Fig 1: A subset of metaplastic cells express overlapping sets of genes with stomach pit cells, and are localized to PanINs.a–c UMAP showing the expression level of highly expressed genes in cluster A_15 cells that we found to include Pit-like cells. In each chart, the expression level of one gene is indicated, a Gkn1, b Gkn2, and c Tff1. High expression level—red, low expression level —gray. Scale is on the right and relevant gene name on the top of each chart. d Dot plot showing the expression level of sets of genes (x-axis) in different subsets of cells (y-axis). Subsets of cells are based on the clusters in Fig. 2b early acinar/ductal cells (control, 17 days and 6 weeks PTI samples), late (3, 5, and 9 months PTI samples). The average expression level is shown by the size of the dot and the percentage of cells that express the relevant gene is indicated by the color. e Distances matrix of all clusters of acinar, ductal, metaplastic, and stomach epithelial cells shown in Fig. 2b. Cluster numbers are indicated on the bottom and on the right, clusters were ordered based on the hierarchical clustering analysis. The scale score of overlapping genes is shown in the red-blue bar. The cell types and cell lineages are indicated on the bar color on the right. Genes used for this analysis are based on comparing the expressed genes in the relevant cluster to all the cells shown in Fig. 1 (see “Methods”). f–k Histological sections of mice pancreas. f, i PT control mice, g, j five months PRT, h, k nine months PRT. f–h Staining with anti-Gkn1, i–k staining with anti-Krt19. Black arrows indicate representative cells that are large and therefore may contain mucins, green arrows indicate representative cells that are smaller and without mucins. Scale bars 100 µm.
Fig 2: Acinar metaplastic cells are heterogeneous.In the middle of the figure a snapshot of Fig. 2b is presented, showing tdTomato-positive and stomach cluster cells. a Dot plot of selected differentially expressed genes in early (control, 17 days and 6 weeks PTI samples) and late (3, 5, and 9 months PTI samples), acinar, ductal and metaplastic clusters of cells as indicated on the y-axis. Dot size represents the expression level and color represents the percentage of cells that express the indicated gene, in each cluster. b Histological sections of mouse pancreas 4 months PTI, immunostaining with anti-Ins1. A green arrow indicates an islet; a black arrow indicates a stained cell that is localized to PanIN. Scale bar 100 µm. c Quantities analysis of metaplastic cell-types and states in PanIN lesions and in ductal structures. Data collected from slices from three different mice for each antibody (n = 3), and is based on the counting of 24,808 cells, see Supplementary Data 9. The bars represent the mean values and ±SD. d, e, h Metaplastic tuft-like cells. Immunostaining using anti-Dclk1 antibody, d control, 5 months PT mouse, e 5 months PRT mouse, scale bars 100 µm. h Violin plot showing the expression of Dclk1 and Pou2f3. f, g, i Senescent cells. Immunostaining using anti-Tgfb1, f control, 5 months PT mouse, g 5 months PRT mouse, scale bars 100 µm. i Violin plot showing the expression of Gjb4, Tgfb1, and Cdkn2a. j Metaplastic chief-like cells, violin plot showing the expression of Muc6, Pgc. m, n, k Metaplastic stomach pit-like cells. Immunostaining using anti-Tff1 antibody, m control, 5 months PT mouse, n 5 months PRT mouse, scale bars 100 µm. k Violin plot showing the expression of Gkn1, Tff1, and Muc5ac. o, p, l Metaplastic cycling cells. Immunostaining with anti-Mki67 antibody, o control, 5 months PT mouse, p 5 months PRT mouse, scale bars 100 µm. l Violin plot showing the expression of Mki67.
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