Chronic lung allograft dysfunction small airways reveal a lymphocytic inflammation gene signature

Abstract

Chronic lung allograft dysfunction (CLAD) is the major barrier to long-term survival following lung transplantation, and new mechanistic biomarkers are needed. Lymphocytic bronchitis (LB) precedes CLAD and has a defined molecular signature. We hypothesized that this LB molecular signature would be associated with CLAD in small airway brushings independent of infection. We quantified RNA expression from small airway brushings and transbronchial biopsies, using RNAseq and digital RNA counting, respectively, for 22 CLAD cases and 27 matched controls. LB metagene scores were compared across CLAD strata by Wilcoxon rank sum test. We performed unbiased host transcriptome pathway and microbial metagenome analysis in airway brushes and compared machine-learning classifiers between the two tissue types. This LB metagene score was increased in CLAD airway brushes (P = 0.002) and improved prediction of graft failure (P = 0.02). Gene expression classifiers based on airway brushes outperformed those using transbronchial biopsies. While infection was associated with decreased microbial alphadiversity (P ≤0.04), neither infection nor alpha-diversity was associated with LB gene expression. In summary, CLAD was associated with small airway gene expression changes not apparent in transbronchial biopsies in this cohort. Molecular analysis of airway brushings for diagnosing CLAD merits further examination in multicenter cohorts.

Rapid molecular detection of airway pathogens in lung transplant recipients

“…In addition to being immunosuppressed, lung transplant recipients have impaired mucociliary clearance and denervation of the lung allograft resulting in impaired cough reflex 14 . Single lung transplant recipients may also be at risk of infection spread from the native lung, IPF recipients appear at particular risk of aspiration 15 , and CF lung transplants are at particular risk of recolonization from the untransplanted airway 16 .…”

Molecular diagnostics for CLAD: When and where?

“…3,6 Further, direct comparison of CLAD-associated differential gene expression between TBB and small airway brushes showed increased signal to noise in the small airways, such that classifiers using airway brushes outperformed those based on TBB tissue. 3 Similarly, sampling the alveolar compartment more than the small airways might contribute to the lack of inflammatory signals observed relative to other studies. 4 The Parkes et al study is the most comprehensive assessment of a molecular signature for CLAD in TBBs to date, leveraging clinically obtained samples as part of standard clinical practice.…”

“…At the same time, the observation of evolving molecular pathways across the time course of CLAD suggests that the most differentially expressed gene list will be highly dependent on how cases and controls are divided. 3 Another issue influencing the results of molecular diagnostic and biomarker studies in CLAD is the method of tissue sampling and where within the lung allograft is sampled. Obliterative bronchiolitis is the predominant histopathologic feature of the bronchiolitis obliterans syndrome (BOS) subtype of CLAD and frequently identified in the restrictive allograft syndrome (RAS) subtype as well.…”

Lung Allograft Epithelium DNA Methylation Age Is Associated With Graft Chronologic Age and Primary Graft Dysfunction

“…Small airway brushing was performed in the distal airways as part of routine 1-year post-transplant surveillance bronchoscopy (16). Following bronchoalveolar lavage (BAL) and before transbronchial biopsies, a cytology brush (Conmed #129) was advanced under fluoroscopic guidance into a basilar segment airway to about 3-4 cm from the periphery.…”