Fig. 4: Transcriptional programs in nascent carcinoma at single cell resolution.

a Experimental approach for scRNAseq of tongue epithelia. Created in BioRender. https://BioRender.com/o87g113. b UMAP of physiologic and transgene-associated epithelial cell states, n = 12,771 cells (n = 2 mice per group). c Individual contribution of each transgenic condition to overall epithelial cell UMAP shown in b. n = 2 mouse tongue epithelia per transgenic condition; N = 3,783, E = 4,529, Y = 2,311, EY = 2,148 cells. d Distribution of cell states in tongue epithelial cells from each transgenic condition. n cells = total cells per transgenic condition. e Relative expression of representative cell state associated genes and the HPV^E6E7 and YAP1^S127A transgenes by cluster. f GSEA of molecular signatures and recurring cancer cell states across the transgene-enriched clusters generated using fgsea⁴⁵ (see Methods for details). Dot color indicates enrichment (purple) or depletion (green). Dot size encodes the absolute value (abs) of the normalized enrichment score (NES). Circle opacity represents -log₁₀ of the adjusted p-value (p_adj); circles are hollow if p_adj > 0.05. For gene set details see Supplementary Data 3. g IGV tracks of YAP CUT&Tag, H3K27ac CUT&Tag, and ATACseq peaks at the Pdpn gene locus. Black bars indicate significant peaks. Red bars indicate EY-gained peaks. h Representative images of H2B-GFP and PDPN protein expression in N and EY epithelia 10 days after transgene induction. Dashed white line indicates the basement membrane. Scale bars: 10μm except where indicated as 50μm (left N panel) or 100μm (left EY panel); n = 5 mice per group.