Fig. 2: CAR T had an impaired effector program and defective antigen receptor signaling in AML.

A, B GSEA results from running RNAseq data of U937^CD33 co-incubated- versus Nalm6^CD33 co-incubated-CD33 CAR T cells (A). Nominal P values, FDR q values, and normalized enrichment score (NES) were calculated using GSEA software (Broad Institute). Heat maps (B) indicating the expression of genes enriched in GSEA from (A) and the known related genes not included in the GSEA gene set. The genes shown in heatmaps meet the parameters: fold change ≥ 1.5-fold in each of the two biological replicates. Each RNA sample was pooled from three technical replicates with T cells from one donor, and we conducted experiment with two different donors, n = 2. C Intensity of intracellular calcium in CAR T cells co-incubated with tumor cells, n = 3. Percentage of phosphorylated ZAP70 (D), phosphorylated ERK1/2 (E), phosphorylated C-JUN (F), and phosphorylated JNK (G) in CD33 CAR T cells pre-incubated with tumor cells and re-stimulated with U937 cells, n = 3. For all bar plots, data are shown as mean ± SD. Assays were performed on day 10 after T-cell initial activation. Two-sided unpaired t-tests were used to assess significance in (C–G). All numbers defined by “n” indicate the number of biological replicates with different human donors. Data are representative of two independent experiments. NS not significant. Source data are provided in the Source Data file.