Extended Data Fig. 5: Benign papilloma and invasive SCC display distinct epigenetic signatures.
From: Ras drives malignancy through stem cell crosstalk with the microenvironment
a, ATAC sequencing is performed on FACS-purified α6hiβ1hi basal populations of interfollicular epidermis (IFE, Sca1+), bulge hair follicle stem cells (HFSCs, CD34+), and tumour cells (CD44hi) either positive or negative for TGFβ-responsiveness (mCherry). Peaks are clustered according to their openness in each population by k-mean clustering. b, Venn diagram showing marked divergence of ATAC peaks from TGFβ-responding tumour basal cells and their non-responding neighbours between papilloma and SCC stages (n = 2 for each condition, each stage). c, Motif enrichment analysis of the 7 ATAC peak clusters. d, Quantifications of the Lepr cis-regulatory region boxed in Fig. 2f. e, Immunofluorescence images reveal that transcription factors RUNX1 and FOS are not detected in normal homeostatic skin but are enriched progressively during tumorigenesis. Scale bars, 50 µm. See also pSMAD2 immunofluorescence quantifications in Extended Data Fig. 1a. f, Lepr EGFP reporter and TGFβ mCherry reporter show minimal activity in papillomas but co-localize at the invasive fronts of SCC. Note numerous SCC cells marked by EGFP cytoplasm and mCherry nucleus. Integrin (white) denotes invasive fronts. For the original images, scale bars, 20 μm. For the magnified insets, scale bar, 10 μm. The percentages of reporter double-positive (DP) cells in these invasive regions are significantly higher in SCC than in papilloma. Majority of the TGFβ mCherry reporter+ cells are these DP cells in SCC compared to the ones in papilloma. (n = 4 for papilloma, n = 3 for SCC; top right: p = 0.0477; bottom right: p < 0.0001). All statistics were using unpaired two-tailed Student’s t -test: ns, p ≥ 0.05); *, p ≤ 0.05); **, p ≤ 0.01; ***, p ≤ 0.001; ****, p ≤ 0.0001. Data are presented as mean ± s.e.m.
