Fig. 3

Single-cell analyses and immune cell signaling. a Single-cell proteomic analyses of one pure DCIS and one mixed invasive tumor. Two selected ROIs from each sample are shown. Left panels: ID-09 (pure DCIS), right panels: ID-08 (mixed invasive tumor). Top: Composite immunofluorescence images of selected markers. EpCam (green), SMA (gray), CD19 (cyan), CD8 (red), CD4 (magenta), CD68 (yellow), DAPI (DNA, blue). Bottom: Maps of cell types estimated by CELESTA cell phenotyping indicated by colors for the different cell types. b Correlation between chemokine gene expression and B cell abundance in stromal segments surrounding DCIS. B-cell abundance estimated using immune cell deconvolution is shown on the x-axis and chemokine expression in stromal segments on a log₂ scale is shown on the y-axis. Pearson correlation coefficients and corresponding P values are given. c Gene Set Enrichment of genes expressed in DCIS cancer segments correlating with B cell abundance in corresponding stromal segments. Normalized Enrichment Score is shown for the top five signatures positively correlated with B cell abundance (NES > 0) and the top five signatures negatively correlated with B cell abundance (NES < 0). Colored bars indicate significant signatures (FDR < 0.1)