The onset of chronic lung allograft dysfunction (CLAD) represents the greatest long-term challenge in lung transplantation (LT). Here we aimed to identify early molecular signals of CLAD by analyzing the effects of bronchoalveolar lavage (BAL)-derived extracellular vesicles (EVs) on airway cells and validating these findings in patient lung tissues. In our BAL biobank, we identified 13 LT patients with a BAL sample at CLAD diagnosis and 13 patients with a stable graft function and a BAL sample obtained at least 12 months post LT (Ctrl). All patients were then followed for at least 18 months. EVs were isolated, immunophenotyped, and co-cultured with airway cells. The cells’ transcriptome and proteome were profiled. Selected targets were validated by immunohistochemistry. Logistic regression and survival analyses were performed for prediction of CLAD progression. During follow-up, 7 CLAD patients experienced allograft dysfunction aggravation, and one control developed CLAD. CLAD patients showed more EVs originating from epithelial cells and leukocytes than stable LT recipients. Exposure of airway cells to CLAD-EVs led to the up-regulation of p70S6K and canonical NF-κB signaling, altering their intracellular and extracellular proteome. Activation of NF-κB was also detected at the onset of CLAD in transbronchial biopsies and BAL cytology, and it persisted throughout the progression to end-stage CLAD. RelA overexpression was associated with poorer graft performance and worse outcomes. RelA-driven NF-κB activation is a key factor in the development of CLAD by promoting persistent inflammation. This pathway may be a promising therapeutic target to improve long-term graft survival after LT.

Chronic lung allograft dysfunction (CLAD) remains the principal limitation to long-term survival after lung transplantation (LT). Early molecular alterations within the graft may precede clinically overt functional decline, but their biological significance remains incompletely defined. In this single-center exploratory pilot study, 16 bilateral lung transplant recipients underwent bronchoalveolar lavage (BAL) sampling at 7 days, 15 days, and 3 months post-transplantation. BAL-derived microRNA (miRNA) profiles were analyzed longitudinally and correlated with long-term clinical outcomes, including CLAD development and phenotypic classification into bronchiolitis obliterans syndrome (BOS) or restrictive allograft syndrome (RAS), over extended follow-up (mean 98 months). Distinct early miRNA signatures were detectable within the first weeks after transplantation and were associated with divergent long-term clinical trajectories. Specific miRNAs, namely let-7e-5p and miR-30d-3p, were associated with subsequent CLAD, whereas differential expression patterns distinguished trajectories toward BOS or RAS. Enrichment analyses highlighted networks related to innate immune activation, hypoxia, tissue remodeling, and PI3K–mTOR signaling. Notably, the occurrence of acute rejection did not differ significantly between patients who developed CLAD and those who remained stable. These findings, although preliminary, suggest that early BAL-derived miRNA profiles may reflect biologically distinct graft states associated with long-term CLAD phenotypes.