Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis

The anatomical source of infection is a major determinant of sepsis outcomes; however, how distinct sites shape immunity remains unclear. Here we applied multi-omic profiling, integrating single-cell transcriptomics, single-cell T cell receptor and B cell receptor sequencing, CITE-seq, bulk RNA sequencing and plasma proteomics, to analyze peripheral blood mononuclear cells and plasma from 281 adult and pediatric individuals with sepsis and controls. We identified an NR4A2⁺ central memory CD4⁺ T cell subset enriched in abdominal, pulmonary and skin sepsis, with features of exhaustion; genetic perturbations showed Nr4a2 loss improved survival, while overexpression worsened it. Proinflammatory CD8⁺ T, natural killer and natural killer T subsets expressing CCL4, CCL3 and tumor necrosis factor expanded in adult abdominal and pulmonary sepsis, while pediatric pulmonary sepsis featured proliferative CD14⁺ monocytes, findings validated in external single-cell cohorts and confirmed in 164 independent individuals. Plasma proteomics revealed shared mediators including interleukin-6 and EN-RAGE across anatomical sites and ages. Together, our findings delineate anatomical-specific and age-specific immune programs in sepsis, highlighting candidate targets for precision immunotherapy.