Longitudinal Immune Profiling in Sepsis Reveals Transient Expansion of a CD14+Monocyte State and Persistent T Cell Suppression

ABSTRACT Sepsis is a dynamic syndrome of immune dysregulation and a leading cause of global mortality. Although immune suppression is recognized as a hallmark of sepsis, the temporal dynamics and mechanistic drivers of immune dysfunction remain incompletely understood. Here, we performed longitudinal single-cell transcriptomic and proteomic profiling of peripheral blood from 98 adults with sepsis or sterile inflammation, alongside 12 healthy controls, capturing immune trajectories from initial clinical presentation through recovery. Integration of RNA and surface protein data revealed an early expansion of a transcriptionally reprogrammed CD14+ monocyte population (MS1) exhibiting features of monocytic myeloid-derived suppressor cells (M-MDSCs), including downregulation of HLA-DR and upregulation of alarmins (S100A8, S100A9), resistin, and clusterin. M-MDSCs arise from emergency myelopoiesis and contribute to adaptive immune suppression through impaired antigen presentation and T cell inhibition. MS1 abundance peaked at initial presentation and declined progressively during the first week of clinical management in most patients. In contrast, CD8+ naive and CD4+ memory T cells exhibited sustained depletion, with recovery occurring at convalescence in only a subset of patients. Plasma proteomic profiling identified cytokines and growth factors, including IL-6 and resistin, that may contribute to MS1 induction and suppressive activity. IL-6 exhibited a kinetic trajectory that closely paralleled MS1 abundance, peaking early and declining during recovery. Resistin levels were positively correlated with MS1 abundance across all timepoints from acute sepsis through convalescence. These dynamics suggest temporally distinct cytokine roles in initiating and sustaining immunosuppressive myeloid responses in sepsis. Together, these findings define a high-resolution, time-resolved immune atlas of human sepsis, linking emergency myelopoiesis to downstream adaptive immune suppression. Our results suggest that coordinated dynamics between myeloid and lymphoid compartments shape early immune trajectories in sepsis and highlight MDSC-targeting pathways as potential therapeutic avenues. Competing Interest Statement M.R is an employee of Genentech, Inc. and owns equity in Roche. P.C.B. serves as a consultant to or equity holder in several companies including 10X Technologies/10X Genomics, GALT/Isolation Bio, Next Gen Diagnostics, Cache DNA, Concerto Biosciences, Stately Bio, Ramona Optics, Bifrost Biosystems, and Amber Bio. P.C.B.'s lab has received funding from Calico Life Sciences, Merck, and Genentech for unrelated research. N.H. holds equity in BioNTech and is an advisor for Related Sciences/Danger Bio. Funding Statement This work was supported in part by the National Institutes of Health (NIH R01AI153142). 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: The Institutional Review Board of the Massachusetts General Hospital gave ethical approval for this work (IRB number 2017P001681) 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. 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 Data Availability All data produced in the present study are available upon reasonable request to the authors