Fig. 5: Longitudinal T cell changes during trial therapy.

a Uniform manifold approximation and projection (UMAP) of scRNA-seq data from CD4 + T cells. Colors and numbers indicate scRNA-seq clusters. b Distribution of CD4 + T cell clusters across groups. Left bar plot showing the relative proportion of cells from all patients for each CD4 + T cell subset. Heat map showing tissue prevalence estimated by the ratio of observed to expected cell number (Ro/e). Pre_R (n = 3; baseline samples from patients that demonstrated an objective response to trial therapy), Pre_NR (n = 9; baseline samples from patients that did not demonstrate an objective response to trial therapy), Post (n = 4; samples collected at the C2 timepoint), and EOT (n = 3; samples collected at the EOT timepoint). c UMAP view of CD4 + T cell clusters (top) and cell density (bottom) displaying CD4 + T cell distribution across four groups. Downsampling was applied and 1,345 cells were included for each group. High relative cell density is shown as bright magma. d Heat map illustrating expression of 17 curated gene signatures across CD4 + T cell clusters. Heat map was generated based on the scaled gene signature scores. e Radar plot showing enrichment of selected five CD4 + T cell states. f UMAP of scRNA-seq data from CD8 + T cells. Colors and numbers indicate scRNA-seq clusters. g Distribution of CD8 + T cell clusters across groups. Left bar plot showing the relative proportion of cells from all patients for each CD8 + T cell subset. Heat map showing tissue prevalence estimated by Ro/e. h Heat map illustrating expression of 20curated gene signatures across CD8 + T cell clusters. Heat map was generated based on the scaled gene signature scores. i Radar plot showing enrichment of selected five CD8 + T cell states. Source data are provided in the Source Data file.