Overexpression of a group of genes in T cells when proximal to tumor cells. Six genes were detected as induced by both differential expression and machine learning when T cells are proximal to tumor cells: RPSA, CD63, LYZ, TMSB4X, S100A14, and LAMA1. (A) Sequencing reads locations (red spots) of these genes are overlaid on the DAPI staining of the nuclei, as well as the segmentation of T cells in blue and tumor cell types in yellow. The cell bodies were detected using InSituSeg, and the cell types were identified using clustering of the gene expression profiles. Only segmentations of T cells and tumor cells are presented. Genes up-regulated in T cells because of proximity to tumor cells have more red spots (overexpression) when proximal to tumor cells (exemplars in full red arrows vs. hollow red arrows). (B) The biopsy with DAPI staining. Each panel in A shows a max projection of a subset region from the biopsy (orange square in B), acquired with a 40× objective, 100 × 100 µm in size (before expansion).
