Fig. 6: CD8⁺ CAR-T cells in the infusion product form four transcriptionally distinct clusters.

a PCA plot of single-cell gene expression residuals in CD8⁺ CAR-T cells isolated from the IP and blood at early, late, and very late time points. Gene expression residuals were calculated after adjusting for known sources of heterogeneity: the cellular detection rate, subject, and time point using MAST. Data were downsampled within each patient to account for differences in sample sizes between time points. b Unsupervised clustering was performed after concatenation of the scRNA-seq data across all time points and patients. Left, t-SNE plot highlighting the four transcriptionally distinct CD8⁺ CAR-T cell clusters identified in the IP. Each dot represents a single CD8⁺ CAR-T cell from the IP (colored) or from the early, late, and very late time points (gray). Right, the percentage of each identified cluster among CD8⁺ CAR-T cells in the IP is shown for each patient. c Heatmap displaying selected genes that are differentially expressed between clusters in the IP. Within each patient, differential gene expression analysis was performed by pairwise comparisons between clusters and only genes that were differentially expressed between clusters in all four patients were represented in the heatmap (FDR = 0.05, log2FC = 1.5). Color scale represents gene expression levels as a z-score.