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. 2017 Jan 19;12(1):e0169894.
doi: 10.1371/journal.pone.0169894. eCollection 2017.

Gene Expression Profiling of Bronchoalveolar Lavage Cells Preceding a Clinical Diagnosis of Chronic Lung Allograft Dysfunction

Free PMC article

Gene Expression Profiling of Bronchoalveolar Lavage Cells Preceding a Clinical Diagnosis of Chronic Lung Allograft Dysfunction

S Samuel Weigt et al. PLoS One. .
Free PMC article


Background: Chronic Lung Allograft Dysfunction (CLAD) is the main limitation to long-term survival after lung transplantation. Although CLAD is usually not responsive to treatment, earlier identification may improve treatment prospects.

Methods: In a nested case control study, 1-year post transplant surveillance bronchoalveolar lavage (BAL) fluid samples were obtained from incipient CLAD (n = 9) and CLAD free (n = 8) lung transplant recipients. Incipient CLAD cases were diagnosed with CLAD within 2 years, while controls were free from CLAD for at least 4 years following bronchoscopy. Transcription profiles in the BAL cell pellets were assayed with the HG-U133 Plus 2.0 microarray (Affymetrix). Differential gene expression analysis, based on an absolute fold change (incipient CLAD vs no CLAD) >2.0 and an unadjusted p-value ≤0.05, generated a candidate list containing 55 differentially expressed probe sets (51 up-regulated, 4 down-regulated).

Results: The cell pellets in incipient CLAD cases were skewed toward immune response pathways, dominated by genes related to recruitment, retention, activation and proliferation of cytotoxic lymphocytes (CD8+ T-cells and natural killer cells). Both hierarchical clustering and a supervised machine learning tool were able to correctly categorize most samples (82.3% and 94.1% respectively) into incipient CLAD and CLAD-free categories.

Conclusions: These findings suggest that a pathobiology, similar to AR, precedes a clinical diagnosis of CLAD. A larger prospective investigation of the BAL cell pellet transcriptome as a biomarker for CLAD risk stratification is warranted.

Conflict of interest statement

The authors have declared that no competing interests exist.


Fig 1
Fig 1. Sample selection flow chart.
LTR, lung transplant recipient. BAL, bronchoalveolar lavage. CLAD, chronic lung allograft dysfunction. RIN, RNA integrity number.
Fig 2
Fig 2. BAL cell differential.
(A) Percentage of neutrophils among the BAL cells by sample. (B) Percent neutrophils analysis (Mann Whitney test) by CLAD Free versus Incipient CLAD group. (C) Percentage of lymphocytes among the BAL cells by sample. (D) Percent lymphocytes analysis (Mann Whitney test) by CLAD Free versus Incipient CLAD group.
Fig 3
Fig 3. Volcano plot visualization of differential gene expression.
DAE generated a candidate list of 55 probe sets, 51 over- and 4 under-expressed in the incipient CLAD as compared to the CLAD free group.
Fig 4
Fig 4. Principal component analysis.
Principal component analysis based on the 40 differentially expressed candidate genes demonstrates modest separation of incipient CLAD and CLAD free groups. The percentage of total variance accounted for by the first principal component was 63.2%, and for the second principal component was 15.1%.
Fig 5
Fig 5. Hierarchical clustering and heat map.
Hierarchical clustering and heat map based on the expression index of n = 40 candidate genes.

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