Fig. 1: LY6D marks a pre-existing spatially localized basosquamous BCC population.

a scRNA-Seq study design (left) and H/E of the various histological features from different human BCCs used for scRNA-Seq experiments. Scale bar = 50 μm. n = 7 humans and n = 1 mouse. b UMAP plot of scRNA-Seq data from seven merged human BCC tumor epithelial samples with seven distinct clusters. c BCC vs SCC scoring superimposed onto the UMAP plot from b. Merged-Hu-C6 from b is circled. d Gene scoring for Keratinocyte Differentiation GO term for the seven different clusters from b. e Cell type scoring for various skin epithelial cell types for the seven different clusters from (b). f Tumor sample proportions in clusters Merged-Hu-C3, Merged-Hu-C2, and Merged-Hu-C6. g Feature plots highlighting the expression of key surface markers (TACSTD2, LYPD3, CLDN4, and LY6D) with the specificity of LY6D for Merged-Hu-C6 indicated. h UMAP plot of scRNA-Seq data from mouse BCC tumor epithelial sample with eight distinct clusters. i Gene scoring for Keratinocyte Differentiation Score for the eight different clusters from h. j Feature plot of Ly6d in mouse BCC tumor. k Marker gene overlap between Merged-Hu-C6 and Mouse-C5. l Spatial localization of TACSTD2 (white), LYPD3 (red), and LY6D (yellow) transcripts in human BCCs, which are co-stained with K14 protein (green). LY6D expression is also shown alone without other markers. Zoomed regions indicated by yellow boxes. Yellow arrows point to LY6D⁺ regions. n = 3. m Spatial localizations of basosquamous markers in human BSC, mouse BCC, human SCC, and human IFE. The markers shown are TACSTD2 (white), LYPD3 (red), and LY6D/Ly6d (yellow). n = 2 for human examples. n = 3 for mouse. n Feature plot human BCC21 showing expression of GLI1 and LY6D. o Spatial localization of basosquamous state and GLI1 transcripts in naive human BCCs and BSCs. Red arrows point to GLI1⁺ regions. Yellow (LY6D⁺) and white (LYPD3⁺) arrows point to basosquamous regions. n = 2. p Diagram indicating the spatial localizations of the basosquamous markers with respect to GLI1⁺ cells. q Histology of various human BCCs, BSC, and SCC with the corresponding indication of LY6D levels. Yellow arrows point to squamous features. Length of each scale bar is noted in figure.