Fig. 7: Analysis of non-immune cells and CIP-Associated Clusters.

a UMAP embedding of the epithelium, with cells color-coded by their inferred cell types. b Bubble plot showing expression levels of selected marker genes for epithelial clusters. c Box plot showing the frequencies of AT2_AT1-inter and AT1 cells in CTL (n = 7) and CIP (n = 9) groups. A two-tailed Mann–Whitney U test was performed. d Box plots showing differences in the expression of CD24, MMP7 and WFDC2 in CTL (n = 29) and CIP (n = 7) patients based on bulk RNA-seq data. P values were determined by a two-tailed Mann–Whitney U test. e Bar plot showing GO analysis for AT1 cells compared with other epithelial clusters. P values were calculated using the hypergeometric test and adjusted with the Benjamini–Hochberg procedure. f Volcano plot showing gene expression fold change of epithelial cells. P values were calculated using a two-tailed Gaussian approximation of the U statistic and adjusted with the Benjamini–Hochberg procedure. g Analysis of Hallmark gene sets enriched in epithelium of CIP. P values were estimated using an adaptive multi-level split Monte Carlo approach and subsequently corrected with the Benjamini–Hochberg method. NES, normalized enrichment score. h UMAP embedding of the stromal with cells color-coded by their inferred cell types. i Box plot showing the fraction of Fibro-POSTN cells in CTL (n = 7) and CIP (n = 9) patients. A two-tailed Mann–Whitney U test was performed. j Heatmap showing the expression of Fibro-POSTN signature genes from bulk RNA-seq data in CTL and CIP patients. k Kaplan–Meier curves showing differences in overall survival probability between OAK cohort patients with high or low levels of Fibro-POSTN gene signature levels. P value was obtained using the two-sided log-rank test. In the box plots (c, d and i), the centre line represents the median, the bounds of the box correspond to the 25th and 75th percentiles, the whiskers extend to the largest and smallest values within 1.5× the interquartile range from the quartiles, and individual points beyond the whiskers indicate outliers.