Quantifying stimulus-response specificity to probe the functional state of macrophages

Immune sentinel macrophages initiate responses to pathogens via hundreds of immune response genes. Each immune threat demands a tailored response, suggesting that the capacity for stimulus-specific gene expression is a key functional hallmark of healthy macrophages. To quantify this property, termed stim-ulus-response specificity(SRS), we developed a single-cell experimental workflow and analytical approaches based on information theory and machine learning. We found that the response specificity of macrophages is driven by combinations of specific immune genes that show low cell-to-cell heterogeneity and are targets of separate signaling pathways. The response specificity profile,a systematic comparison of multiple stimulus-response distributions, was distinctly altered by polarizing cytokines, and it enabled an assessment of the functional state of macrophages. Indeed, the response specificity profile of peritoneal macrophages from old and obese mice showed characteristic differences, suggesting that SRS may be a ba-sis for measuring the functional state of innate immune cells.A record of this paper's transparent peer review process is included in the supplemental information.

Automated summary

Immune sentinel macrophages respond to pathogens through immune response genes. The capacity for stimulus-specific gene expression, known as stimulus-response specificity (SRS), is crucial for macrophage function. Using information theory and machine learning, we developed an experimental workflow to quantify SRS and found that it is influenced by specific immune genes with low heterogeneity and separate signaling pathways.