A Single-Cell Atlas of the Human Healthy Airways

Marie Deprez,Kevin Lebrigand,Marie-Jeanne Arguel,Marin Truchi,Virginie Magnone,Charles-Hugo Marquette,Christophe Becavin,Sandra Ruiz García,Frédéric Brau,Dana Pe’Er,Magali Plaisant,Agnès Paquet,Sophie Abelanet,Pascal Barbry,Sylvie Leroy,Laure-Emmanuelle Zaragosi

doi:10.1164/rccm.201911-2199oc

Abstract

Rationale: The respiratory tract constitutes an elaborate line of defense that is based on a unique cellular ecosystem.Objectives: We aimed to investigate cell population distributions and transcriptional changes along the airways by using single-cell RNA profiling.Methods: We have explored the cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. A total of 77,969 cells were collected at 35 distinct locations, from the nose to the 12th division of the airway tree.Measurements and Main Results: The resulting atlas is composed of a high percentage of epithelial cells (89.1%) but also immune (6.2%) and stromal (4.7%) cells with distinct cellular proportions in different regions of the airways. It reveals differential gene expression between identical cell types (suprabasal, secretory, and multiciliated cells) from the nose (MUC4, PI3, SIX3) and tracheobronchial (SCGB1A1, TFF3) airways. By contrast, cell-type-specific gene expression is stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuroendocrine cells, and brush cells and identifies a related population of NREP-positive cells. We also report the association of KRT13 with dividing cells that are reminiscent of previously described mouse "hillock" cells and with squamous cells expressing SCEL and SPRR1A/B.Conclusions: Robust characterization of a single-cell cohort in healthy airways establishes a valuable resource for future investigations. The precise description of the continuum existing from the nasal epithelium to successive divisions of the airways and the stable gene expression profile of these regions better defines conditions under which relevant tracheobronchial proxies of human respiratory diseases can be developed.

Highlights

The prevalence of chronic respiratory diseases is thought to increase in the future by raising exposure to diverse atmospheric contaminants
We identified 14 epithelial cell types, including 12 for the surface epithelium and 2 for submucosal glands, which collectively represented 89.1% of total cells (Figure 1C-1E, Table E2; See our interactive web tool https://www.genomique.eu/cellbrowser/Human Cell Atlas (HCA)/?ds=HCA_airway_epithelium)
We have established a reference single-cell atlas of normal human airways after analyzing 35 fresh tissue samples collected by bronchoscopy in 10 healthy volunteers, resulting in a largescale gene expression profiling that integrated spatial information of each sample

Summary

Introduction

The prevalence of chronic respiratory diseases is thought to increase in the future by raising exposure to diverse atmospheric contaminants (pollution, allergens, smoking). While nose and bronchus are sharing many cellular properties, which has led to the definition of a pathophysiological continuum in allergic respiratory diseases [1, 2], they differ by features such as host defense against viruses, oxidative stress [3], or anti-bacterial mechanisms [4]. The recent advent of single-cell RNA sequencing offers an excellent opportunity to carefully analyze and compare cellular composition and gene expression from nasal to the successive generations of the lung airways. The resulting picture defines a relatively stable cellular composition and gene expression across the first 12 successive generations of the tracheobronchial tree. Our work better defines the conditions under which the nose can be considered as a relevant bronchial surrogate for studying human lung pathologies, and underlines the relative stability of gene expression in the proximal tracheobronchial compartment of the airways

Methods

Results

Conclusion