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. Author manuscript; available in PMC: 2024 Mar 16.
Published in final edited form as: Cell. 2023 Mar 16;186(6):1127–1143.e18. doi: 10.1016/j.cell.2023.02.021

Figure 6: Immunosuppressive niches surround Tpex and Tex-int in metLN after anti-PD-L1 ICB.

Figure 6:

A) Paired differential abundance (DA) analysis of main immune cell populations between uiLN and metLN (n = 9; paired Wilcoxon Rank Sum Test). The log2 fold changes are plotted against the negative log10 (nominal p-values). Colors indicate if cell populations are significantly more abundant in uiLN (purple), tumor (blue), or not differentially abundant (False, grey) after Benjamini-Hochberg correction, FDR < 0.1. B) Cluster 8 and 14 abundances (as percentage of non-naïve CD8+ T cells) in paired samples from uiLN and metLN. P-values obtained by generalized linear mixed models. C) Number of cluster 16 neighbors for cluster 18 cells in ui-cores (global) and met-cores (global) from SOC and anti-PD-L1 treated patients. D) Expression of PD-1 on cluster 18 and cluster 16 cells with a DC neighbor in ui-cores (global) and met-cores (global) from SOC and anti-PD-L1 treated patients. E) Expression of CD39, IDO1, PD-L1, and TIM3 on DCs neighboring Tpex (cluster 18 cells) in ui-cores (global) and met-cores (global) from SOC and anti-PD-L1 treated patients. F) Expression of FOXP3 and TIM3 on Tregs neighboring Tpex (cluster 18 cells) in ui-cores (global) and met-cores (global) from SOC and anti-PD-L1 treated patients. G) Expression of CD45RO and TCF-1 on CD4+ T cells neighboring Tpex (cluster 18 cells) in ui-cores (global) and met-cores (global) from SOC and anti-PD-L1 treated patients. H) Representative images of a metLN (patient 10) and uiLN (patient 01) from anti-PD-L1 treated patients showing the spatial localization of CD4 T cells, Tregs, DCs, Tpex (cluster 18), Tex-int (cluster 16), and keratin+ cells. Cell identity overlaid onto the segmentation mask. Highlighted region is colored by the expression of CD4+ (cyan), CD45RO (red), CD11c (purple), PD-L1 (red), TCF-1 (yellow), IDO1 (yellow), FoxP3 (purple), TIM-3 (green), and CD39 (green). I) Log2 fold changes of cluster 5 and 9 abundances at time of surgery vs baseline stratified into patients with metastatic LN (Met) and patients without metastatic LN (No met). J) Log2 fold changes of cluster 2 and 5 frequencies of proliferating cells at time of surgery vs baseline stratified into patients with metastatic LN (Met) and patients without metastatic LN (No met). C-G) P-values obtained by Wilcoxon Rank Sum Test. See also Figure S6.