GSE193683
Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro [scRNA-seq]
Rationale: Although epithelial-mesenchymal transition (EMT) is a common feature of fibrotic lung disease, its role in fibrogenesis is controversial. Recently, aberrant basaloid cells were identified in fibrotic lung tissue as a novel epithelial cell type displaying a partial EMT phenotype. The developmental origin of these cells remains unknown. Objectives: To elucidate the role of EMT in the development of aberrant basaloid cells from human bronchial epithelium by mapping EMT-induced transcriptional changes at the population and single-cell level. Methods: Human bronchial epithelial cells (HBECs) grown as submerged or air-liquid interface (ALI) cultures with or without EMT induction were analyzed by bulk and single-cell RNA-Sequencing. Measurements and Main Results: Comparison of submerged and ALI cultures revealed differential expression of 9,868—protein coding (PC) and long non-coding RNA (lncRNA)—genes and revealed epithelial cell-type-specific lncRNAs. Similarly, EMT induction in ALI cultures resulted in robust transcriptional reprogramming of 6,927—PC and lncRNA—genes. While there was no evidence for fibroblast/myofibroblast conversion, cells displayed a partial EMT gene signature and an aberrant basaloid-like cell phenotype. Conclusions: The substantial transcriptional differences between submerged and ALI cultures highlights that care must be taken when interpreting data from submerged cultures. This work supports that lung epithelial EMT does not generate fibroblasts/myofibroblasts and confirms ALI cultures provide a physiologically relevant system to study aberrant basaloid-like cells and mechanisms of EMT. We provide a catalog of PC and lncRNA genes and a data visualization package for further exploration for potential roles in the lung epithelium in health and lung disease. Overall design: 3 individual healthy donor bronchial epithelial tissue samples were used for single-cell RNA sequencing analysis. The single-cell RNA-seq data were generated in two ALI libraries, AW20003 and AW21001, and one submerged cultures library, SC2100310. (1) AW20003 contained the data of donor ID 34 (11 years old Caucasian male). Hashtag-oligos (HTOs) 5 and 6 labelled the Day 0 cells, HTOs 3 and 4 the Day 1 cells and HTOs 1 and 2 the Day 5 cells. (2) AW21001 combined the data of donor IDs 27 (60 years old black male) and 54 (19 years old black female) in different HTOs. HTOs 1 and 4 labelled the Day 0 cells of each donor respectively. Similarly, HTOs 2 and 5 and HTOs 3 and 6 held the data of Days 1 and 5. (3) SC2100310 combined the data of all three donors with HTO 1 marking the cells of donor IDs 27, HTO 2 the cells of donor ID 34 and HTO 3 the cells of donor ID 54.