Single-cell transcriptomics identifies different immune signatures between macrophage activation-like syndrome and immune paralysis in sepsis

Different immune phenotypes characterize sepsis patients, including hyperinflammation and/or immunosuppression, but the biological mechanisms driving this heterogeneity remain largely unknown. We used single-cell RNA sequencing to profile circulating leukocytes of healthy controls and sepsis patients classified as either hyperinflammatory (macrophage activation-like syndrome [MALS]), immune paralysis , or unclassified (when criteria for neither of these two immune subgroups were applicable). Pronounced differences were detected in the transcriptional signature of monocytes from sepsis patients, with clear distinction between MALS and immune paralysis patients. Unsupervised clustering analysis revealed the existence of MALS-specific monocyte clusters, as well as one sepsis-specific monocyte cluster that was linked to disease severity. In separate cohorts, urosepsis was characterized by heterogeneous MALS and immunosuppression monocyte signatures, while MALS-specific monocyte clusters showed overlapping transcriptional signatures with severe COVID-19. In conclusion, our findings shed light on the heterogeneous immune landscape underlying sepsis, and provide opportunities for patient stratification for future therapeutic development. ### Competing Interest Statement E.J. Giamarellos-Bourboulis has received honoraria from AbbVie USA, Abbott CH, Brahms GmbH, InflaRx GmbH, MSD Greece, Sobi and XBiotech Inc.; independent educational grants from Abbott, bioMerieux Inc, Johnson & Johnson, InflaRx GmbH, Sobi; and funding from the Horizon2020 Marie-Curie Project European Sepsis Academy (granted to the National and Kapodistrian University of Athens), and the Horizon 2020 European Grant ImmunoSep and RISCinCOVID (granted to the Hellenic Institute for the Study of Sepsis). M.G. Netea is a scientific founder of Trained Therapeutix Discovery, and has received research grants from Trained Therapeutix Discovery, GSK, ViiV Healthcare and Ono Pharma. The other authors have declared that no conflict of interest exists. ### Clinical Trial NCT 03332225 ### Funding Statement This study was supported by a Horizon 2020 ImmunoSep grant (#847422). Y.L. was supported by an ERC starting Grant (948207) and a Radboud University Medical Centre Hypatia Grant (2018). C.J.X. was supported by Helmholtz Initiative and Networking Fund (1800167). M.G.N. was supported by an ERC Advanced Grant (833247) and a Spinoza Grant of the Netherlands Organization for Scientific Research. E.J.G.B. has received honoraria from AbbVie USA, Abbott CH, Brahms GmbH, InflaRx GmbH, MSD Greece, Sobi and XBiotech Inc.; independent educational grants from Abbott, bioMerieux Inc, Johnson & Johnson, InflaRx GmbH, Sobi; and funding from the Horizon2020 Marie-Curie Project European Sepsis Academy (granted to the National and Kapodistrian University of Athens), and the Horizon 2020 European Grant ImmunoSep and RISCinCOVID (granted to the Hellenic Institute for the Study of Sepsis). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: From all study subjects, informed consent was obtained from the participant or from their legal representatives prior to participation (ethical approval by the National Ethics Committee of Greece 78/17). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as [ClinicalTrials.gov][1]. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors. [1]: https://ClinicalTrials.gov