Fig. 2: Composition of alveolar epithelial and immune cells and their correlations in regenerating alveolar niche in IPF lungs.

a Representative ROI from Early disease stage showing KRT17/7 and CD206 protein expression (IMC staining). b–e Corresponding cell centroid maps for (a) showing location of ABIs, basal cells and AT II cells. No ABI_b is visible in keeping with their very low numbers. f Expression density plot for EPCAM, KRT17/7, KRT5, Ki67 and ProSP-C for all epithelial cell clusters in alveolar niche. Blue vertical lines represent background staining. ATII cells are the only cells with high ProSP-C expression; they also showed no/low KRT5 expression by gene expression analysis (see Supplementary Fig. 3b, c) and immunofluorescence staining (Supplementary Fig. 6). g High magnification of H&E images from ‘a’ and ‘b’ boxes in (A). These show that the morphology of ABI_a and ABI_b-DC ADJ cells are in keeping with formal histopathology feature of type II alveolar metaplasia. AM- alveolar macrophages. h Proposed points for ABIs, basal cells and ATII cells in the differentiation trajectory of abnormal alveolar epithelium as shown by Kathiriya’s¹¹ human alveolar organoid studies. Broken blue boxes identifies markers used in our study. Diagram adapted from Kathiriya JJ et al.¹¹; AEC 2 – type 2 alveolar epithelial cells. i Proportion (mean, for all 53 ROIs) of different epithelial and immune cells (as % of total epithelial and immune cells, respectively). j Number (cells/mm² of tissue) of immune (left graph) and epithelial (right graph) cells in Early, Intm and Adv disease stages. Bar plot provided for visualisation, showing mean and S.D. ***p < 0.001 is 7.2e-06 **p < 0.01 is 5.0e-03 [comparison derived using generalised linear model (GLM) model statistics, with area as a normalising factor]. k Correlation in abundance of cells (per mm² of tissue) between alveolar epithelial cell types and immune cells. Values are ‘r’ derived using Pearson’s correlation (complete data in Supplementary Fig. 7). Only positive correlation shown; grey boxes—no significant correlation **p < 0.01; ***p < 0.001; Benjamini—Hochberg correction was applied for multiple comparisons. I Correlation plots for ABI-immune cell pairs with three highest r values for each disease stage (as shown in k). All analyses performed on data derived from 53 ROIs, n = 7 patients (see Fig. 1). Source data are available in Source Date File.