Fig. 6: Evaluating the persisting transcriptional signature across T cells, including adult long-lived CAR-T cells.

a, UMAP plots show expression of the strongest markers of the late-persisting CAR-T signature. Red arrows highlight persisting CAR-T cells between the CARPALL (CAT CAR-T) and CTL019 studies. b, Heat map demonstrates logistic regression cell-to-cell matching. CTL019-persisting CD4 CAR-T cells match strongly to late double-negative CAT CAR-T cells from the CARPALL study, as indicated by the red arrows. c, Box plots show the per-cell distribution of the late score as defined by the late-persisting CAR-T signature. Scores are shown for CAR-T, cancer and normal datasets. Publicly available datasets analyzed in this study are described in Supplementary Table 6. The red line represents the median of the late double-negative (DN TEM) cells from the CARPALL study. Colored cell types refer to CARPALL CAR-T cells. Red arrows indicate persisting CAT CAR-T cells from CARPALL and persisting CTL019 cells. Box plots show the first quartile (the lower end of the box) and the third quartile (the upper other end of the box) as well as the median values (center line) per dataset. The ‘whiskers’ extend from the ends of the box to a maximum and minimum of 1.5 times the interquartile range beyond the box. Outliers are shown as dots. AXICEL, axicabtagene ciloleucel CAR-T cells (infusion products); BRCA, breast cancer; ChiCTR, BCMA CAR-T (ChiCTR, 1800017404); CRC, colorectal cancer; DN, double-negative; GBM, glioblastoma; HCC, hepatocellular carcinoma; JCAR014, Fred Hutchinson Cancer Center CAR-T cells; NB, neuroblastoma; NPC, nasopharyngeal carcinoma; NSCLC, non-small lung cell carcinoma; SKCM, skin cutaneous melanoma (1 = Li; 2 = Yost; 3 = Jerby-Anon); TCM, central memory; TEM, effector memory. The numbers of cells and samples used in this figure are described in Supplementary Table 6.