Single-cell gene expression profiles of mouse macrophages stimulated with immune ligands.

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 Response Specificity, we developed a single-cell experimental workflow and analytical approaches based on information theory and machine learning. We found that 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 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 Response Specificity may be a basis for measuring the functional state of innate immune cells. Overall design: Macrophages were collected from the mouse peritoneum or differentiated from myeloid progenitors, and stimulated with a panel of immune ligands for 3hrs. Cells were collected into suspension and scRNAseq was performed using the BD Rhapsody platform.