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Firsova, A.B.* ; Marco Salas, S.* ; Kuemmerle, L. ; Abalo, X.M.* ; Sountoulidis, A.* ; Larsson, L.* ; Mahbubani, K.T.* ; Theelke, J.* ; Andrusivova, Z.* ; Alonso Galicia, L.* ; Liontos, A.* ; Balassa, T.* ; Kovács, F.* ; Horvath, P. ; Chen, Y. ; Gote-Schniering, J.* ; Stoleriu, M.-G. ; Behr, J. ; Meyer, K.B.* ; Timens, W.* ; Schiller, H.B. ; Luecken, M. ; Theis, F.J. ; Lundeberg, J.* ; Nilsson, M.* ; Nawijn, M.C.* ; Samakovlis, C.*

Spatial single-cell atlas reveals regional variations in healthy and diseased human lung.

Nat. Commun. 16:9745 (2025)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
Integration of scRNA-seq data from millions of cells revealed a high diversity of cell types in the healthy and diseased human lung. In a large and complex organ, constantly exposed to external agents, it is crucial to understand the influence of lung tissue topography or external factors on gene expression variability within cell types. Here, we apply three spatial transcriptomics approaches, to: (i) localize the majority of lung cell types, including rare epithelial cells within the tissue topography, (ii) describe consistent anatomical and regional gene expression variability within and across cell types, and (iii) reveal distinct cellular neighborhoods in specific anatomical regions and examine gene expression variations in them. We thus provide a spatially resolved tissue reference atlas in three representative regions of the healthy human lung. We further demonstrate its utility by defining previously unknown imbalances of epithelial cell type compositions in chronic obstructive pulmonary disease lungs. Our topographic atlas enables a precise description of characteristic regional cellular responses upon experimental perturbations or during disease progression.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Fetal
ISSN (print) / ISBN 2041-1723
e-ISSN 2041-1723
Journal Nature Communications
Quellenangaben Volume: 16, Issue: 1, Pages: , Article Number: 9745 Supplement: ,
Publisher Nature Publishing Group
Publishing Place London
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Human-Centered AI (HCA)
Research Unit Precision Regenerative Medicine (PRM)
Institute of Lung Health and Immunity (LHI)
Grants Erling-Persson Foundation, Number 2023-0035
Vetenskapsrdet (Swedish Research Council)
Cancerfonden (Swedish Cancer Society)