Fig. 2: Shift in the myeloid compartment in non-responders compared to responders.

a Stacked bar plot representing the relative proportions of annotated immune cells versus non-immune cells and myeloid versus lymphoid cell types, stratified by therapy response. b Representative IMC images indicating the different identified myeloid cell types. The scale bar in overview images is 50 μm. The scale bar is 20 μm in inserts. c Hierarchical clustering heatmap of the median marker intensity per patient indicated for the 7 annotated myeloid cell types. d Uniform Manifold Approximation and Projection (UMAP) of single cells of all ROIs combined using lineage marker intensities, color-coded by annotated myeloid cell lineages. e Stacked bar plot representing the proportions of annotated myeloid cell types stratified by therapy response. f Violin plots indicating the median expression of immune checkpoints in the identified myeloid cell clusters. Every dot is a single cell. Cell type is indicated in colors. Bars indicate the median with a 95% confidence interval. g Dot plots of the median abundance of annotated myeloid cell clusters, stratified by therapy response. Each dot is a patient. The bars indicate the median with a 95% confidence interval. Nonparametric T-tests were used to calculate the statistical difference between non-responders and responders. h Representative IMC images illustrating a high abundance of M2 MP (CD68⁺CD163⁺) in non-responders and a high abundance of MDM (CD68⁺CD14⁺) in responders. The scale bar is 50 μm.