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

Area of Science:

• Cellular signaling
• Molecular biology
• Systems biology

Background:

• Transcription factor dynamics are crucial for gene regulation but vary at the single-cell level.
• Understanding the origins of this heterogeneity is key to deciphering cellular responses.
• The nuclear factor κB (NF-κB) pathway is a critical signaling cascade with dynamic behavior.

Purpose of the Study:

• To investigate the sources of heterogeneity in nuclear factor κB (NF-κB) signaling dynamics.
• To determine how variations in gene expression influence NF-κB response.
• To link single-cell signaling differences to transcriptional outcomes.

Main Methods:

• Utilized clonal populations of immortalized fibroblasts derived from a single mouse embryo.
• Stimulated cells with tumor necrosis factor ɑ (TNF-ɑ) and interleukin-1β (IL-1β).
• Combined transcriptomics, single-cell analysis, and computational simulations to model NF-κB dynamics.

Main Results:

• Identified distinct NF-κB activation patterns (persistent, oscillatory, weak) within clonal fibroblast populations.
• Demonstrated that less than two-fold differences in key gene expression levels predict varied NF-κB dynamics.
• Showed that these dynamic differences lead to distinct target gene transcription patterns.

Conclusions:

• Small variations in gene expression within a transcription factor's regulatory circuit can drive significant signaling heterogeneity.
• This heterogeneity is observable even in genetically identical cell populations.
• Findings have implications for understanding cellular responses across different cell types and conditions.