mRNA-Seq of WTBE and CFBE cells

Cystic fibrosis (CF) is characterized by chronic inflammation and excessive cytokines secretion in the lung. Isogenic human CF bronchial epithelial (CFBE41o-) cell lines stably expressing wt-CFTR (WTBE) or F508del mutant (CFBE) are widely used tools in understanding responses to stimuli or drugs and CF pathogenesis in vitro. However, their intrinsic cellular differences in culture are unknown. Hence, we performed integrative analyses at protein, mRNA and chromatin levels on these isogenic cell lines cultured in submerged and transwell condition. CFBE and WTBE cells displayed different secretion patterns on IL-6, IL-8, CXCL1, CXCL10, and CCL5 . The ALI culture dramatically increased cytokines secretion in both cells. ATAC-seq results showed that CFBE cells exhibited higher genome-wide chromatin accessibility than WTBE cells in both culture methods, but the relative openness of cytokine genes between two cells varied individually. Differentially expressed genes between two cell lines from mRNA sequencing were highly concentrated in immunity-related pathways. While the mRNA stability of CXCL10 and CXCL1 exhibited the most significant differences between cell lines in SUB culture, most cytokines had comparable mRNA stabilities within same culture method. Moreover, polarization of cells via transwell culture remodeled the chromatin accessibility and transcriptome. This multilayered studies presents a comprehensive baseline activities of CFBE and WTBE cells, further facilitating their usage and data interpretation as CF cell models. Overall design: transcriptome profile of WTBE and CFBE cells under different culture models.