Immune checkpoint molecules as biomarkers of Staphylococcus aureus bone infection and clinical outcome

Abstract Background Staphylococcus aureus prosthetic joint infections (PJIs) are broadly considered incurable, and clinical diagnostics that guide conservative vs. aggressive surgical treatments don’t exist. Understanding the human T cell response to chronic S. aureus osteomyelitis may lead to improved patient outcomes and inform new therapeutic strategies. Methods We performed multi-omics studies, including flow cytometry, scRNA-seq, and immunofluorescence in a humanized NSG-SGM3 BLT mouse model and with human clinical samples to characterize the human T cell landscape in S. aureus osteomyelitis. Results Human T cells are remarkably heterogeneous in gene expression and abundance. Notably, the CD4 Th1/Th17 cells comprise a mixed population of activated, progenitor-exhausted, and terminally-exhausted states with increased expression of immune checkpoint proteins (LAG-3, TIM-3). Importantly, these proteins are upregulated in the serum and the bone marrow of patients with S. aureus PJI. In a clinically informative pilot cohort, a multiparametric diagnostic integrating high serum immune checkpoint protein levels with low proinflammatory cytokine levels (IFN-γ, IL-2, TNF-α, IL-17) reveals that TIM-3 was highly predictive of adverse disease outcomes (AUC = 0.89). Conclusions T cell impairment, marked by immune checkpoint expression and exhaustion, could serve as a functional biomarker for S. aureus PJI disease outcome, and therapeutic blockade of checkpoint proteins may represent a potential strategy to improve outcomes following surgery.