Fig 2: In-Depth Analysis of Relationships in the Tumor Ecosystem, Related to Figure 6(A) Frequencies of selected T cell clusters for juxta-tumoral and tumor samples. (B) Chord diagrams of the relationships between T cell, myeloid, and epithelial clusters in tumors and matched juxta-tumoral tissue for 41 patients (p = 0.001). (C) Frequencies of selected clusters that differed in correlation between tumor and juxta-tumoral tissue. (D) Absolute number of correlations between clusters for juxta-tumoral (JT) and tumor (T) tissue and table of the fold change between JT and T tissue. (E) Frequency of T cell and TAM phenotypes associated with immunosuppression for TIG1-3. (F) Pseudo-brightfield images of EpCAM and pan cytokeratin on tumor tissue. Rectangles highlight the areas shown at higher magnification in Figure 6E. Scale bar, 50 µm. Spearman correlation and Wilcoxon rank-sum test were used for statistical analysis. * p < 0.05, ** p < 0.01, *** p < 0.001.

Fig 3: Residual SARS-CoV-2 detected in the appendix and skin tissues of patient 1 using multiplex immunohistochemistry and RNAscope (A, D) Representative images of the (A) appendix and (D) skin tissues stained with hematoxylin and eosin, with differentiated staining of nuclear (hematoxylin) and cytoplasmic (eosin) components. (B, E) Representative images of the (B) appendix and (E) skin tissues stained for DAPI (blue), CK/EpCAM (red), CD45 (cyan), SARS-CoV-2 nucleocapsid protein (COVID NP; green), and CD68 (yellow). (C, F) Representative images of the (C) appendix and (F) skin tissues stained for DAPI (blue), SARS-CoV-2 nucleocapsid protein (COVID NP; green), and CD68 (red). (G–I) Representative images of the (G, H) appendix tissue obtained from patient 1 and (I) normal colon tissue obtained from patients not affected by COVID-19, subjected to RNAscope in situ hybridization with a nuclear component (hematoxylin) counterstained. SARS-CoV-2 spike RNAs are labelled as green dots, examples of the green dots are marked by black arrows. (A–F) Scale bar, 100 µm. (G–I) Scale bar, 20 µm.

Fig 4: Enteric neurons are part of the tumor microenvironment. (A and C) Representative photographs of human colorectal adenocarcinoma sections immunostained for the neuronal marker ß-tubulin III (red) and the epithelial marker EpCAM (green) showing the (A) center of the tumor and the (C) tumor front, showing the presence of enteric neurons in the tumor microenvironment. Scale bars: 250 µm. (B and D) Higher-magnification confocal micrographs (white boxed regions from panels A and C), illustrating the close proximity between tumor epithelial cells and enteric nervous structures. Scale bars: 25 µm. (B) Of note, nonspecific autofluorescence signal is visible in the lower left and upper right corners. DAPI, 4',6-diamidino-2-phenylindole.

Fig 5: A Single-Cell Proteomic Atlas of Breast Cancer Ecosystems(A) Experimental approach.(B) t-SNE plots of EpCAM, CD45, CD31, and FAP expression in 58,000 cells from all samples using a 0 to 1 normalization.(C) t-SNE as in (B), colored by cell type.(D and E) Frequencies of live epithelial cells, immune cells, endothelial cells, and fibroblasts for (D) mammoplasty (M), juxta-tumoral (JT), and tumor (T) samples and (E) tumor subtypes.Wilcoxon rank-sum test was used for statistical analysis. *p < 0.05, **p < 0.01, ***p < 0.001. See also Figure S1.