Nine cancer tissue sections fit on the large Xenium capture area. Here we explore a human pancreatic cancer section. All high quality transcripts are shown as a density map, and then viewed as per-gene localization plots. Yellow is high expression, green is mid-level expression, and blue is low or zero expression.

All expected pancreatic cell types are clearly identified: acinar (secretory exocrine cells), endocrine cells, and ductal cells. A diversity of immune cells can also be distinguished, including lymphatic endothelial cells. At least three different tumor subtypes are resolved. One subtype is distinguished by lack of CFTR (cystic fibrosis transmembrane conductance regulator) expression, a gene critical to the ductal secretory function of the pancreas. Another subtype consists of metaplastic acinar cells which have acquired tumor and ductal gene expression.

Pancreatic cancer cell types are overlaid and registered to an H&E image derived from the same section stained post-Xenium and post-immunofluorescence.

Immunofluorescence staining with B cell marker CD20 (white), tumor marker TROP2 (red), and endocrine F cell marker PPY (green) was performed on the same section post-Xenium. Registration with the Xenium data allows for the overlay of cell segmentation and RNA transcripts such as PPY. Correlation plot between Xenium PPY transcript count (Q-Score ≥ 20) and PPY immunofluorescence (AU = arbitrary units of fluorescent intensity) yields a Spearman’s r of 0.8.

For each cell type, a K-D Tree was queried to identify all the other cell centroids that fall within a certain radius. Using the resulting indices from each query, cell types were tallied and neighborhood proportions for each cell type were plotted as stacked bar plots. Using the lasso tool in Xenium Explorer, cell proportions were validated and compared to the secondary analysis.

Stacked bar plots of cell type proportions for tumor cells, metaplastic cells, CFTR− tumor cells, and acinar cells, excluding “self” identities. Tumor cells are surrounded predominantly by other tumor subtypes. Metaplastic tumor cells (which express acinar genes such as ANPEP) neighbor other acinar cells and tumor cells. CFTR− tumor cells are predominantly adjacent to macrophages, suggesting that this cell subtype is more likely to be associated with tumor growth, progression, and invasiveness (Poh & Ernst, 2021).