Extended Data Fig. 4: Identification of morphologically benign acinar with somatic copy number alterations (SCNAs).

a, UMAP of epithelial cells in snRNA-seq data colored by expression level of given marker genes of intraepithelial neoplasia (PIN) in ST slice sampled from the transition zone of HP09. b, Spatial transcriptomic slice of the transition zone of HP09 colored by the expression level of selected marker genes of the PIN in this slice. c, Heatmap showing CNA in each single nucleus identified as luminal cell sampled from the peripheral zone of HP09. d, Sampling strategy of HP12 (upper left) and H&E staining of this slice. Selected region in the dashed box was used to perform Visium analysis. e, Enlarged partition of slice sampled from the peripheral zone of HP12. f, Spatial transcriptomic slices of HP12 colored by CNV Leiden clusters. g, Heatmap grouped by CNA Leiden clusters of the peripheral zone slice of HP12. h, Spatial transcriptomic slice colored by expression level of Type 2 luminal signature in each spot. i, Enlarged partition of the slice expressing high level of Type 2 luminal signature. j, Sampling strategy of HP13. k, Spatial transcriptomic slices of HP13 colored by CNV Leiden clusters. l, Heatmap grouped by CNA Leiden clusters of the peripheral zone slice of HP13. m, Enlarged partition of the slice sampled from the peripheral zone of HP13 expressing high level of Type 2 luminal signature. The region in dashed line is an early prostate cancer (PCa) lesion. n, Spatial transcriptomic slices of HP13 colored by expression level of Type 2 luminal signature.