Introduction

Single-cell sequencing (SCS) is an emerging technology used to understand the function and gene expression status of individual cells, as well as interactions that occur at the single-cell level by use of single-cell suspensions, preparations, single-cell capture and labeling methods, library preparation and sequencing, and data analysis [1]. Currently, SCS technologies have been used in genome sequencing (scDNA-seq), transcriptome sequencing (scRNA-seq), DNA methylation sequencing, histone modification sequencing, and chromatin structure sequencing (scATAC-seq). SCS studies conducted on heterogeneous diseases have demonstrated significant advantages when compared to studies conducted using traditional sequencing methods [1, 2]. For instance, SCS technology has been widely used in the field of upper and lower airway diseases, such as inflammatory diseases, viral infections, and cancers [3]. Moreover, it can be used to identify rare subgroups, circulating inflammatory cells, tumor or immune microenvironments, cancer stem cells, and to classifry the heterogeneity and molecular subtypes of airway inflammations and tumors[4]. Futhermore, SCS can be used to study various mechanisms associated with disease onset, progression, tumor metastasis, evolution, relapse, and treatment resistance. Here we provide a systematic review of current advances in the application of several common SCS techniques in the upper and lower airways.

1. SCS in airway inflammatory diseases

The upper and lower inflammatory airway diseases discussed in this review are allergic rhinitis (AR), chronic rhinosinusitis (CRS), bronchial asthma (BA), chronic obstructive pulmonary disease (COPD), and idiopathic pulmonary fibrosis (IPF). These diseases are characterized by pathological features such as luminal inflammation, epithelial chemosis and hyperplasia of the basement membrane, smooth muscle and submucosal cells, as well as glandular hyperplasia. Their common features are epithelial barrier dysfunction, including defective tight junctions (TJs) between cells and increased epithelial permeability. ScRNA-seq is widely used in the field of immune diseases due to its advantages of high cell throughput, low cost of library construction, and short capture cycle. At present, scRNA-seq studies of upper and lower airway diseases have revealed that the airway has a complex structure and contains multiple cell types, such as epithelial cells that act as a barrier, and immune cells for antimicrobial defense. ScRNA-seq is also used to understand airway biology, disease pathogenesis, and disease progression between the upper and lower inflammatory airways. Here, we discuss the use of single cell sequencing in several different airway inflammatory diseases on individual basis.