An Atlas of Airways at a Single Cell Level in Chronic Obstructive Pulmonary Disease, Idiopathic Pulmonary Fibrosis and Controls

The increasing incidence of chronic respiratory disease is a public health problem that affects hundreds of thousands of people worldwide at all ages. Directly exposed to atmospheric airborne contaminants (pollution, allergens), the respiratory tract represents a complex ecosystem involving different cells (multiciliated, basal, mucosecretory, neuroendocrine, etc.) that develop complex interactions with the surrounding connective tissue but also with their rich immune environment and the local microbiota. Although a pathophysiological continuum is postulated between the nasal and bronchial airways in certain diseases, such as allergic diseases, investigators have demonstrated large gene expression gradients between samples taken from the nasal and bronchial airways in different studies. Specifying the cellular variability throughout the respiratory tree in a normal physiological situation is one of the major objectives defined in the establishment of an atlas of all airway cells, as defined in the objectives of the international consortium Human Cell Atlas.

The sequencing of the RNAs present specifically in each individual cell ("single-cell RNAseq"), and its comparison with neighbouring cells allows to document the precise cellular contributions, as well as the signalling pathways involved. The development of tissue sampling, stabilization, transport and single cell analysis procedures can be performed on primary respiratory epithelium cultures and can also be extended to respiratory samples from healthy volunteers.

This project will analyze gene expression profiles at the single cell level (single cell RNAseq) in volunteers with chronic obstructive pulmonary disease, interstitial pulmonary fibrosis and compared to healthy subjects of the same age. The technical modalities of the samples will be brushing and staged airway biopsies for direct analysis of the samples. This approach will be complemented by an air-liquid interface culture to allow secondary analysis in single cell RNAseq and three-dimensional mapping of the distribution of these cells with single cell in situ analysis.

Thanks to sampling at several levels of the respiratory tree (nose, bronchioles, bronchioles), cellular and gene expression variations along the tracheobronchial axis will be exhaustively documented in subjects of different ages, healthy or suffering from pathologies such as chronic obstructive pulmonary disease and interstitial pulmonary fibrosis. These data will serve as worldwide references for comparisons in different physiological and pathological contexts.