Small transcriptional differences among cell clones lead to distinct NF-κB dynamics

Abstract

Transcription factor dynamics is fundamental to determine the activation of accurate transcriptional programs and yet is heterogeneous at single-cell level. The source of this dynamic variability is not completely understood. Here we focus on the nuclear factor κB (NF-κB), whose dynamics have been reported to cover a wide spectrum ranging from oscillatory to non-oscillatory. We show that clonal populations of immortalized fibroblasts derived from a single mouse embryo (that can hence be considered quasi-identical) display robustly distinct dynamics upon tumor necrosis α (TNF-α) stimulation. Combining transcriptomics, data-constrained mathematical modelling, and mRNA interference we show that small differences in the expression of genes belonging to the NF-κB regulatory circuit are predictive of the distinct responses to inflammatory stimuli observed among the clones. We propose that this transcriptional fine-tuning can be a general mechanism to produce cell subpopulations with distinct dynamic responses to stimuli within homogeneous cell populations.

Insights on the NF-κB System Using Live Cell Imaging: Recent Developments and Future Perspectives

“…Along these lines, a clever combination of computer vision, live cell imaging and computer modeling revealed that the levels of IκBα relative to p65 determine the responsiveness of NF-κB to TNF-α in 3T3 cells ( 68 ). We have proposed that the overall transcriptional differences in the expression of regulatory elements upon TNF-α stimulation are a major driver of the differences in the response of cells to stimuli ( 69 ), which suggests that the dynamical variation of the levels of the negative feedbacks can produce distinct NF-κB dynamics. This is in line with results obtained on an easily tunable synthetic NF-κB-like circuit reconstructed in yeast, which demonstrate how different strengths in the negative feedbacks of the circuit lead to different dynamics ( 70 ).…”