Extended Data Fig. 9: Clustering analysis of patient CAR T cells activated with IL-4 supplementation.

a, Expression distribution of Proliferation Score, Type-1 Score, Type-2 Score, and Cytotoxic Score on the UMAP in Fig. 3j. Genes defining each module are listed below. b, Differentially expressed genes (DEGs) specific to Cluster 4 in comparison to all other clusters in Fig. 3j. c, Corresponding signalling pathways regulated by the DEGs identified in Cluster 4 in Fig. 3j. Functional pathways are downregulated in this cluster, whereas T cell exhaustion and death receptor signalling are activated. d, Dot plot showing expression profile of type 2 receptor genes across all clusters identified in Fig. 3j, with notable high expression observed in Clusters 1 and 4. The size of circle represents proportion of single cells expressing the gene, and the colour shade indicates normalized expression level. e, Comparison of signalling pathways in BCA2 patient CAR T cells supplemented with 10 ng/mL IL-4 relative to the original condition, with or without the exclusion of dysfunctional cytotoxic Cluster 4 cells in Fig. 3j. A statistical comparison of the activation z score for functional signalling pathways (n = 21), including those regulating metabolism, immune function, and proliferation, was conducted. In c and e, pathway terms are ranked by –log 10 (p-value). z score is computed and used to reflect the predicted activation level (z > 0, activated/upregulated; z < 0, inhibited/downregulated; z ≥ 2 or z ≤ −2 can be considered significant). Significance levels were calculated with two-tailed Mann-Whitney test (b), right-tailed Fisher’s Exact Test (c), or two-tailed Wilcoxon matched-pairs signed rank test (e).