Fig. 5: Single-cell transcriptome of infused CAR-T cells are distinct from CAR-T cells in blood.

a Left, t-SNE representation of 62,167 CD8⁺ CAR-T cells concatenated from the IP, early, late, and very late time points of four additional patients. Single cells from the early time point are overlaid on single cells at the late time point. Right, t-SNE analysis of concatenated CD8⁺ CAR-T cells from each time point in each patient. b Heatmap displaying the expression of genes that are differentially expressed between each time point with selected genes highlighted. Only genes that were differentially expressed between time points in all four patients are represented in the heatmap (FDR = 0.05, log2FC = 1.5). Color scale represents gene expression levels as a z-score. c GSEA using indicated gene sets was performed on CD8⁺ CAR-T cells isolated from the IP and blood at distinct time points after adoptive transfer. A combined Z-score was calculated for pairwise comparisons between CD8⁺ CAR-T cells from each post-infusion sample relative to the IP. A negative Z-score represents higher expression of the gene set in CD8⁺ CAR-T cells from the IP. Each point represents an individual patient. FDR = 0.01, absolute continuous Z-score > log2(1.5), absolute discrete Z-score > log2(1.5). d Violin plot of MKi67 gene expression at the IP, early, late, and very late time points. e Co-expression of zero to seven inhibitory markers, including PD-1, LAG-3, TIM-3, KLRG1, TIGIT, 2B4, and CD160 on CD8⁺ CAR-T cells from the IP and isolated at the early, late, and very late time points after infusion. Source data underlying Fig. 5e is provided as a Source Data file.