Fig. 3: Spatially resolved immune cell landscape in OCCC with and without PPP2R1A mutations.

a, The antibody panel applied in CODEX assay. The diagram was created using BioRender. b,c, The cellular densities of proliferating B cells (CD20⁺Ki-67⁺; b) and germinal centre B cells (CD20⁺CD21⁺Ki-67⁺; c) in pretreatment samples. d, A representative CODEX image showing TLSs from the pretreatment sample of a patient with mutant PPP2R1A (patient 160). Scale bars, 100 μm (large image) and 200 μm (small images). e. Schematic of the multicellular neighbourhood analysis. The diagram was created using BioRender. f,g, The numbers of PD-1⁺CD8⁺ T cells (CD45⁺CD3e⁺CD8⁺CD4⁻PD-1⁺CD39⁻) and CD45RO⁺PD-1⁻CD8⁺ T cells (CD45⁺CD3e⁺CD8⁺CD4⁻CD45RO⁺GZMB⁻PD-1⁻CD39⁻) in the neighbourhood of all (f) and MHC-I⁺ (g) tumour cells. In f, the numbers of cells in each group are as follows: 7,043 (mutant PPP2R1A, pretreatment), 12,758 (mutant PPP2R1A, on treatment), 17,346 (WT PPP2R1A, pretreatment) and 66,177 (WT PPP2R1A, on treatment). In g, the numbers of cells in each group are as follows: 523 (mutant PPP2R1A, pretreatment), 1,532 (mutant PPP2R1A, on treatment), 212 (WT PPP2R1A, pretreatment), 2,536 (WT PPP2R1A, on treatment). AvgFC, average fold change. h,i, Representative CODEX images showing PD-1⁺CD8⁺ T cells and CD45RO⁺PD-1⁻CD8⁺ T cells in the neighbourhood of tumour cells in PPP2R1A-mutant (patient 157; h) and wild-type (patient 137; i) on-treatment samples. Scale bars, 50 μm (h,i). For the box plots (b,c,f and g), the centre line represents the median value; the lower and upper hinges correspond to the first and third quartiles, respectively; and the whiskers represent 1.5 × interquartile range. P values were calculated using two-sided Wilcoxon rank-sum tests.

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