Extended Data Fig. 1: CAR T cells in B cell ALL and melanoma show different single-cell transcriptomes.
From: FOXP1 and KLF2 reciprocally regulate checkpoints of stem-like to effector transition in CAR T cells
a, Upper left: Leukemia burden in E2A-PBX1-bearing mice that were untreated or treated with 106 CD19 CAR T cells (n = 5 mice per group). Upper right: Tumor burden in B16-CD19-bearing mice that were untreated (n = 5 mice) or treated (n = 10 mice) with 5 × 106 CD19 CAR T cells. Lower panel: Gating strategy for sorting CAR T cells (huEGFR+CD45.1+) from treated mice as in Fig. 1a. b, scRNA-seq profiles from different individual mice (replicates) in the same group are shown in separate UMAP plots. scRNA-seq is described in Fig. 1a. c, scRNA-seq profiles from different individual mice (replicates) in the same group are combined in the same UMAP plot. Cells are color-coded by the cluster defined in Fig. 1a. d, Single-cell expression of selected genes in CD8+ CAR T cells from mice with E2A-PBX1 as described in Fig. 1e is shown in UMAP plots. The mRNA level is color-coded. e, Single-cell expression of selected genes in CD8+ CAR T cells infiltrating B16-CD19 as described in Fig. 1h is shown in UMAP plots. The mRNA level is color-coded. f, Projection of cells in clusters 2, 4, 5 and 7 (black) in Fig. 1a to the reference map of ProjecTILs. Color codes of T cell subsets are based on the original ProjecTILs paper. g, A volcano plot comparing the transcriptome between CD8+ CAR T cells responding to E2A-PBX1 and those responding to B16-CD19. Statistical significance in a is determined by a two-sided Student’s t-test. Data in a are representative of two independent experiments. Circles in a left panel represent individual mice. Data in a right panel represent Mean ± SEM.
