Stimulus-response signaling dynamics characterize macrophage polarization states

Area of Science:

• Cellular and Molecular Biology
• Immunology
• Systems Biology

Background:

• Cellular functions are shaped by their microenvironment.
• Polarizing cytokines significantly alter macrophage transcriptomes and epigenomes.
• Understanding macrophage functional responses to stimuli is crucial.

Purpose of the Study:

• To characterize functional responses of differentially polarized macrophage populations.
• To measure the dynamics of transcription factor nuclear factor κB (NF-κB) in response to various stimuli.
• To develop methods for distinguishing cell states based on dynamic signaling patterns.

Main Methods:

• Measuring single-cell NF-κB trajectories in response to 8 stimuli across 6 polarized macrophage populations.
• Applying machine learning to time-series data to analyze stimulus distinguishability.
• Identifying informative trajectory features ("signaling codons") for cell state mapping.
• Inferring kinetic parameters using a mechanistic NF-κB network model.

Main Results:

• Macrophage polarization leads to a loss of stimulus distinguishability in NF-κB dynamics, indicating canalized effector functions.
• "Signaling codons" were identified, enabling the mapping of a cell state landscape and localization of conditioned macrophages.
• Kinetic parameters from a network model provided an alternative cell state mapping and predicted biochemical findings.

Conclusions:

• Dynamic trajectories of a single analyte, like NF-κB, can distinguish functional cell states.
• This approach reveals the underlying molecular network states governing cell behavior.
• The findings offer a novel method for characterizing cell states and their functional specializations.