Fig. 6: The suppressive immune environment is shaped by tumor cell states.

a Representative CD68 IHC staining of 5 AML tumors and 4 matched normal samples. b Higher expression of TIM3 (HAVCR2) and VISTA (VSIR) in macrophages obtained from tumors compared to macrophages obtained from matched normal kidneys. Left panel: violin plot showing expression of HAVCR2and VSIR; right panel: dot plot showing scaled expression and the percentage of cells expressing these genes. c Nanostring digital spatial profiling of one SLS-dominant and one IS-dominant tumor. Left panel: a representative ROI (Region of Interests) from SLS-dominant tumor; middle panel: a representative ROI from IS-dominant tumor; right panel: expression of ACTA2 across all ROIs after Q3 normalization (From left to right columns are 12 SLS-dominant tumor ROIs and 12 IS-dominant tumor ROIs). Scale bars, 100 μm. d Inferred interactions between tumor cells and macrophages calculated by integrative analysis of spatial transcriptomics of the representative SLS-dominant tumor (12 ROIs) and scRNA-seq. x axis displays relative expression of genes in single-cell data. Only genes that are expressed in both single-cell data and spatial transcriptomics data are shown. Left side are genes relatively highly expressed in tumor cells; right side are genes relatively highly expressed in macrophages. Y axis displays Pearson Correlation Coefficient (PCC) of gene expression with macrophage frequency in spatial transcriptomics data. Genes with log-ratio <−1.5 and correlation coefficient higher than 0.4 are colored. APOE: PCC = 0.49, p = 0.1 (correlation test, two-sided). e Interactions between tumor cells and other cell types calculated as the product of the average ligand expression and average receptor expression (only interactions with a score greater than 1 across any cell type pair are displayed). Each column shows a pair of cell types, and each row shows the ligand-receptor pair. The color indicates interaction score. Column label: cell type expressing the ligand and cell type expressing the receptor are separated by “_”. Row label: ligand and receptor are separated by “_”. f tSNE plot of macrophages colored by cluster (downsampled to have equal number of cells from SLS or IS tumors). g tSNE plot of macrophages colored by sample type of origin. h Fraction of macrophages obtained from subtypes of tumors or from matched normal across clusters. i Average expression of IL7R, GZMK, GZMH, and IFITM1. j M2 module score calculated by relative expression of CD163, MRC1, VEGFA, GPNMB, and TREM2. k Feature plot showing expression of TREM2 and TYROBP (DAP12). l Violin plot showing expression of APOE and APP in tumor cells (SLS vs. IS). m Spatial transcriptomic profiling of an independent AML tumor using 10× Visium platform. Panels from left to right: (1) H&E-stained tissue, (2) averaged expression of CTSK and PMEL; spots with the expression of CTSK and PMEL higher than the median of all spots were annotated as tumor (yellow), (3) SLS spots (blue) and IS spots (green) were identified by marker gene expression; averaged expression of TREM2 and TYROBP are displayed in red, (4) expression of APOE.