Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing

Abstract

Standalone and consortia-led single-cell atlases of healthy and diseased human airways generated with single-cell RNA-sequencing (scRNA-seq) have ushered in a new era in respiratory research. Numerous discoveries, including the pulmonary ionocyte, potentially novel cell fates, and a diversity of cell states among common and rare epithelial cell types have highlighted the extent of cellular heterogeneity and plasticity in the respiratory tract. scRNA-seq has also played a pivotal role in our understanding of host–virus interactions in coronavirus disease 2019 (COVID-19). However, as our ability to generate large quantities of scRNA-seq data increases, along with a growing number of scRNA-seq protocols and data analysis methods, new challenges related to the contextualisation and downstream applications of insights are arising. Here, we review the fundamental concept of cellular identity from the perspective of single-cell transcriptomics in the respiratory context, drawing attention to the need to generate reference annotations and to standardise the terminology used in literature. Findings about airway epithelial cell types, states and fates obtained from scRNA-seq experiments are compared and contrasted with information accumulated through the use of conventional methods. This review attempts to discuss major opportunities and to outline some of the key limitations of the modern-day scRNA-seq that need to be addressed to enable efficient and meaningful integration of scRNA-seq data from different platforms and studies, with each other as well as with data from other high-throughput sequencing-based genomic, transcriptomic and epigenetic analyses.

TNFRSF1B Signaling Blockade Protects Airway Epithelial Cells from Oxidative Stress

“…Of note, this proof-of-concept study has two potential limitations. Firstly, the heterogeneity and plasticity of the respiratory epithelium is well known, with common and rare epithelial cell types in different sections of the respiratory tract [ 34 ], thus our results employing two particular cell types may not be fully extrapolatable due to the inherent complexity of the airways. Secondly, the relevance of the TNFR2 blockade for oxidative stress protection should be further validated in well-differentiated primary CF and non-CF airway epithelial cell cultures, which more closely recapitulate the in vivo morphology and pathophysiology of human airway epithelia.…”