Fig. 3: scRNA-seq of primary tissues shows cell-state changes mediated by DDR1. | Nature Communications

Fig. 3: scRNA-seq of primary tissues shows cell-state changes mediated by DDR1.

From: Breast tissue regeneration is driven by cell-matrix interactions coordinating multi-lineage stem cell differentiation through DDR1

Fig. 3: scRNA-seq of primary tissues shows cell-state changes mediated by DDR1.

a scRNA-seq data from all cells (n = 1467) from patient-derived hydrogel-grown tissues projected onto two dimensions using t-SNE on the top eight principal components across 7193 variable genes. b Bar chart of an embryonic stem cell gene set enrichment in each of the epithelial clusters. c, d Volcano plot visualizing differential gene expression between clusters 0 and 1 (c) and between clusters 4 and 6 (d). Cell cycle genes are highlighted in green. Ki67 (MKI67, www.ncbi.nlm.nih.gov/gene/4288) is labeled individually. The likelihood ratio test was used, p-values not corrected for multiple tests. e Inferred lineage relationships of all cells (black) were projected onto two dimensions as basal and luminal differentiation trajectories, using Monocle. Cluster 0 (red; left panel) and cluster 1 (yellow; right panel) cells are highlighted. f–g Stacked bar charts indicating the distribution of basal (f) and luminal (g) clusters in control, DDR1i, and DDR1i Rel tissues. h Heatmap of enriched gene sets using the Broad Institute’s MAigDB dataset with the hypergeometric test (FDRs were calculated) on DDR1i and DDR1i Rel tissues. i Cells treated with DDR1i, released from DDR1i and untreated controls projected onto basal and luminal differentiation trajectories, using Monocle. j Proposed model for the role of DDR1 in mammary epithelial cell differentiation. Source data are provided as a Source data file.

Back to article page