A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung

• Published in: Nature cell biology Vol. 25; no. 2; pp. 351 - 365
• Main Authors: Sountoulidis, Alexandros, Marco Salas, Sergio, Braun, Emelie, Avenel, Christophe, Bergenstråhle, Joseph, Theelke, Jonas, Vicari, Marco, Czarnewski, Paulo, Liontos, Andreas, Abalo, Xesus, Andrusivová, Žaneta, Mirzazadeh, Reza, Asp, Michaela, Li, Xiaofei, Hu, Lijuan, Sariyar, Sanem, Martinez Casals, Anna, Ayoglu, Burcu, Firsova, Alexandra, Michaëlsson, Jakob, Lundberg, Emma, Wählby, Carolina, Sundström, Erik, Linnarsson, Sten, Lundeberg, Joakim, Nilsson, Mats, Samakovlis, Christos
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 2023; Nature Publishing Group
• Subjects: 13/51; 14/19; 14/32; 14/63; 38/39; 38/91; 631/136/142; 631/136/1660/1986; 631/208/514/1949; 631/337/2019; Biomedical and Life Sciences; Bronchoconstriction; Cancer Research; Cell Biology; Cell differentiation; Cell Differentiation - genetics; Cell interactions; Developmental Biology; Differentiation (biology); Embryo, Mammalian; Embryos; Epithelium; Fibroblasts; Gene expression; Gene Expression Profiling; Gene sequencing; Heterogeneity; Humans; Life Sciences; Lung; Lung diseases; Lungs; Medicin och hälsovetenskap; Muscles; Origins; Parasympathetic nervous system; Progenitor cells; Resource; Respiratory tract; Smooth muscle; Stem Cells; Topography; Transcriptomics
• ISSN: 1465-7392; 1476-4679; 1476-4679
• DOI: 10.1038/s41556-022-01064-x

The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases. Sountoulidis et al. provide a spatial gene expression atlas of human embryonic lung during the first trimester of gestation and identify 83 cell identities corresponding to stable cell types or transitional states.