Abstract
Despite significant advances in understanding lung development, the intricate cellular interactions and spatial organization of the developing human lung remain incompletely defined. Spatial transcriptomics enables gene expression profiling within the native tissue context, providing unprecedented insights into complex developmental processes. In this study, we applied the 10X Genomics Visium platform to characterize spatially resolved transcriptional profiles of prenatal human lungs during the pseudoglandular and canalicular stages.Spatial transcriptomic analysis of 12 prenatal lung samples (13–20 weeks gestation) identified 10 distinct transcriptional niches corresponding to unique combinations of epithelial, mesenchymal, endothelial, and immune cell populations. Unsupervised clustering revealed developmental shifts in spot/niche composition from the pseudoglandular to canalicular stage, with a progressive increase in alveolar epithelial spots and a concomitant decline in mesenchymal regions, particularly in peripheral lung areas. Differential gene expression analysis demonstrated stage-specific transcriptional transitions in individual spot types, including downregulation of cell cycle and structural pathways and upregulation of secretory pathways as the lung matures. Spatial organization analysis revealed increasing compartmentalization of pulmonary cell types, highlighting the progressive structuring of the distal lung microenvironment. In summary, this study provides a spatial map of the developing human lung, offering novel insights into pulmonary lineage dynamics and cellular interactions during early organogenesis.
Data availability
Raw and processed data associated with the study are available in Gene Expression Omnibus (GEO) and can be retrieved using accession number GSE310610.
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Acknowledgements
We wish to acknowledge the technical support from John Ashton, Jeffrey Malik, Cameron Baker, and Elizabeth Pritchett in the University of Rochester Genomics Research Center (URGRC).
Funding
This work is funded by the NIH/NHLBI through the Developing Lung Molecular Atlas Program (LungMAP) Pilot grant (to SB).
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SB and TJM conceptualized the study. SD, GD, and IG processed the samples and performed experiments. YR and SB analyzed the data. YR, SD, GD, TJM and SB wrote and edited the manuscript. No honorarium or other form of payment was given to anyone to produce the manuscript. There are no prior publications or submissions with any overlapping information, including studies and patients. All authors have read the manuscript and have approved of its submission and declare no conflicts of interest.
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Ren, Y., Danopoulos, S., Deutsch, G.H. et al. Spatial transcriptomics of developing human lungs defines cellular phenotypes associated with age, lineage and location. Sci Rep (2026). https://doi.org/10.1038/s41598-025-34594-z
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DOI: https://doi.org/10.1038/s41598-025-34594-z
