Cellular heterogeneity in the 16HBE14o (−) airway epithelial line impacts biological readouts

The airway epithelial cell line, 16HBE14o(−), is an important cell model for studying airway disease. 16HBE14o(−) cells were originally generated from primary human bronchial epithelial cells by SV40‐mediated immortalization, a process that is associated with genomic instability through long‐term culture. Here, we explore the heterogeneity of these cells, with respect to expression of the cystic fibrosis transmembrane conductance regulator (CFTR) transcript and protein. We isolate clones of 16HBE14o(−) with stably higher and lower levels of CFTR in comparison to bulk 16HBE14o(−), designated CFTR(high) and CFTR(low). Detailed characterization of the CFTR locus in these clones by ATAC‐seq and 4C‐seq showed open chromatin profiles and higher order chromatin structure that correlate with CFTR expression levels. Transcriptomic profiling of CFTR(high) and CFTR(low) cells showed that the CFTR(high) cells had an elevated inflammatory/innate immune response phenotype. These results encourage caution in interpreting functional data from clonal lines of 16HBE14o(−) cells, generated after genomic or other manipulations.