Molecular Analysis of Transbronchial and Mucosal Biopsies in Patients with CLAD

Abstract

Purpose Chronic lung allograft dysfunction (CLAD) is a clinical/functional diagnosis that cannot be defined by histology in transbronchial biopsies (TBBs). Moreover, understanding the biology of CLAD is crucial for prevention and potential treatment. We studied gene expression associated with CLAD in TBBs, but also studied mucosal biopsies from the third bronchial bifurcation (3BMBs). Methods 223 highly alveolated TBBs (54 CLAD, 169 no CLAD) and 182 3BMBs (43 CLAD, 139 no CLAD) were collected from 7 centers and processed on microarrays. The top 100 non-overlapping genes associated with a diagnosis of CLAD prior to biopsy were identified, annotated, and used for gene set analysis and gene ontology (GO) biological process analysis. Results The top genes associated with CLAD reflected de-differentiation (expression loss), injury (expression gain), and inflammation in both TBBs and 3BMBs. These associations were stronger in 3BMBs. Pathway analysis using the top genes also suggested parenchymal de-differentiation (e.g. loss of transcriptional regulation and mitochondrial function in TBBs) and inflammatory pathway activation, particularly in 3BMBs (Table 1). Gene sets previously annotated in atrophy-scarring, including immunoglobulin transcripts (plasma cells), were elevated in CLAD in TBBs and 3BMBs, but 3BMBs also showed more inflammation-related changes (e.g. interferon gamma effects). Conclusion Molecular changes associated with CLAD were apparent in TBBs and especially in 3BMBs, and indicate that CLAD is a combination of atrophy/scarring, function loss, and, particularly in 3BMBs, inflammation. Molecular assessment of 3BMBs is a particularly promising opportunity to dissect CLAD biology and potentially gain insight into the BOS variant. ClinicalTrials.gov: NCT02812290