Single Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis

Abstract

Cystic fibrosis (CF) is a life-shortening multisystem hereditary disease caused by abnormal chloride transport. CF lung disease is driven by innate immune dysfunction that perpetuates inflammation. The airways provide a window into CF pathogenesis, as immune cells display exaggerated inflammatory responses and impaired phagocytic function, contributing to tissue injury. In order to define the transcriptional profile of this airway immune dysfunction, we performed the first single-cell transcriptome characterization of CF sputum. We show that the airway immune cell repertoire shifted from alveolar macrophages in HC to a predominance of recruited monocytes and neutrophils in CF. Recruited lung mononuclear phagocytes were abundant in CF, separated into three archetypes: activated monocytes, monocyte-derived macrophages, and heat-shock activated monocytes. Neutrophils were most prevalent in CF, with a dominant immature proinflammatory archetype. While CF monocytes exhibited proinflammatory features, both monocytes and neutrophils showed transcriptional evidence of abnormal phagocytic and cell-survival programs. Our findings offer an opportunity to understand subject-specific immune dysfunction and its contribution to divergent clinical courses in CF. As we progress towards personalized applications of therapeutic and genomic developments, we hope this inflammation profiling approach will enable further discoveries that change the natural history of CF lung disease.

Topography-dependent gene expression and function of common cell archetypes in large and small porcine airways

“…We found airway common cell types that seemingly share the same gene expression biomarkers and have similar morphology by light microscopy may have very different gene expression profiles when in two different locations. Whereas single cell RNA-seq has previously revealed common “sub-sets” or “cell states” that further sub-classify cell types, the sheer magnitude with hundreds or thousands of differentially expressed genes between corresponding cell archetypes (Montoro et al, 2020; Schupp et al, 2020) in large and small airways was striking.…”

“…CFTR expression varies alongside that of many other genes in different cell types, and gene expression can vary greatly in tissue of diseased CFTR -/- animal models or in people with cystic fibrosis in the presence of infection and inflammation (Schupp et al, 2020). But does CFTR itself regulate expression of other genes via protein-protein interactions or via ion transport-mediated transcriptional regulation?…”

“…Here, we studied the key differences in large and small airway epithelial composition and gene expression and hypothesized that the gene expression profile of a given cell archetype (Montoro et al, 2020; Schupp et al, 2020) would depend on its location. We used airway microdissection to isolate freshly-obtained small airway epithelial cells (Li et al, 2016) which in newborn pigs correspond to those less than 200 μm diameter.…”

Reproducible Single-Cell Genomic Research in Pulmonary and Critical Care Medicine

“…Hence, single-cell technologies have rapidly become a logical method of choice to study lung biology and disease (2). Specifically, single-cell RNA-seq has been applied to create reference atlases of normal human lung tissue (3-6), to study cellular cross-talk in multicellular lung cancer niches (7,8), to discover novel cell types in the normal lung (9) or in pulmonary fibrosis (10)(11)(12)(13)(14)(15)(16), to evaluate remodeling of the airway epithelium in asthma (17) or as a result of smoking (18), to study the immune response in cystic fibrosis (19), and in COVID-19 (20)(21)(22). By applying the power of single-cell techniques to causal experiments in model organisms or in vitro systems, investigators were able to provide mechanistic insights about the role of specific cell types to disease pathogenesis (23)(24)(25).…”

Spelunking in Sputum: Single-Cell RNA Sequencing Sheds New Insights into Cystic Fibrosis

“…In this issue of the Journal , Schupp and colleagues (pp. 1419–1429 ) conducted an unbiased analysis by performing single-cell RNAseq analyses in sputum between nine CF subjects and five healthy control subjects ( 7 ).…”