Fig. 3: Nascent tumour heterogeneity in the epithelial compartment is linked to stromal remodelling.
From: Precancerous niche remodelling dictates nascent tumour persistence
a, Microdissection of squamous upper gastrointestinal tract 8 months after DEN treatment for single-cell RNA sequencing. b, Uniform manifold approximation and projection (UMAP) showing cell-type annotation. Krt, keratinocytes. c, Heterogeneous expression of Pdgfra in fibroblasts in the UMAP space. The inset shows fibroblast clusters. d, Violin plots showing levels of Pdgfra and Fn1 expression in fibroblast clusters. Black line, mean. e, Representative images from 6 mice of the DEN area and nascent tumour stroma 10 days after DEN treatment, showing the accumulation (white arrowhead) of fibronectin (FN1, green) in the niche. Blue, DAPI. Scale bars, 10 µm. f, Heatmap (left) of the top 1,500 differentially expressed genes along the basal keratinocyte pseudotime trajectory. Pseudotime trajectories, top right (blue, committed; yellow, basal; magenta, tumour). Populations representing two tumour transcriptional modules (tumour 1, red; and tumour 12, cyan; bottom right UMAP). g, Representative images from 6 mice, showing tumour 12 markers in nascent tumours 10 days after DEN treatment, showing homogeneous KRT6A (red) and KRT17 (yellow); heterogenous SOX9 and EGR1 (cyan); and AREG and RUNX1 (magenta); DAPI (blue). Scale bars, 10 µm. h, Representative images showing SOX9 distribution in Niche− and Niche+ tumours 10 days after DEN treatment. White arrowheads highlight SOX9+ keratinocytes (cyan), KRT6A (red) and PDGFRα (grey). Scale bars, 10 µm. i, Images of SOX9+ clusters in DEN-treated tumour-free areas 10 days after DEN treatment. The control was the adjacent area negative for SOX9. Blue, DAPI; cyan, SOX9; grey, PDGFRα. Scale bars, 10 µm. White arrowheads highlight keratinocyte to fibroblast proximity; the white dashed line shows the epithelia to stroma border. j, Left, experimental protocol: Krt14CreER;Sox9flox/flox mice received tamoxifen (TAM) followed by DEN. Tissues were collected 1 month after DEN treatment and compared with DEN-treated uninduced controls. Right, quantification of tumour burden; n = 3 mice per condition; data shown as mean ± s.e.m.; one-tailed Mann–Whitney test. Images captured by confocal microscopy. Illustrations in a and j were created in BioRender; Alcolea, M. https://BioRender.com/xjxwb1m (2026).
