Single-cell proteome profiling reveals distinct immunological patterns in the lungs of patients with severe acute respiratory failure

Summary In this study, we provide a comprehensive characterization of the alveolar immune landscape in patients suffering from severe acute respiratory failure, predominantly caused by pneumonia or acute respiratory distress syndrome, conditions defined by intense pulmonary inflammation and immune dysregulation. Despite diverse underlying causes, the overall composition of alveolar immune cells was largely consistent, with neutrophils and macrophages comprising the majority of cells. However, the maturation and activation states of immune cell subsets varied significantly, not only between patients with and without pneumonia, but also among pneumonia cases stratified by pathogen type. We also observed dynamic shifts in immune cell subsets over the disease course and found that an increased proportion of CD123 bright immature neutrophils and a reduction in alveolar resident macrophages were associated with increased 28-day mortality. Integration with alveolar cytokine profiles revealed strong correlations between immune cell populations and the local cytokine milieu. These findings highlight the importance of assessing immune cell function, not merely abundance, through broad and longitudinal investigation to better understand the pathophysiology of acute respiratory failure and to guide precision immunomodulatory therapy.