Fig. 2

Cell phenotyping and total cell proportion analysis. A 55 clusters were resolved by Phenograph at leiden resolution 2 following integration by Harmonypy. B Annotated clusters were merged into 19 cell types. C Cell types were defined by canonical marker expression. D Over 90% of 210,945 cells in total cohort were phenotyped. E, G TMA cores consisted of heterogenous proportions of each cell type. F, H Analysis of cell types by outcome did not show clear differences between patient groups. I Principal component analysis indicated that sample variance was driven by proportions of CD4⁺, CD8⁺, macrophage and B immune cells. J,K) Differential enrichment indicated higher levels of Treg cells in non-responding patients. Significant results p < 0.05 in volcano shown in red. Not adjusted for multiple testing