Single-cell transcriptomic analysis deciphers heterogeneity and transcriptional regulatory programs of sepsis with different prognosis

Sepsis has a high mortality rate, yet the cellular heterogeneity and transcriptional regulatory programs associated with divergent clinical outcomes remain incompletely understood. Here, we integrated two peripheral blood single-cell RNA-seq cohorts to explore prognosis-associated immune remodeling patterns in sepsis. Using reference-based annotation, pySCENIC-inferred regulon activity, pathway enrichment, and CellChat based ligand-receptor inference, we observed broad differences in cell composition, transcriptional programs, and intercellular communication between survivors and non-survivors. Non-survivors exhibited relative decrease of monocytes, B-cells, NK cells, and CD4/CD8 T cells, together with relative platelet expansion. cDC2 and plasmablasts showed relatively large transcriptional disturbance compared to other cell types. In cDC2, poor outcome was associated with increased TNF-α and NF-κB related regulon activity, which linked to AP-1 transcription factors (JUN, FOSL2, CEBPB, NFIL3, KLF6, and FOSB), together with reduced STAT1 and STAT2-associated interferon signaling. Gene regulatory network analysis highlighted cell type-specific transcription factor and target gene relationships. CellChat suggested that cDC2 may occupy a more connected position in survivors, whereas connectivity appeared reduced in non-survivors. Independent bulk transcriptomic validation supported increased FOSL2 and CEBPB expression, and a multivariable eight-transcription-factor model showed preliminary discriminatory performance. Overall, this study suggests that poor-outcome sepsis may be associated with altered cDC2 regulatory states and reduced cDC2 centered intercellular coordination.