Extended Data Fig. 3: scATAC-seq+scRNA-seq of CAR T cells after leukemia clearance.
From: BACH2 dosage establishes the hierarchy of stemness and fine-tunes antitumor immunity in CAR T cells
a–e, scATAC-seq+scRNA-seq experiment is described in Fig. 3. a, Single-cell expression of selected genes in each transcriptome-defined cluster. b, A volcano plot of differentially expressed (DE) genes between stem-like and LT stem-like CAR T cells. Adjusted P values (adj P) were calculated using a two-sided Wilcoxon rank-sum test with Bonferroni correction to account for multiple comparisons. c, The protein level of TOX in stem-like (CD62Lint PD1+) and LT stem-like (CD62Lhi PD1−) CD8+ CD19 CAR T cells from E2A-PBX1 inoculated mice (n = 6 mice) on day 20 after CAR T-cell infusion. Circles represent individual mice. Statistical significance was calculated with a two-sided paired Student’s t-test. Data are representative of two independent experiments. *P < 0.05. d, Genes in CD8+ CD19 CAR T cells are ranked by the number of correlated scATAC-seq peaks. Genes with more than five correlated peaks are highlighted in red. e, Transcription factors (TFs) in CD8+ CD19 CAR T cells are ranked by the number of target genes. f, Single-cell enrichment of the open chromatin signature associated with Asxl1 KO long-lived stem-like T cells (GSE274863) in LT stem-like CAR T cells (ATAC_3) versus stem-like CAR T cells (ATAC_0) as defined in Fig. 3e. The P value was calculated using a two-sided Student’s t-test.
