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. 2022 Apr 27;3(5):100621. doi: 10.1016/j.xcrm.2022.100621

Figure 3.

Figure 3

Transcriptional programs of intratumoral and stromal T cells

(A) t-SNE plot of all iCD3+ T cells (red triangles); sCD3+ T cells (blue squares), and melanoma cells (green circles) harvested by LCM illustrates overlap of iCD3+ and sCD3+ cells. Genes with raw read count >100 are used in the t-SNE algorithm.

(B) Venn diagram of expressed genes for iCD3+ and sCD3+ T cells. An expressed gene is defined as 75% quantile ≥1 TPM in the samples (PAL75). The plot shows 1,489 and 449 unique genes expressed by iCD3+ or by sCD3+ T cells, respectively.

(C) Heatmap representing top 50 genes in iCD3+ T cells (green and red) and sCD3+ T cells (orange and blue) across all CD3+ T cells harvested by LCM.

(D) Violin plots of gene expression for PRF1, GZMH, TIGIT, CXCL14, IL15, CCR7, UTP14C, PBX2, TMC4 across all iCD3 and sCD3+ T cells harvested by LCM. Gene expression is calculated in log2 TPM value. Line at median with 95% CI. Wilcoxon paired test.