Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts biological readouts

Abstract

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.