Alveolar Immune Profiling Identifies Distinct Subphenotypes of Acute Respiratory Failure

Acute respiratory failure causes millions of deaths worldwide each year, highlighting the need for a better understanding of its pathophysiology and approaches to identify treatment-responsive subphenotypes of patients. Although subphenotypes of acute respiratory failure have been described using peripheral blood biomarkers, it remains unclear whether lung-specific molecular profiles can define biologically and clinically meaningful subphenotypes. In this study, we identified four distinct subphenotypes based on the measurement of twenty-five soluble proteins in alveolar fluid collected from 466 patients with acute respiratory failure. Forty-eight of these participants also underwent immunophenotyping by spectral flow cytometry to characterize immune cell populations. Twenty-eight-day mortality was significantly different across the four subphenotypes. The subphenotype with lowest mortality (12.7%) showed elevated levels of soluble PD-L1, enrichment of T cell-related chemokines, and the highest proportion of memory CD8⁺ T cells. A subphenotype characterized by globally low soluble protein levels and higher proportions of exhausted T cell subsets had a mortality rate of 22.1% despite relatively moderate illness severity. The subphenotype with the highest mortality (29.4%) exhibited increased pyrogenic and neutrophil-associated alveolar mediators. Severity of respiratory failure varied markedly between subphenotypes, while non-pulmonary organ failures were similar across groups. We developed a parsimonious classifier to predict subphenotypes in two additional cohorts totaling 122 patients. The clinical differences between the subphenotypes were similar across cohorts, although associations with mortality were not detected in the smaller validation cohorts. These findings identify novel subphenotypes of acute respiratory failure and support integrating lung-specific molecular measures into future studies to advance precision-medicine approaches.