Extended Data Fig. 4. Spatial and molecular analysis of BLM-induced mouse lung fibrosis.
a) H&E-stained sections of mouse lung tissues collected at day 7 (d7) and day 21 (d21) post-BLM or saline vehicle treatment that were used for Visium analysis. b) Summarizing statistics of Visium spot count used and histopathological annotations. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range. c) Volcano plots depicting differential expression analysis results between BLM and vehicle-treated lungs at d7 and d21, highlighting genes with significant (adj. p < 0.01) changes in expression. d) Network of top significant (p value < 0.0001) canonical pathway enrichment results based on human hsNMF-F14hi C0 and mouse mmNMFd21-F14hi C0 marker genes (adj. p < 0.05), with specific pathways within each node cluster annotated. Inner nodes illustrate groups of regulators sharing genetic influences, and outer nodes represent contributing marker genes. e) Spatial plots of mmNMF-F14hi C0-C2 and regions histologically annotated as fibrotic tissue (gray) for all the BLM-challenged lungs collected at d21. f) To quantify the spatial localization of the mmNMF-F14hi clusters in relation to fibrotic tissue, the same strategy as presented in Extended Data Fig. 2h was employed, except for using regions annotated as fibrotic to extract radial distances. g) Z-scores for each cluster plotted across each distance bin, relating to the distance from fibrotic regions (yellow shaded areas) across all tissue samples. P-values were computed from the Z-scores using a two-tailed test (dark blue: p < 0.01; light blue: p < 0.05; gray: ≥ 0.05). mmF14hi C0 was significantly enriched within the border of fibrotic areas, especially at 150-350 µm distances into the fibrotic tissue. On the other hand, there was an underrepresentation of mmF14hi C0 spots in areas outside the fibrosis. H&E, Hematoxylin and eosin.