Gene expression variability across cells and species shapes innate immunity

As the first line of defence against pathogens, cells mount an innate immune response, which varies widely from cell to cell. The response must be potent but carefully controlled to avoid self-damage. How these constraints have shaped the evolution of innate immunity remains poorly understood. Here we characterize the innate immune response's transcriptional divergence between species and variability in expression among cells. Using bulk and single-cell transcriptomics in fibroblasts and mononuclear phagocytes from different species, challenged with immune stimuli, we map the architecture of the innate immune response. Transcriptionally diverging genes, including those that encode cytokines and chemokines, vary across cells and have distinct promoter structures. Conversely, genes that are involved in the regulation of this response, such as those that encode transcription factors and kinases, are conserved between species and display low cell-to-cell variability in expression. We suggest that this expression pattern, which is observed across species and conditions, has evolved as a mechanism for fine-tuned regulation to achieve an effective but balanced response.We thank N. Eling, M. Fumagalli, Y. Gilad, O. Laufman, A. Marcovitz, J. Marioni, K. Meyer, M. Muffato, D. Odom, O. Stegle, A. Stern, M. Stubbington, V. Svensson and M. Ward for discussions; G. Emerton, A. Jinat, L. Mamanova, K. Polanski, A. Fullgrabe, N. George, S. Barnett, R. Boyd, S. Patel and C. Gomez for technical assistance; the Hipsci consortium for human fibroblast lines; and members of the Teichmann laboratory for support at various stages. This project was supported by ERC grants (ThDEFINE, ThSWITCH) and an EU FET-OPEN grant (MRG-GRAMMAR No 664918) and Wellcome Sanger core funding (Grant No WT206194). T.H. was supported by an HFSP Long-Term Fellowship and by EMBO Long-Term and Advanced fellowships. V.P. is funded by Fondazione Umberto Veronesi.