Fig. 1

Overall study design and cellular composition of immune cells in the TME. A Schematic design for the study. B Patient clinical outcome in response to BA therapy. C Longitudinal patient sampling for scRNA-seq. D UMAP (Uniform Manifold Approximation and Projection) plot of all sequenced cells (n = 40,093) that passed QC (Quality Control) for subsequent analyses in this study. Each dot indicates an individual cell; color denotes cell types. E Gene expression heatmap analyzed by scRNA-seq. Expression value is the z-score normalized mean expression. F Boxplots showing the proportion of lymphoid (left panel) and myeloid (right panel) cells among immune cells. G Pairwise comparison of the fraction of CTLs of pre- vs post-treatment samples