles into multimeric IκBsome complexes, which BAFF neutralizes in order to potentiate cRel activity and B cell expansion. Indeed, moderation of p100 expression or disruption of IκBsome assembly circumvented the BAFF requirement for full B cell expansion. Our studies emphasize the importance of p100 in determining distinct NFκB network states during B cell biology, which causes BAFF to have context-dependent functional consequences.

The transcription factor NFκB is a regulator of inflammatory and adaptive immune responses, yet only IκBα has been shown to limit NFκB activation and inflammatory responses. We investigated another negative feedback regulator, IκBε, in regulating B cell proliferation and survival. The loss of IκBε showed increased B cell proliferation and survival in response to both antigenic and innate stimulation. NFκB activity was elevated during late phase activation, but the dimer composition was stimulus-specific. In response to IgM, cRel dimers were elevated in IκBε-deficient cells, yet in response to LPS, RelA dimers were elevated also. The corresponding dimer-specific sequences were found in the promoters of hyper-activated genes. Using a mathematical model of the NFκB signaling system in B cells, we demonstrated that kinetic considerations of the IKK signaling input and IκBε’s interactions with RelA- and cRel-specific dimers could account for this stimulus-specificity. cRel is known to be the key regulator of B cell expansion. We found that RelA-specific phenotype in LPS-stimulated cells was physiologically relevant: unbiased transcriptome profiling identified the inflammatory cytokine, interleukin 6 (IL-6) to be hyper-activated in IκBε−/− B cells. When the IL-6 receptor was blocked, LPS-responsive IκBε−/− B cell proliferation was specifically reduced to near wild type levels. Our results provide novel evidence of a critical role of immune-response functions for IκBε in B cells; it regulates proliferative capacity via at least two mechanisms involving cRel and RelA-containing NFκB dimers. This study illustrates the importance of kinetic considerations in understanding the functional specificity of negative feedback regulators.

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Understanding the functions of multi-cellular organs in terms of the molecular networks within each cell is an important step in the quest to predict phenotype from genotype. B-lymphocyte population dynamics, which are predictive of immune response and vaccine effectiveness, are determined by individual cells undergoing division or death seemingly stochastically. Based on tracking single-cell time-lapse trajectories of hundreds of B cells, single-cell transcriptome, and immunofluorescence analyses, we constructed an agent-based multi-modular computational model to simulate lymphocyte population dynamics in terms of the molecular networks that control NF-κB signaling, the cell cycle, and apoptosis. Combining modeling and experimentation, we found that NF-κB cRel enforces the execution of a cellular decision between mutually exclusive fates by promoting survival in growing cells. But as cRel deficiency causes growing B cells to die at similar rates to non-growing cells, our analysis reveals that the phenomenological decision model of wild-type cells is rooted in a biased race of cell fates. We show that a multi-scale modeling approach allows for the prediction of dynamic organ-level physiology in terms of intra-cellular molecular networks.

Key Points NF-κB family members RelB and cRel are coordinately activated by BAFF and provide distinct survival signals. In vivo and in vitro B-cell developmental defects are observed when both RelB and cRel are deleted.