NFAT and NF-κB dynamically co-regulate TCR and CAR signaling responses in human T cells

While it has been established that the responses of T cells to antigens are combinatorially regulated by multiple signaling pathways, it remains elusive what mechanisms cells utilize to quantitatively modulate T cell responses during pathway integration. Here, we show that two key pathways in T cell signaling, calcium/nuclear factor of activated T cells (NFAT) and protein kinase C (PKC)/nuclear factor κB (NF-κB), integrate through a dynamic and combinatorial strategy to fine-tune T cell response genes. At the cis-regulatory level, the two pathways integrate through co-binding of NFAT and NF-κB to immune response genes. Pathway integration is further regulated temporally, where T cell receptor (TCR) and chimeric antigen receptor (CAR) activation signals modulate the temporal relationships between the nuclear localization dynamics of NFAT and NF-κB. Such physical and temporal integrations together contribute to distinct modes of expression modulation for genes. Thus, the temporal relationships between regulators can be modulated to affect their co-targets during immune responses, underscoring the importance of dynamic combinatorial regulation in cellular signaling. [Display omitted] •Single-cell analysis of dynamic TCR and CAR signaling responses in human T cells•Temporal relationships between NFAT and NF-κB are modulated in an analog mode•Co-target genes with different functions decode temporal relationships differently•TCR and CAR signaling responses share similar dynamic regulatory principles Huang et al. show that the temporal relationships between the nuclear localization dynamics of NFAT and NF-κB are modulated by signal strength and type during TCR or CAR signaling in human T cells. The temporal relationships between two regulator dynamics are decoded to tune the expression of immune response genes.