Transcriptomic analysis of Paired Nasal and Bronchial brushes in Cystic Fibrosis Patients

Abstract

Abstract Cystic Fibrosis is a genetic disorder affecting approximately 30,000 people in the United States. CF mainly affects the lungs and digestive track, leaving individuals with CF more susceptible to lung infections. Transcriptomic analysis of bronchial brushing can be used to identify gene signatures of inflammatory lung diseases such as asthma and CF. However, due to the invasiveness of this technique, the application is limited in pediatric patients. We sought to determine whether nasal brushes could be used as an alternative for transcriptomic analysis of the airway by determination of the similarities and differences in nasal and bronchial gene expression, and whether there is a correlation between nasal transcriptomes and their bronchial counterparts. To address this, we compared five pairs of Nasal and Bronchial Brushes obtained from pediatric CF patients. The initial principal component analysis (PCA) analysis showed distinct clustering of the bronchial and nasal data. A Pearson correlation test was run on each pair of nasal and bronchial data sets for all genes and revealed both weak and strong correlations with correlation coefficient value ranging from 0.244 to 0.872. To visualize the correlation of CF specific genes, we generatedheatmaps of a few subsets of genes chosen from published literature including top differentially expressed genes in CF vs non-CF. Our finding suggested that patients with overall higher correlation coefficient tend to have better correlations in top genes down-regulated in CF versus non-CF bronchial epithelium. However, further analysis and data set collection might be necessary due to the heterogeneous nature of these samples.