Molecular Pathway Analysis of Chronic Lung Allograft Dysfunction: Results from a Multicenter International Cohort

Purpose The molecular pathogenesis of chronic lung allograft dysfunction (CLAD) is poorly understood. We hypothesized that microarray analysis of TBBs and mucosal biopsies from the third bronchial bifurcation (3BMBs) would provide insight into biological pathways through gene ontology (GO) analysis. Methods We performed gene expression microarray analysis of 498 TBBs and 324 3BMBs from 10 international centers, comparing CLAD+ and CLAD- cases. CLAD was defined per 2019 ISHLT guidelines. Bayes-moderated t-tests were used to identify CLAD-associated genes. We performed GO biological process analysis with CLAD-associated genes with false discovery rate Results In TBBs CLAD-associated GO terms described lung development regulation, injury response, epithelial proliferation, epithelial-mesenchymal transition, and angiogenesis (Fig. 1A). In 3BMBs the GO terms included endocytosis and intracellular trafficking, cell-cell/cell-substrate adhesion, collagen/matrix metabolism, but unlike TBBs included immunity (Fig. 1B). Time correction did not affect transcript associations with CLAD in TBBs but diminished them in 3BMBs. Excluding biopsies with coexistent rejection or infection removed associations in TBBs but strengthened them in 3BMBs even after correcting for time post-transplant. Conclusion In our biopsy set the molecular CLAD phenotype resembles a parenchymal response to wounding that overlaps other pathologies. CLAD-associated molecular changes were independent of time in TBBs but not 3BMBs, suggesting that CLAD is primarily a time dependent airway process involving injury and either adaptive or innate immunity. Unlike TBBs, molecular changes in 3BMBs were identifiable despite coexistent rejection or infection, suggesting this biopsy format may better capture CLAD information.