Distinct transcriptomic signatures discriminate hyperinflammation from immune paralysis in sepsis: a single-cell RNA sequencing study

Abstract Background Sepsis is a highly heterogeneous syndrome characterized by variable immune dysregulation states, including hyperinflammation and immunosuppression. Previous immunotherapy attempts in sepsis have largely failed, likely due to a “one-size-fits-all” approach that ignores each patient’s immune status. The recent ImmunoSep randomized clinical trial demonstrated that precision immunotherapy guided by the presence of either macrophage activation–like syndrome (MALS) or immune paralysis can improve early organ dysfunction in sepsis patients. However, the molecular mechanisms underlying these immune endotypes remain unclear. Objectives To identify the immunological signatures that distinguish MALS and immune paralysis. Methods We used single-cell RNA sequencing to profile circulating leukocytes of 6 healthy controls and 16 sepsis patients classified as MALS, immune paralysis or unclassified (when criteria for neither of these two immune endotypes were applicable). Classification was based on surrogate biomarkers ferritin and HLA-DR expression on monocytes. Thereafter, the transcriptional programs of these groups were compared. Results Pronounced differences were detected mainly in the transcriptional signature of monocytes from these patients, with a clear distinction between MALS and immune paralysis. Unsupervised clustering analysis revealed the existence of MALS-specific monocyte clusters, as well as one sepsis-specific monocyte cluster that was linked to greater comorbidity burden and may reflect increased clinical vulnerability in sepsis. These findings were validated in two independent cohorts, in which urosepsis was characterized by heterogeneous MALS and immune paralysis monocyte signatures. Moreover, MALS-specific monocyte clusters showed overlapping transcriptional signatures with severe COVID-19. Conclusions Our findings shed light on the heterogeneous immune landscape underlying sepsis and provide opportunities for patient stratification for future therapeutic development.