Extended Data Fig. 7: Niche of growing tumours recruits other stromal cells; (Corresponds to Fig. 3).
From: Precancerous niche remodelling dictates nascent tumour persistence
a, Experimental protocol for targeted DNA sequencing of stromal niche 7 m after DEN treatment. b, Substitutions per megabase (Sb/Mb) were calculated and used as indicative of the mutation burden in stroma across conditions. n = 6 control (from 4 animals), 13 DEN (from 6 animals) and 18 tumour (from 6 animals). Epithelial tissue (12 m after DEN treatment) was used as benchmark and includes both tumour and tumour-free tissues (DEN+Tmr; from 3 mice). Data is expressed as mean±s.e.m. Two-tailed Welch’s t-test comparing tumour stroma with internal or external control stroma or with epithelium. c, Stacked bar plot showing scRNA-seq captured cell type distribution across conditions. d, Representative 3D-rendered confocal image of an early tumour (KRT6A, red) 4 m (left) and 7 m (right) post-DEN withdrawal showing the recruitment of immune cells (CD45, green) and blood vessels (CD31, orange) to the persisting tumour niche. DAPI (blue). Scale bar, 50 µm. e, Heatmap showing expression of representative marker genes across the 14 immune cell types identified in the scRNA-seq data. Log-transformed normalised expression levels were averaged by cluster for each gene and scaled across all cells belonging to each group. Scale bar denotes expression range (scale: -2 to 2). f, UMAP of identified immune cell types split by condition. g, Top, stacked bar plot showing immune cell type enrichment across conditions. Significance was assessed by a one-sided Chi-square test. (Bottom) heatmap showing standardised residuals values from Chi-square test. Asterisk (*) marks cell types used in CellChat analysis. h, Heatmaps representing outgoing (left) and incoming (right) interaction strengths as identified by CellChat and rescaled to their row maxima. Cumulative interaction strength is depicted by bars on the right. Months (m). Illustration in a was created in BioRender; Alcolea, M. https://BioRender.com/udeggcf (2026). Source data (b).
