Fig. 2: Mapping carcinoma-TME interactions in human colorectal cancer.

A Uniform Manifold Approximation Projection (UMAP) single cell transcriptomes from all cells collected in vivo, with cell types indicated. B Cell type composition in primary tumor and normal adjacent samples. Cell counts of each microenvironment cell type are normalized by total number of epithelial cells. Tumor samples are ordered based on MSI/MSS status and tumor stage. C Left panel: CODEX image of normal adjacent tissues and primary tumor from patient 86, highlighting seven cell-type markers – ECAD, CD68, CD3E, CD20, VIM, α-SMA and CD31 (scale = 50 μm). Right panel: post-segmented image colored by cell type. A section approximately 1.5 mm by 1.5 mm in size from the H&E slides was scanned, the exact dimensions of which vary based on the patient tissue acquired. A segment of this tile scan is presented here. D Composition of cell neighborhood based on CODEX image analysis. Each row represents the average cell type composition of a k-nearest-neighbors (k = 6) surrounding a particular cell type and the values sum to 1. E Receptor-ligand interactions up-regulated in primary tumors. Each edge indicates a predicted interaction between a receptor upregulated in primary tumor carcinoma cells compared to normal adjacent epithelial cells, and a ligand expressed by indicated cell type in the TME. Edge widths indicate the number of patients (samples) in which the receptor is significantly up regulated. Receptors were ranked based on the number of patients with increased expression and the graph degree, which represents the number of ligands from each cell type that communicate with the receptor. EP [R] receptors expressed on epithelial cells, B B cells, T T cells, EN endothelial cells, F fibroblasts, MF Myofibroblasts, M/D Macrophage/dendritic cells, MA mast cells. F Same as E, but highlighting the ligands up-regulated in primary tumor carcinoma cells compared to normal adjacent epithelial cells, and corresponding receptors expressed by TME cells. EP [L] ligands expressed on epithelial cells, PL plasma B cells. Source data are provided as a Source Data file.