Fig. 4: Guiding the selection of CAR variants through transcriptional mapping on TILs. | Nature Communications

Fig. 4: Guiding the selection of CAR variants through transcriptional mapping on TILs.

From: speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing

Fig. 4

a UMAP embedding resulting from the integration of CD8+ CAR library T cells with CD8+ TILs recovered from patients with non-small-cell lung cancer pre- and post-anti-PD-1 ICB treatment26. CAR T cells are highlighted and colored based on the cluster annotations from Fig. 2. CICs = CAR-induced clusters. b Enrichment of CAR library T cells across the 19 different clusters generated from unsupervised cell clustering. c UMAP plots highlighting cells from clusters 8 and 12. CAR library T cells and TILs are separated in two individual plots. d Volcano plots showing differentially expressed genes for TILs between clusters 8 or 12 and all the rest of clusters. Statistical significance was determined though the adjusted p-values generated using the FindMarker() function of Seurat package (two-sided Wilcoxon Rank Sum test). Source data are provided as a Source Data file. e Violin plots showing the expression levels of a selection of marker genes (only TILs). f Enrichment of cells in clusters 8 and 12 across different CAR variants. Only variants with at least 20 CD8 T cells are shown. In all panels, TCR- refers to T cells without a TCR.

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