CLAD_sequence_files

<b>Background </b>Progression of chronic lung disease often leads to the requirement for a lung transplant (LT). Despite improvements in short-term survival after LT, chronic lung allograft dysfunction (CLAD) remains a critical challenge for long-term survival. This study investigates the relationship between the metabolome of bronchoalveolar lavage fluid (BALF) from subjects post-LT with underlying lung disease and CLAD severity.<b>Methods </b>Untargeted LC-MS/MS metabolomics was performed on 960 BALF samples collected over 10 years from LT recipients with alpha-1-antitrypsin disease (AATD, n=22), cystic fibrosis (CF, n=46), chronic obstructive pulmonary disease (COPD, n = 79) or pulmonary fibrosis (PF, n=47). Datasets were analyzed using random forest (RF) machine learning and multivariate statistics for associations with underlying disease and final CLAD severity.<b>Results. </b>BALF metabolomes varied by underlying disease state, with AATD LT recipients being particularly distinctive (PERMANOVA, <i>p</i>= 0.001, F= 3.91). We also found a significant association with the final CLAD severity score (RF variance explained = 11.08%, PERMANOVA, <i>p</i>=0.001), especially those with underlying CF. Association with CLAD severity was driven by changes in phosphoethanolamine and phosphocholine lipids that increased and decreased, respectively, and metabolites from the bacterial pathogen <i>Pseudomonas aeruginosa</i>. <i>P. aeruginosa </i>siderophores, quorum-sensing quinolones, and phenazines were detected in BALF, and 4-hydroxy-2-heptylquinoline (HHQ) was associated with the final CLAD stage in samples from CF patients (<i>R</i>= 0.34; <i>p </i>≤ 0.01, CI 95% = 3.61e⁺⁰⁶; -6.95e⁺⁰⁵). Relationships between CLAD stage and <i>P. aeruginosa</i> metabolites were especially strong in those with CF, where 61% of subjects had at least one of these metabolites in their first BALF sample after transplant.<b>Conclusions:</b> BALF metabolomes after LT are distinctive based on the underlying disease and reflect the final CLAD stage. In those with more severe outcomes, there is a lipid transition from phosphocholine to phosphoethanolamine. The association of <i>P. aeruginosa</i> metabolites with CLAD stages in LT recipients with CF indicates this bacterium and its metabolites may be drivers of allograft dysfunction.