Fig. 3: Cellular neighborhoods reveal differences in the spatial TME organization in responders and nonresponders.

a Cellular neighborhood (CN) analysis schematic. [1] Selection of computational parameters, including the window size (five in this schematic) and the number of CNs to be computed (five in this schematic). [2] Assignment of an index cell (i, center of window) to a given CN based on the composition of cell types within its corresponding window the clustering of windows. [3] Heatmap of cell type distribution for each CN and assignment of CN names. [4] Visualization of CNs as a Voronoi diagram. b Identification of 10 conserved CNs in the CTCL TME using a window size of 10. c Representative Voronoi diagram of the 10 CNs in a responder post-treatment, with the corresponding H&E and seven color fluorescent CODEX images. Scale bar, 20 µm. d–e Voronoi diagrams of CNs in a responder (d) and nonresponder (e) post-treatment, highlighting CN-5 (tumor and dendritic cells), CN-8 (tumor and CD4⁺ T cells) and CN-10 (Treg enriched). f–h Frequencies of CN-5 (f), CN-8 (g) and CN-10 (h) per tissue microarray spot across patient groups (mean, red bar). P values calculated with a linear mixed-effect model with Bonferroni’s corrections for multiple comparisons. i–k Frequencies of ICOS⁺ CD4⁺ T cell (i), Ki-67⁺ CD4⁺ T cell (j) and ICOS⁺ Treg (k) as a percentage of all immune cells per tissue microarray spot across patient groups (mean, red bar). P values calculated with a linear mixed-effect model with Bonferroni’s corrections for multiple comparisons. Source data are provided as a Source Data file.