Extended Data Fig. 3: Comparison of pathologic mesenchymal niche subsets arising from IPF and cultured AHLM.
From: Human alveolar type 2 epithelium transdifferentiates into metaplastic KRT5+ basal cells
(a, b) IF analysis of hAEC2s-derived organoids co-cultured with human adult normal lung (AHLM) and IPF mesenchyme at D7, and quantified by the percentage of SFTPC + , KRT5 + , and SFTPC + /KRT5 + cells in total cells. Data are expressed as the mean ± SD, representative of n = 3 technical replicates. * p = 0.0182 and ** p = 0.0066. Representative of n = 2 independent experiments. (c) UMAP plots of mesenchyme from each individual IPF or normal donor that was used in scRNA-seq analysis. (d) Comparison of top 100 markers in CTHRC1 + (left) and HAShigh/BMP anatgonisthigh (right) clusters of uncultured IPF (IPF fresh) and cultured AHLM with statistical comparison for degree of gene overlap of two independent gene sets denoted by representation factor (see methods). (e, f, and g) UAMP plots show BMP antagonists and TGFB1 expression in IPF lungs (from IPF Cell Atlas, Habermann et al.). Data are expressed as the mean ± SD. * indicates p < 0.05 and ** indicates p < 0.01 as determined by unpaired one-tailed student’s t-test. Each data point on the graph represents a technical replicate.
