Extended Data Fig. 3: Identification and single cell transcriptomic characterization of progenitor-like and dysfunctional T cell subsets.
From: The T cell differentiation landscape is shaped by tumour mutations in lung cancer
(a) Full gating strategy to identify the CD4 Early, CD8 Naïve-like, CD8 Tdys and CD8 TDT subsets by single T cell RNA expression. (b, c) Confirmation of CD4 (n=590 cells; b) and CD8 (n=206 cells; c) subset identity by evaluating expression of genes not used in the gating strategy but whose relative expression is known based on analysis of flow cytometry data. Each point represents an individual T cell and two-sided Wilcoxon rank sum test p-values are shown (***p<0.0001). Violin plots show the median and interquartile range. (d, e) GSEA to evaluate enrichment of gene sets upregulated in published T cell dysfunction datasets (d) and sorted CD8 Tdys and multimer reactive cells (e), amongst genes ranked by their expression in CD4 TDT vs. Early (143 vs. 175 cells) and CD8 TDT vs Naive-like populations (143 vs. 19 cells). For each gene set tested, the top 200 most differentially expressed genes were selected. Normalized enrichment scores (NES) and FDR adjusted p-values from permutation tests are shown. (f) GSEA to confirm the T central memory like transcriptional status of CD4 Early vs. Tdys/TDT subsets (175 vs. 415 cells). Normalized enrichment scores (NES) and FDR adjusted p-values by permutation test are shown.
