A pairwise cytokine code explains the organism-wide response to sepsis [Spatial transcriptomics by Array-seq]

Sepsis is a systemic response to infection with life-threatening consequences. Our understanding of the molecular and cellular impact of sepsis across organs remains rudimentary. Here, we characterize the pathogenesis of sepsis by measuring dynamic changes in gene expression across organs. To pinpoint molecules controlling organ states in sepsis, we compare the effects of sepsis on organ gene expression to those of 6 singles and 15 pairs of recombinant cytokines. Strikingly, we find that the pairwise effects of tumor necrosis factor plus interleukin (IL)-18, interferon-gamma or IL-1 suffice to mirror the impact of sepsis across tissues. Mechanistically, we map the cellular effects of sepsis and cytokines by computing changes in the abundance of 195 cell types across 9 organs, which we validate by whole-mouse spatial profiling. Our work decodes the cytokine cacophony in sepsis into a pairwise cytokine message capturing the gene, cell and tissue responses of the host to the disease. Overall design: We performed whole-mouse spatial transcriptomics. Overall, 4 datasets (2 datasets/condition) were genenrated from the following experiments and samples: (1) whole-body section from naive mice, (2) whole-body section from LPS-injected mice (5 mg/kg, 24 hours).