Fig. 4: Spatial transcriptomic characterization of human IPMN tissue slices.

A Summary of the IPMN study. B H&E slices of IPMN tumor excised from three patients (bottom two rows) and their corresponding spatial transcriptomic spots (top two rows) arranged based on increasing CLDN4 expression. The spatial transcriptomes between the IPMN slices were merged, clustered, and projected on the Uniform Manifold Approximation and Projection (UMAP) dimension in (C) and projected to their H&E slices. Scale bar = 3 mm. C Leiden clustering of IPMN transcriptome projected on UMAP space. Dot plot of one-sided hypergeometric t test results of all clusters in IPMN based on cell type signatures. D Heatmap of Leiden clusters with genes selected from the PDAC cell surfaceome atlas with greater than 80% expression across sequenced PDAC cells. Scale represents z-score of log-normalized gene counts. E–G Differential expression of Cluster 6 (E) and Cluster 12 (F) versus all remaining clusters and G) Cluster 12 versus Cluster 6. H Cancer surfaceome score based on average normalized and scaled gene expression of all cells and all cancer cell surfaceome PDAC genes in each cluster. I Pearson’s correlation similarity matrix of select cancer cell surfaceome genes based on the IPMN spatial transcriptome. J Pearson’s correlation of all spots for S100P vs key markers of interest. K KEGG pathway enrichment of Cluster 6 and Cluster 12. Each calculation is based on n = 18 samples. For box plots, the center is the median and the lower and upper bound of the box are 25% and 75% of the distribution, respectively. The lower whisker is the lower 25% − 1.5 x interquartile range (IQR). The upper whisker is the upper 75% + 1.5 x IQR. Differential expression analysis in (E), (F) and (G) were based on non-parametric Wilcoxon rank sum test, which is a default setting in Seurat’s FindMarkers function. Gene enrichment analysis in (K) was done with hypergeometric t test based on clusterProfiler package. Source data are provided as a Source Data file.