Extended Data Fig. 7: The molecular and cellular basis of clinically relevant PF histopathologies.

a, Each sample was assigned a pathology score based on a semiquantitative scale assessing the number/severity of pathologic features. Here we show a representative sample (VUILD107MA; IPF diagnosis) with annotated features. Features are represented by colors and symbols as shown: §, hyperplastic airway epithelial cells (AECs); ^, remodeled epithelium; #, epithelial detachment; †, large airway; $, goblet cell metaplasia; *, mixed inflammation; ‖, muscularized artery; Δ, fibroblastic focus; ‡, fibrosis; =, severe fibrosis. b, Cell types significantly associated with pathology score are labeled in the volcano plot. The horizontal and vertical dashed lines show the significance threshold (FDR < 0.01) and split the plot into cell types negatively and positively associated with pathology score, respectively. Cell types on the right are present in higher proportions in samples with high pathology scores. c, The cell-type composition of select annotations of interest, as a proportion of the number of cells across an annotation (each column sums to 1; columns indicated by gray lines). See Supplementary Fig. 17a for an expanded version of this plot with all cell types and annotations. d, Examples of select annotations on semi-transparent H&E images overlain with cell types in the annotated region. Each point represents a cell centroid. Cell-type colors are matched to b. Scale bars represent 20 µm. Example annotations were taken from the following samples: granuloma—VUILD96MA (sarcoidosis); tertiary lymphoid structure (TLS)—VUILD110LA (CTD-ILD); microscopic honeycombing (partial)—VUILD78MA (IPAF); goblet cell metaplasia—VUILD104MA2 (IPF); hyperplastic AECs—VUILD107MA (IPF); fibroblastic focus—VUILD104MA1 (IPF).