Multi-omic analysis of PBMCs in sepsis reveals widespread cytotoxic dysfunction and an increased population of CD69 expressing naïve CD4+ T cells

Joshua Flynn^1,2,3Anne-Marie Baird^1,2Eamon Breen^2,4Michael Carty⁵Ciara S McNevin^1,3Lisa Mcdermott^2,6Elaine Kenny^2,6John Davis Coakley⁷Thomas Ryan⁷Derek G Doherty^1,2,8Orla Sheils^1,2,3*

• ¹School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin 8, Ireland
• ²Trinity St James's Cancer Institute, Dublin 8, Ireland
• ³Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin 8, Ireland
• ⁴Flow Cytometry Core, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin 8, Ireland
• ⁵Department of Clinical Microbiology, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin 8, Ireland
• ⁶TrinSeq, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin 8, Ireland
• ⁷Department of Intensive Care Medicine, St James’s Hospital, Dublin 8, Ireland
• ⁸Department of Immunology, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin 8, Ireland

Sepsis is responsible for 1 in 5 deaths globally and the majority of those who survive have lasting health issues. A hallmark of sepsis is a deregulated inflammatory response to infection, with leukocytes playing a critical role. This study utilised a targeted single-cell multi-omics approach to characterise peripheral blood mononuclear cell (PBMC) populations and their transcriptomic profiles in an Irish cohort of people patients with (i) sepsis and (ii) bacteraemia without sepsis (defined as clinically significant positive blood culture without sepsis as assessed by the Clinical Microbiology). Variable leukocyte distributions were identified, with decreased cytotoxic lymphocytes, including CD8+ T cells, natural killer cells, CD56+ T cells, γδ T cells, mucosal-associated invariant T cells, and increased T helper (Th) cell subsets within sepsis samples. Additionally, PBMCs from sepsis samples displayed an impaired expression profile in effector T cells, resulting in widespread suppression of PBMC cytotoxic activity. These results identify potential mechanisms underlying the functional impairment witnessed in sepsis. Such mechanisms may inform future diagnostic and treatment strategies.