The discovAIR project: a roadmap towards the Human Lung Cell Atlas

Abstract

The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell-cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions.

FIGURE 1

discovAIR approach and workflow. The discovAIR consortium aims to establish a first draft of the Human Lung Cell Atlas by integrating existing single-cell RNA sequencing (scRNA-seq) datasets from the Lung Biological Network of the HCA (HCA-Lung) into a single embedding, allowing analyses on the integrated dataset (A). This dataset will be enriched by additional datasets generated by the discovAIR consortium: a multi-omics characterisation of lung tissue from five healthy donor lungs sampled at five locations (“deep dive”) (B) and a cohort of healthy controls (at least n=50) and patients with lung disease (at least n=50) (C). The “deep dive” tissue samples will also be used to generate spatially resolving datasets on matched tissue sections using Visium, in situ sequencing, SCRINSHOT (single-cell resolution in situ hybridisation on tissues) and laser capture microdissection (LCM)-guided single-nucleus RNA sequencing (snRNA-seq) analysis (D). Samples from the discovAIR cohort (patients and controls) will be used for spatial mapping using SCRINSHOT (E) and for establishment of the lung cell perturbation atlas (F). In the lung cell perturbation atlas, stimulations of ex vivo cultured primary cells or precision-cut lung tissue slices will be used to map cell state trajectories of healthy cells to diseased cell states (G). These novel datasets will be ingested into the next iterations of the integrated Human Lung Cell Atlas, used to establish consensus annotations for the different lung cell types and submitted to the appropriate data repositories (H) as open data using novel visualisation modalities for the spatial datasets. Finally, the integration of the Human Lung Cell Atlas (including datasets from lung disease) and the lung cell perturbation atlas will generate novel insights into mechanisms of disease, and help guide identification of drug targets and biomarkers for disease inception or treatment response. ISS: in situ sequencing; snATAC-seq: single-nucleus sequencing assay for transposase-accessible chromatin.