Signals trigger state-specific transcriptional programs to support diversity and homeostasis in immune cells

Defining macrophage states Macrophages are immune cells that play a major role in maintaining tissue homeostasis. Because of their high plasticity, macrophages can rapidly respond to various external and internal cues, such as exposure to infectious agents or metabolic stress. Through single-cell analyses of mRNA and proteins in macrophage populations and computational analysis, Fischer et al. characterized the differential transcriptional programs driven by the microbial product LPS and the free fatty acid palmitate, both of which engage the same cell surface receptor, TLR4. These data helped to characterize the pro- and anti-inflammatory macrophage states induced by both stimuli, determine how antagonistic genes interacted with each other, and measure transcriptional signaling efficiency in these cells. Macrophages play key roles in the immune systems of humans and other mammals. Here, we performed single-cell analyses of the mRNAs and proteins of human macrophages to compare their responses to the signaling molecules lipopolysaccharide (LPS), a component of Gram-negative bacteria, and palmitate (PAL), a free fatty acid. We found that, although both molecules signal through the cell surface protein Toll-like receptor 4 (TLR4), they stimulated the expression of different genes, resulting in specific pro- and anti-inflammatory cellular states for each signal. The effects of the glucocorticoid receptor, which antagonizes LPS signaling, and cyclic AMP–dependent transcription factor 3, which inhibits PAL-induced inflammation, on inflammatory response seemed largely determined by digital on-off events. Furthermore, the quantification of transcriptional variance and signaling entropy enabled the identification of cell state–specific deregulated molecular pathways. These data suggest that the preservation of signaling in distinct cells might confer diversity on macrophage populations essential to maintaining major cellular functions. Single-cell data reveal the major transcriptional regulators for distinct macrophage states. Single-cell data reveal the major transcriptional regulators for distinct macrophage states.