Heritable single-cell gene expression states shape functional variability in innate immune responses.

Area of Science:

• Immunology
• Cell Biology
• Systems Biology

Background:

• Innate immunity exhibits significant single-cell heterogeneity, but the underlying mechanisms of this variability are not fully understood.
• Understanding how gene expression variability is maintained across cell divisions is crucial for deciphering immune responses.

Purpose of the Study:

• To quantify transcriptional heritability in the Toll-like receptor (TLR) system at the single-cell level.
• To investigate how environmental context and population density influence heritable gene expression states.
• To link transcriptional heritability to functional immune outcomes and cellular organization.

Main Methods:

• Integration of transcriptomics (RNA-seq), high-content imaging, and mathematical modeling.
• Utilized RNA-seq-based fluctuation tests to identify heritable genes in clonal macrophage populations.
• Employed high-content microscopy to visualize protein-level dynamics and spatial organization.

Main Results:

• Identified a subset of Toll-like receptor 4 (TLR4)-dependent genes with stable transcriptional heritability for over 25 cell divisions.
• Observed gene-specific heritability dynamics, with CD36 showing stable, cell density-reinforced states and IL1β exhibiting transient states.
• Demonstrated that heritable states interact with population context to drive emergent spatial organization and heterogeneous infection susceptibility, exemplified by Listeria monocytogenes.

Conclusions:

• Transcriptional heritability is a key driver of innate immune heterogeneity.
• Heritable cellular states dynamically interact with population density and environmental cues to shape complex immune behaviors.
• Heritable CD36 expression directly influences macrophage susceptibility to bacterial infection, highlighting functional relevance.